https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Hao+LuProteopedia - User contributions [en]2026-09-19T01:51:43ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387454Sandbox Reserved 4942012-05-03T03:54:23Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported the isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from '''<FONT COLOR="#E42217"> '''adenosine diphosphate </FONT> (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>. Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''', and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
--[[User:Hao Lu|Hao Lu]]</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387443Sandbox Reserved 4942012-05-03T03:46:16Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported the isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from '''<FONT COLOR="#E42217"> '''adenosine diphosphate </FONT> (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>. Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''', and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387439Sandbox Reserved 4942012-05-03T03:44:10Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported the isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''', and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387437Sandbox Reserved 4942012-05-03T03:42:04Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported the isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387433Sandbox Reserved 4942012-05-03T03:40:41Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387430Sandbox Reserved 4942012-05-03T03:38:12Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functional mitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387429Sandbox Reserved 4942012-05-03T03:37:06Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387426Sandbox Reserved 4942012-05-03T03:35:52Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level (2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387422Sandbox Reserved 4942012-05-03T03:34:31Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. PDB code of ATP synthase is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387421Sandbox Reserved 4942012-05-03T03:33:48Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>. Its PDB codes is [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387419Sandbox Reserved 4942012-05-03T03:32:39Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c (in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387418Sandbox Reserved 4942012-05-03T03:32:06Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by '''<FONT COLOR="#E42217"> SDS-polyacrylamide gel electrophoresis </FONT>'''(SDS-PAGE) ,'''<FONT COLOR="#F535AA"> high-performance liquid chromatography </FONT>'''(HPLC) analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387036Sandbox Reserved 4942012-05-02T22:14:30Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">''Saccharomyces cerevisiae''</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387035Sandbox Reserved 4942012-05-02T22:13:54Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in '''<FONT COLOR="#571B7e">Saccharomyces cerevisiae</FONT>''' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387033Sandbox Reserved 4942012-05-02T22:12:38Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' , and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387026Sandbox Reserved 4942012-05-02T22:06:22Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387024Sandbox Reserved 4942012-05-02T22:05:53Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref name="PP"> PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue<ref name="PP"/>.]].<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387020Sandbox Reserved 4942012-05-02T22:01:45Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE)</FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387018Sandbox Reserved 4942012-05-02T22:00:53Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA"> (HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387017Sandbox Reserved 4942012-05-02T21:59:49Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>. ATP synthase has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution <ref>PMID: 10840052</ref>.An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1387012Sandbox Reserved 4942012-05-02T21:57:24Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The protein has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene> and <scene name='Sandbox_Reserved_494/Helices/1'>helices</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386999Sandbox Reserved 4942012-05-02T21:50:44Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The protein has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene>. The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. <br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386996Sandbox Reserved 4942012-05-02T21:47:10Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly. The protein has many <scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene><br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386995Sandbox Reserved 4942012-05-02T21:45:20Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>hydrophobic residues</scene><br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386993Sandbox Reserved 4942012-05-02T21:44:10Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<scene name='Sandbox_Reserved_494/Hydrophobic_residues/1'>TextToBeDisplayed</scene><br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386979Sandbox Reserved 4942012-05-02T21:36:49Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry αβ<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
As a motor protein, ATP synthase offers a rare research opportunity. Structure of the F<sub>1</sub> motor, both rotor and stator in the same assembly, are known in atomic detail for the first time, and rotation can be analyzed at sub-millisecond time resolution. An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386972Sandbox Reserved 4942012-05-02T21:28:29Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase<ref name="MM"/>.]]<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386963Sandbox Reserved 4942012-05-02T21:22:10Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_Ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase.]]<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=File:1c17_Ligand.jpg&diff=1386960File:1c17 Ligand.jpg2012-05-02T21:21:41Z<p>Hao Lu: </p>
<hr />
<div></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386958Sandbox Reserved 4942012-05-02T21:20:56Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref>.<br />
<br />
[[Image:1c17_ligand.jpg | thumb|frame|Octahedral coordination of Mg<sup>2+</sup> in the catalytic site of ATP synthase.]]<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1386947Sandbox Reserved 4942012-05-02T21:04:53Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalyticsites of ATP synthase have proceeded extensively in the ''E. coli'' enzymes, somewhat less so in ''Saccharomyces cerevisiae'' and ''Bacillus'' PS3, and to far lesser extent in other species. Almost without exception, detailed in vitro biochemical analyses of purified mutant enzymes have been limited to the ATP hydrolysis reaction. However, in both yeast and E. coli, growth tests on nonfermentable substrates provide sensitive if quantative assays of ATP synthesis in the cell. Ligands to the Mg<sup>2+</sup> cation have been studied in detail by mutagenesis and functional analysis <ref>PMID: 9425083 </ref> .<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384592Sandbox Reserved 4942012-05-02T17:54:01Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384591Sandbox Reserved 4942012-05-02T17:53:57Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
Mutagenesis of catalytic cites<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384587Sandbox Reserved 4942012-05-02T17:47:55Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
The energy for ATP synthesis is provided from proton transport along the gradient of electrochemical potential of protons across membranes (△H). When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384585Sandbox Reserved 4942012-05-02T17:41:48Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Reaction analysis of the catalytic sites== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384572Sandbox Reserved 4942012-05-02T17:30:40Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase<ref name="CV" />.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384571Sandbox Reserved 4942012-05-02T17:30:08Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV"> PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase.<ref name="CV" />]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384569Sandbox Reserved 4942012-05-02T17:26:30Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /></div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384564Sandbox Reserved 4942012-05-02T17:24:50Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384562Sandbox Reserved 4942012-05-02T17:22:56Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV" PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384559Sandbox Reserved 4942012-05-02T17:20:47Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref name="CV" PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase <ref name="CV"/>.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384558Sandbox Reserved 4942012-05-02T17:18:09Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb|frame|Two structural domains of ATP synthase.]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384553Sandbox Reserved 4942012-05-02T17:15:16Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384552Sandbox Reserved 4942012-05-02T17:15:15Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]|frame|Two major structrual domains.]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384547Sandbox Reserved 4942012-05-02T17:07:56Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384546Sandbox Reserved 4942012-05-02T17:07:26Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref name="MM">PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR. <ref name="MM"/>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384527Sandbox Reserved 4942012-05-02T16:58:09Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref>PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR. <ref>PMID: 11997128</ref>. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384521Sandbox Reserved 4942012-05-02T16:55:29Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>PMID: 11533724</ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref>PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384520Sandbox Reserved 4942012-05-02T16:53:47Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>Masasuke Yoshida, Eiro Muneyuki and Toru Hisabori, ATP synthase-a marvellous rotary engine of the cell, Molecular Cell Review. 2: 669-677, (2001). </ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref>PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>PMID: 12788493</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Luhttps://proteopedia.org/index.php?title=Sandbox_Reserved_494&diff=1384515Sandbox Reserved 4942012-05-02T16:52:20Z<p>Hao Lu: </p>
<hr />
<div>{{Sandbox_Reserved_Robert_B_Rose_1}}<Structure load='1c17' size='300' frame='true' align='right' CAPTION= 'ATP synthase, [[1c17]]' scene='Insert optional scene name here' /><br />
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
><!-- PLEASE DO NOT DELETE THIS TEMPLATE --><br />
<br />
==Background== <br />
ATP synthesis is the most prevalent chemical reaction in the biological world and ATP synthase is one of the most ubiquitous, abuntant proteins on earth. From '''<FONT COLOR="#E42217">''Escherichia coli''</FONT>''' to plants and mammals, this enzyme is one of the most conserved during evolution<ref>Masasuke Yoshida, Eiro Muneyuki and Toru Hisabori, ATP synthase-a marvellous rotary engine of the cell, Molecular Cell Review. 2: 669-677, (2001). </ref>.PDB codes are [[1c17]]. The molecular study of ATP synthase was initiated in 1960 when Efraim Racker and his colleagues reported thia isolation of soluable factor from beef heart mitochondria. ATP synthase produces ATP from adenosine diphosphate (ADP) and inorganic phosphate with the use of energy from a transmembrane proton-motive force generated by respiration or photosynthase<ref>PMID: 10576729</ref>.<br />
<br />
==Structure of ATP synthase== <br />
Strucutre of ATP synthases are basically similiar whatever the source. In their simplest form in prokaryotes, they contain eight different subunits, with stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>10-15</sub>. The total molecular size is about 530kDa<ref>PMID: 11997128</ref>. The enzyme consists of the extramembranous F<sub>1</sub> catalytic domain linked by means of a central stalk to an intrinsic membrane domain called F<sub>0</sub>. In the atomic structure of F<sub>1</sub>, the α and β subunits are arranged alternately around a coiled coil of two antiparallel α helices in the γ subunit <ref>PMID: 19489730</ref>.The catalytic sites are in the β subunits at the α/β subunit interface. The remainder of the γ subunit protrudes from the α<sub>3</sub>β<sub>3</sub> assembly and can be cross linked to the polar loop region of the c subunits in F<sub>0</sub>. In mitochondria, the δ and ε subunits are associated with the γ subunit in the central stalk assembly, as are the bacterial and chloroplast ε subunits, the counterparts of mitochondrial δ. ATP-dependent rotation of γ and ε within an immobilized α<sub>3</sub>β<sub>3</sub> complex from the thermophilic bacterium '''<FONT COLOR="#F535AA">''Bacillus'' PS3</FONT>''' has been observed directly.<br />
<br />
[[Image:1c17_dimor_(3).jpg | thumb]]<br />
<br />
==High resolution structure analysis== <br />
The first atomic-level(2.8Å) resolution structures by '''<FONT COLOR="#F87217">X-ray</FONT>''', strucutures was of bovine mitochondrial F<sub>1</sub> in 1994. The α and β subunits each had similiar three-domain structure, with an N-terminal β-barrel furthest away from the membrane surface, a central nucleotide-binding domain, and a C-terminal helical domain. Also, an '''<FONT COLOR="#571B7e">NMR</FONT>''' structure of isolated ''E. coli'' ε subunit is in good agreement with X-ray structure. The structure of the N-terminal domain of ''E. coli'' δ subunit consisting of residues 1 through 134 was solved also by NMR. In addition, according to analyses by SDS-polyacrylamide gel electrophoresis '''<FONT COLOR="#E42217"> (SDS-PAGE) </FONT>''', high-performance liquid chromatography'''<FONT COLOR="#F535AA">(HPLC)</FONT>''' analysis, and NH<sub>2</sub>-terminal sequencing, the purified complex used here for crystallization consists of subunis α, β, γ, δ, ε, b, d, a, h, f, ATP8, and c(in diminishing apparent molecular weight order for F<sub>1</sub> and F<sub>0</sub> on SDS gels) and is similar to other preparations.<br />
<br />
==Mechanism of action== <br />
When the magnitude of △H is large, as in functionalmitochondrial, downhill proton flow through F<sub>0</sub> causes rotation of the F<sub>0</sub> rotor and hence rotation of the γε-subunits of F<sub>1</sub>. The rotary motion of the γ alternates the structure of the β-subunit so the ATP is synthesized<ref>5</ref>.<br />
<br />
==Perspective== <br />
An emerging possibility of step-size mismatch between the F<sub>1</sub> and F<sub>0</sub> motors provides an opportunity to find a noval coupling mechanism of the two motors that will explain why the mismatch is good for the enzyme. Finally, one can even dream of using this, the world's tiniest motor, as an engine part in the fabrication of nano-machines. The marvel of ATP will continue.<br />
<br />
==Additional Resources==<br />
For additional information, see: [[Photosynthesis]]<br />
<br /><br />
<br />
==References== <br />
<references /><br />
[1] ATP synthase-a marvellous<br />
[2] Molecular Architecture of the rotary motor in ATP synthase<br />
[3] The molecular mechanism of ATP<br />
[4] Essentials for ATP synthesis by F1F0 ATP synthases<br />
[5] ATP synthesis driven by proton tranport in</div>Hao Lu