Mode coupling points to functionally important residues in myosin II
ABSTRACT Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis o...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.1777-1786 |
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| container_issue | 9 |
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| container_title | Proteins, structure, function, and bioinformatics |
| container_volume | 82 |
| creator | Varol, Onur Yuret, Deniz Erman, Burak Kabakçıoğlu, Alkan |
| description | ABSTRACT
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near‐native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non‐Gaussian vibrational modes on fluctutational dynamics. We show that an information‐theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II. Proteins 2014; 82:1777–1786. © 2014 Wiley Periodicals, Inc. |
| doi_str_mv | 10.1002/prot.24531 |
| format | Article |
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Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near‐native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non‐Gaussian vibrational modes on fluctutational dynamics. We show that an information‐theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II. Proteins 2014; 82:1777–1786. © 2014 Wiley Periodicals, Inc.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.24531</identifier><identifier>PMID: 24677138</identifier><language>eng</language><publisher>United States: Blackwell Publishing Ltd</publisher><subject>Allosteric Site ; allostery ; anharmonicity ; Dictyostelium - metabolism ; Energy Transfer ; mode coupling ; Models, Molecular ; molecular dynamics ; Molecular Dynamics Simulation ; Molecular Motor Proteins - chemistry ; Molecular Motor Proteins - metabolism ; myosin II ; Myosin Type II - chemistry ; Myosin Type II - metabolism ; Protein Conformation ; Protozoan Proteins - chemistry ; Protozoan Proteins - metabolism</subject><ispartof>Proteins, structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.1777-1786</ispartof><rights>2014 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5341-a64759790072e744fc85b71860871273ca7fa71d92efcd6ec931123120bc7733</citedby><cites>FETCH-LOGICAL-c5341-a64759790072e744fc85b71860871273ca7fa71d92efcd6ec931123120bc7733</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprot.24531$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.24531$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24677138$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Varol, Onur</creatorcontrib><creatorcontrib>Yuret, Deniz</creatorcontrib><creatorcontrib>Erman, Burak</creatorcontrib><creatorcontrib>Kabakçıoğlu, Alkan</creatorcontrib><title>Mode coupling points to functionally important residues in myosin II</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>ABSTRACT
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near‐native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non‐Gaussian vibrational modes on fluctutational dynamics. We show that an information‐theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II. Proteins 2014; 82:1777–1786. © 2014 Wiley Periodicals, Inc.</description><subject>Allosteric Site</subject><subject>allostery</subject><subject>anharmonicity</subject><subject>Dictyostelium - metabolism</subject><subject>Energy Transfer</subject><subject>mode coupling</subject><subject>Models, Molecular</subject><subject>molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Motor Proteins - chemistry</subject><subject>Molecular Motor Proteins - metabolism</subject><subject>myosin II</subject><subject>Myosin Type II - chemistry</subject><subject>Myosin Type II - metabolism</subject><subject>Protein Conformation</subject><subject>Protozoan Proteins - chemistry</subject><subject>Protozoan Proteins - metabolism</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0ctu1DAUBmCrAtGhsOEBUCQ2VaUUH1_jJb0y1UARGqnsLI_jIJckTu1EZd4eD2m7YFGxOpvv_PLvg9A7wMeAMfk4xDAeE8Yp7KEFYCVLDJS9QAtcVbKkvOL76HVKtxhjoah4hfYJE1ICrRbo7EuoXWHDNLS-_1kMwfdjKsZQNFNvRx9607bbwndDiKPpxyK65OvJpcL3RbcNKY_l8g162Zg2ubcP8wCtL87Xp5_L1fXl8vTTqrScMiiNYJIrqTCWxEnGGlvxjYRK4EoCkdQa2RgJtSKusbVwVlEAQoHgjZWS0gN0OMfmwnf5DaPufLKubU3vwpQ0cJGLSy7Yf1DOBeFC7eiHf-htmGLuPStMQCmS1dGsbAwpRdfoIfrOxK0GrHdX0Lsr6L9XyPj9Q-S06Vz9RB-_PQOYwb1v3faZKP3t-_X6MbScd3wa3e-nHRN_aSFza33z9VJfwI8VZ1cnekX_AKDEnto</recordid><startdate>201409</startdate><enddate>201409</enddate><creator>Varol, Onur</creator><creator>Yuret, Deniz</creator><creator>Erman, Burak</creator><creator>Kabakçıoğlu, Alkan</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201409</creationdate><title>Mode coupling points to functionally important residues in myosin II</title><author>Varol, Onur ; Yuret, Deniz ; Erman, Burak ; Kabakçıoğlu, Alkan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5341-a64759790072e744fc85b71860871273ca7fa71d92efcd6ec931123120bc7733</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Allosteric Site</topic><topic>allostery</topic><topic>anharmonicity</topic><topic>Dictyostelium - metabolism</topic><topic>Energy Transfer</topic><topic>mode coupling</topic><topic>Models, Molecular</topic><topic>molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular Motor Proteins - chemistry</topic><topic>Molecular Motor Proteins - metabolism</topic><topic>myosin II</topic><topic>Myosin Type II - chemistry</topic><topic>Myosin Type II - metabolism</topic><topic>Protein Conformation</topic><topic>Protozoan Proteins - chemistry</topic><topic>Protozoan Proteins - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Varol, Onur</creatorcontrib><creatorcontrib>Yuret, Deniz</creatorcontrib><creatorcontrib>Erman, Burak</creatorcontrib><creatorcontrib>Kabakçıoğlu, Alkan</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Varol, Onur</au><au>Yuret, Deniz</au><au>Erman, Burak</au><au>Kabakçıoğlu, Alkan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mode coupling points to functionally important residues in myosin II</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2014-09</date><risdate>2014</risdate><volume>82</volume><issue>9</issue><spage>1777</spage><epage>1786</epage><pages>1777-1786</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>ABSTRACT
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near‐native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non‐Gaussian vibrational modes on fluctutational dynamics. We show that an information‐theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II. Proteins 2014; 82:1777–1786. © 2014 Wiley Periodicals, Inc.</abstract><cop>United States</cop><pub>Blackwell Publishing Ltd</pub><pmid>24677138</pmid><doi>10.1002/prot.24531</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0887-3585 |
| ispartof | Proteins, structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.1777-1786 |
| issn | 0887-3585 1097-0134 |
| language | eng |
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| source | MEDLINE; Wiley Journals |
| subjects | Allosteric Site allostery anharmonicity Dictyostelium - metabolism Energy Transfer mode coupling Models, Molecular molecular dynamics Molecular Dynamics Simulation Molecular Motor Proteins - chemistry Molecular Motor Proteins - metabolism myosin II Myosin Type II - chemistry Myosin Type II - metabolism Protein Conformation Protozoan Proteins - chemistry Protozoan Proteins - metabolism |
| title | Mode coupling points to functionally important residues in myosin II |
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