User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions

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<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Large Ribosomal Subunit''' ([[1s72]]), resolution 2.4&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene>). <br>
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Large Ribosomal Subunit''' ([[1s72]]), resolution 2.4&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene>). <br>
·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}}  ··</center></td></tr></table>
·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}}  ··</center></td></tr></table>
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72extenvsglb/5'>Globular vs. extended proteins</scene>
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72extenvsglb/6'>Globular vs. extended proteins</scene>
:*Proteins are generally globular.  However, while about half the 27 proteins seen in the crystal structure of the large ribosomal subunit are globular (<font color="orange">shown as orange</font>), interestingly, '''the other half are extended or have large extended regions''' emanating from globular domains (<font color="cyan">shown as cyan</font>).   
:*Proteins are generally globular.  However, while about half the 27 proteins seen in the crystal structure of the large ribosomal subunit are globular (<font color="orange">shown as orange</font>), interestingly, '''the other half are extended or have large extended regions''' emanating from globular domains (<font color="cyan">shown as cyan</font>).   
:*These extended proteins and regions are reminiscent of the [[Intrinsically Unfolded Proteins (IUP)|intrinsically unfolded proteins]] that play roles in many other processes.
:*These extended proteins and regions are reminiscent of the [[Intrinsically Unfolded Proteins (IUP)|intrinsically unfolded proteins]] that play roles in many other processes.


:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/4examples/9'>Particular examples of globular vs. extended proteins</scene>
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/4examples/12'>Particular examples of globular vs. extended proteins</scene>
:Zooming in to see some examples in more detail:   
:Zooming in to see some examples in more detail:   
:*L2, L15, and L39e illustrate proteins with extended regions.   
:*L2, L15, and L39e illustrate proteins with extended regions.   
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:*L39e is extended over its entire length.  
:*L39e is extended over its entire length.  


:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/Extensionpenetrate/3'>Extensions penetrate into the subunit interior</scene>
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/Extensionpenetrate/5'>Extensions penetrate into the subunit interior</scene>
:*View of L2, L15, L39e and L7ae again but with the RNA backbone shown. The extended regions are <font color="cyan">again highlighted in cyan</font>.   
:*View of L2, L15, L39e and L7ae again but with the RNA backbone shown. The extended regions are <font color="cyan">again highlighted in cyan</font>.   
:*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements.   
:*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements.   
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::*One atom in particular corresponds to the carbon of the tetrahedral carbon intermediate of the peptidyl transferase reaction<ref>PMID: 10937990</ref>, and <font color = "red">'''A2486'''</font> (E. coli #2451) of <font color = "red">Domain V</font> approaches this critical atom of the <font color="magenta">Yarus analog</font>.
::*One atom in particular corresponds to the carbon of the tetrahedral carbon intermediate of the peptidyl transferase reaction<ref>PMID: 10937990</ref>, and <font color = "red">'''A2486'''</font> (E. coli #2451) of <font color = "red">Domain V</font> approaches this critical atom of the <font color="magenta">Yarus analog</font>.
::*It is important to note that '''the ribosome is highly conserved, particularly the nucleotides close to the Yarus analog in Domain V and thus the major conclusions reached from the structure are applicable to all ribosomes'''.
::*It is important to note that '''the ribosome is highly conserved, particularly the nucleotides close to the Yarus analog in Domain V and thus the major conclusions reached from the structure are applicable to all ribosomes'''.
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/12'>No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis</scene>
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/13'>No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis</scene>
:*<font color="yellow">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="#228b22">'''L10e'''</font> are the nearest proteins to the <font color="magenta">Yarus analog</font> bound to <font color="red">domain V</font> of the subunit. Note that it may help to start from the <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene> before hitting the above <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/12'>scene link</scene> to get a good sense of these elements in the core of the subunit or use <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewall/2'>this scene with the rest of the subunit shown translucently</scene>. With <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewp/1'>all the proteins shown it is obvious these four proteins are the closest.</scene>
:*<font color="dodgerblue">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="darkgreen">'''L10e'''</font> are the nearest proteins to the <font color="magenta">Yarus analog</font> bound to <font color="red">domain V</font> of the subunit. Note that it may help to start from the <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene> before hitting the above <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/13'>scene link</scene> to get a good sense of these elements in the core of the subunit or use <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewall/3'>this scene with the rest of the subunit shown translucently</scene>. With <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewp/2'>all the proteins shown it is obvious these four proteins are the closest.</scene>
:*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 &Aring; away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small>
:*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 &Aring; away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small>
:*As touched on [[#The rRNA domains:|in an earlier section]], it is in fact, <font color="#fd0162">RNA</font> that is intimately associated with the active site of the ribosome, leaving little doubt that the ribosome is indeed a ribozyme.
:*As touched on [[#The rRNA domains:|in an earlier section]], it is in fact, <font color="#fd0162">RNA</font> that is intimately associated with the active site of the ribosome, leaving little doubt that the ribosome is indeed a ribozyme.
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