Sandbox Reserved 930: Difference between revisions

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{{Sandbox_Reserved_510042_1}}
{{Sandbox_Reserved_510042_1}}


=Scallop myosin head in detached state=
=Scallop myosin head in the detached state=




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• S1 nucleotide-free state corresponding to the near-rigor conformation of myosin [http://www.pdb.org/pdb/explore/explore.do?structureId=1DFK 1DFK]
• S1 nucleotide-free state corresponding to the near-rigor conformation of myosin [http://www.pdb.org/pdb/explore/explore.do?structureId=1DFK 1DFK]


• S1 Mg-ADP • VO4 state corresponding to the pre-power stroke conformation [http://www.pdb.org/pdb/explore/explore.do?structureId=1kk8 1KK8]
• S1 Mg-ADP • BeFx state corresponding to the pre-power stroke conformation [http://www.pdb.org/pdb/explore/explore.do?structureId=1kk8 1KK8]


• S1 Mg-ADP state corresponding to the myosin detached state [http://www.rcsb.org/pdb/explore/explore.do?structureId=1b7t 1B7T]
• S1 Mg-ADP state corresponding to the myosin detached state [http://www.rcsb.org/pdb/explore/explore.do?structureId=1b7t 1B7T]
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==Nucleotide binding pocket: ADP + Mg<sup>2+</sup>==
==Nucleotide binding pocket: ADP + Mg<sup>2+</sup>==


The nucleotide-binding pocket is located at the interface of the 50 kDa upper subdomain and the N-terminal subdomain <ref name="risal2004"> PMID: 15184651</ref>, which is opposite to a deep cleft that bisects the actin-binding domain (Fig. 3).This part of protein involves an arrangement of a secondary structure mainly around the parallel 7-stranded <scene name='57/579700/Strands/1'> β-sheet</scene>. Loops extending from the &beta;-strands interact with the adenine nucleotide.  
The nucleotide binding pocket is located at the interface of the 50 kDa upper subdomain and the N-terminal subdomain <ref name="risal2004"> PMID: 15184651</ref>, which is opposite to a deep cleft that bisects the actin-binding domain (Fig. 3). The nucleotide binding pocket and actin binding domain contained a complex arrangement of secondary structure elements mainly around the parallel 7-stranded <scene name='57/579700/Strands/1'> β-sheet</scene>. Loops extending from the &beta;-strands interact with the adenine nucleotide.  






<scene name='57/579700/Adp/5'>ADP</scene> forms hydrogen bonds with the amino acid side chains around it, <scene name='57/579700/Mg/5'>Mg2+</scene> coordinates with residues Thr183, Ser 241 of the heavy chain, O1B and O3B from ADP and three water molecules as well. The hydrogen bonds between ADP and the amino acid residues together with  the interactions of Mg2+ keep ADP in the nucleotide-binding pocket.
<scene name='57/579700/Adp/5'>ADP</scene> forms hydrogen bonds with the amino acid side chains in the binding pocket. <scene name='57/579700/Mg/5'>Mg2+</scene> coordinates with residues Thr183, Ser 241 of the N-terminal subdomain as well as O1B and O3B from ADP and three water molecules. The hydrogen bonds between ADP and the amino acid residues together with  the interactions of Mg2+ keep ADP in the nucleotide-binding pocket.


In the contractile cycle ATP binding causes a conformational change, which detaches the myosin S1 unit from actin. Then the active site closes, and ATP is hydrolysed to Pi and ADP, leading to the subsequent reattachment of the S1 with the actin. The conformational changes of the acting-binding pocket and the opening and closing of the nucleotide-binding pocket cause the strong and weak acting binding states of myosin, allowing muscle contraction <ref name="houdusse2000"> PMID: 11016966</ref>.
In the contractile cycle ATP binding causes a conformational change, which detaches the myosin S1 unit from actin. Then the active site closes, and ATP is hydrolysed to Pi and ADP, leading to the subsequent reattachment of the S1 with the actin. The conformational changes of the acting-binding pocket and the opening and closing of the nucleotide-binding pocket cause the strong and weak acting binding states of myosin, allowing muscle contraction <ref name="houdusse2000"> PMID: 11016966</ref>.
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Taking part in the organization of the different conformations of the contractile cycle is also the so called switch I, which is a second catalytic loop of the nucleotide-binding pocket. <ref name="houdusse2000"> PMID: 11016966</ref> Switch II forms a specific salt bridge and hydrogen bond interactions with switch I that stabilize the pre-power stroke state  <ref name="himmel2002"> PMID: 12297624</ref>.
Taking part in the organization of the different conformations of the contractile cycle is also the so called switch I, which is a second catalytic loop of the nucleotide-binding pocket. <ref name="houdusse2000"> PMID: 11016966</ref> Switch II forms a specific salt bridge and hydrogen bond interactions with switch I that stabilize the pre-power stroke state  <ref name="himmel2002"> PMID: 12297624</ref>.


In the pre-power stroke conformation of the MD, switch II interacts with the nucleotide-binding pocket and forms the stabilizing hydrogen bond interactions and a salt bridge with switch I <ref name="himmel2002"> PMID: 12297624</ref><ref name="risal2004"> PMID: 15184651</ref>. Rotation of the 50-kDa upper subdomain away from the N-terminal subdomain pulls switches I and II apart breaking the protein- nucleotide interactions between switch I and ADP, as well as changing the conformation of switch II. These changes result in closing of the actin-binding site and opening of the nucleotide-binding pocket, leading to MgADP release. At the same time SH1 helix is unwound and the lever arm is able to change its position enabling sliding of myosin through the actin filament <ref name="himmel2002"> PMID: 12297624</ref>.
In the detached conformation of the MD, switch II interacts with the nucleotide-binding pocket and forms the stabilizing hydrogen bond interactions and a salt bridge with switch I <ref name="himmel2002"> PMID: 12297624</ref><ref name="risal2004"> PMID: 15184651</ref>. Rotation of the 50-kDa upper subdomain away from the N-terminal subdomain pulls switches I and II apart breaking the protein- nucleotide interactions between switch I and ADP, as well as changing the conformation of switch II. These changes result in closing of the actin-binding site and opening of the nucleotide-binding pocket, leading to MgADP release. At the same time SH1 helix is unwound and the lever arm is able to change its position enabling sliding of myosin through the actin filament <ref name="himmel2002"> PMID: 12297624</ref>.




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