Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein
Internal and rigid‐body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid‐body motion is predominant in compariso...
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| Veröffentlicht in: | Journal of computational chemistry 2002-02, Vol.23 (3), p.402-413 |
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| container_title | Journal of computational chemistry |
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| creator | Yoshioki, Shuzo |
| description | Internal and rigid‐body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid‐body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H‐bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H‐bond strength. We see a relationship between vibrational frequencies (assuming rigid‐body motion of the water molecules) and the H‐bond strength of the water taking part in this H‐bonding. Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002 |
| doi_str_mv | 10.1002/jcc.1170 |
| format | Article |
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Water's rigid‐body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H‐bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H‐bond strength. We see a relationship between vibrational frequencies (assuming rigid‐body motion of the water molecules) and the H‐bond strength of the water taking part in this H‐bonding. Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002</description><identifier>ISSN: 0192-8651</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.1170</identifier><identifier>PMID: 11908503</identifier><language>eng</language><publisher>New York: Wiley Periodicals, Inc</publisher><subject>Animals ; bovine pancreatic trypsin inhibitor ; Cattle ; Computer Simulation ; fluctuating protein ; hydrogen bond ; Hydrogen Bonding ; Models, Molecular ; Motion ; normal mode analysis ; Protein Conformation ; Proteins - chemistry ; Trypsin Inhibitors - chemistry ; vibrating water molecule ; Vibration ; Water - chemistry</subject><ispartof>Journal of computational chemistry, 2002-02, Vol.23 (3), p.402-413</ispartof><rights>Copyright © 2002 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3550-b483ffa871dda9a4d691d518c7370e16311dd395a6ab4d18a767fd4d32558bcd3</citedby><cites>FETCH-LOGICAL-c3550-b483ffa871dda9a4d691d518c7370e16311dd395a6ab4d18a767fd4d32558bcd3</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%2Fjcc.1170$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjcc.1170$$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/11908503$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yoshioki, Shuzo</creatorcontrib><title>Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein</title><title>Journal of computational chemistry</title><addtitle>J. Comput. Chem</addtitle><description>Internal and rigid‐body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid‐body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H‐bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H‐bond strength. We see a relationship between vibrational frequencies (assuming rigid‐body motion of the water molecules) and the H‐bond strength of the water taking part in this H‐bonding. Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002</description><subject>Animals</subject><subject>bovine pancreatic trypsin inhibitor</subject><subject>Cattle</subject><subject>Computer Simulation</subject><subject>fluctuating protein</subject><subject>hydrogen bond</subject><subject>Hydrogen Bonding</subject><subject>Models, Molecular</subject><subject>Motion</subject><subject>normal mode analysis</subject><subject>Protein Conformation</subject><subject>Proteins - chemistry</subject><subject>Trypsin Inhibitors - chemistry</subject><subject>vibrating water molecule</subject><subject>Vibration</subject><subject>Water - chemistry</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kE1P4zAQQC3ECkoXiV-AfEJcwnrqOE64oQItCMFld-nNcuwJBPJR7ITSX8FfJlXCroTEaSTP07PmEXIA7AQYm_x6MuYEQLItMgKWREESy8U2GTFIJkEcCdgle94_Mca4iMIdsguQsFgwPiLv5-tKl7nxtM6opktXN5hXVFeWrnSDjpZ1gaYt0FPfOle3lc2rB9o84id7Sudr6-oHrIK07rcpNivEir7mqdPN5uWra-PXNCta07Q9Mdh-kh-ZLjzuD3NM_lxe_J7Og5u72dX07CYwXAgWpGHMs0zHEqzViQ5tlIAVEBvJJUOIOHQLnggd6TS0EGsZycyGlk-EiFNj-Zgc9d7u35cWfaPK3BssCl1h3XolQXAedsHG5LgHjau9d5ippctL7dYKmNrEV118tYnfoYeDs01LtP_BoXYHBD2wygtcfytS19PpIBz43Df49o_X7llF3aFC3d_O1DWHiVzc_lUz_gHkOaAE</recordid><startdate>200202</startdate><enddate>200202</enddate><creator>Yoshioki, Shuzo</creator><general>Wiley Periodicals, 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>7X8</scope></search><sort><creationdate>200202</creationdate><title>Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein</title><author>Yoshioki, Shuzo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3550-b483ffa871dda9a4d691d518c7370e16311dd395a6ab4d18a767fd4d32558bcd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Animals</topic><topic>bovine pancreatic trypsin inhibitor</topic><topic>Cattle</topic><topic>Computer Simulation</topic><topic>fluctuating protein</topic><topic>hydrogen bond</topic><topic>Hydrogen Bonding</topic><topic>Models, Molecular</topic><topic>Motion</topic><topic>normal mode analysis</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>Trypsin Inhibitors - chemistry</topic><topic>vibrating water molecule</topic><topic>Vibration</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yoshioki, Shuzo</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>MEDLINE - Academic</collection><jtitle>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yoshioki, Shuzo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J. 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Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002</abstract><cop>New York</cop><pub>Wiley Periodicals, Inc</pub><pmid>11908503</pmid><doi>10.1002/jcc.1170</doi><tpages>12</tpages></addata></record> |
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| ispartof | Journal of computational chemistry, 2002-02, Vol.23 (3), p.402-413 |
| issn | 0192-8651 1096-987X |
| language | eng |
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| source | MEDLINE; Wiley Journals |
| subjects | Animals bovine pancreatic trypsin inhibitor Cattle Computer Simulation fluctuating protein hydrogen bond Hydrogen Bonding Models, Molecular Motion normal mode analysis Protein Conformation Proteins - chemistry Trypsin Inhibitors - chemistry vibrating water molecule Vibration Water - chemistry |
| title | Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein |
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