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Protein dynamics derived from clusters of crystal structures
A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational chang...
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| Published in: | Biophysical journal 1997-12, Vol.73 (6), p.2891-2896 |
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| Main Authors: | , , , , , |
| Format: | Article |
| Language: | English |
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| cited_by | cdi_FETCH-LOGICAL-c462t-c070c9f88f420b566d6af51da8d32f4f5821644afb87e5afcbe787cc6ed6cfd33 |
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| container_end_page | 2896 |
| container_issue | 6 |
| container_start_page | 2891 |
| container_title | Biophysical journal |
| container_volume | 73 |
| creator | van Aalten, D.M. Conn, D.A. de Groot, B.L. Berendsen, H.J. Findlay, J.B. Amadei, A. |
| description | A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins. |
| doi_str_mv | 10.1016/S0006-3495(97)78317-6 |
| format | article |
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A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins.</description><subject>Animals</subject><subject>Biophysical Phenomena</subject><subject>Biophysics</subject><subject>Crystallization</subject><subject>Crystallography, X-Ray</subject><subject>Models, Molecular</subject><subject>Protein Conformation</subject><subject>Proteins - chemistry</subject><subject>Thermodynamics</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1997</creationdate><recordtype>article</recordtype><recordid>eNqFkM9r2zAUx8VYabN0f0LBp7IevEq2LMlQNkZYu0KhhW5noTw9tSq2lUlyIP99nSaE7dTTO3x_PT6EnDH6lVEmLh8ppaKsedt8aeWFVDWTpfhAZqzhVUmpEh_J7GA5IZ9SeqGUVQ1lx-S45YxXtJ6Rq4cYMvqhsJvB9B5SYTH6NdrCxdAX0I0pY0xFcAXETcqmK1KOI-QxYjolR850CT_v75z8uf75e_GrvLu_uV38uCuBiyqXQCWF1inlps1lI4QVxjXMGmXrynHXqIoJzo1bKomNcbBEqSSAQCvA2bqek2-73tW47NECDjmaTq-i703c6GC8_l8Z_LN-CmvNmGKs5VPB-b4ghr8jpqx7nwC7zgwYxqRly5VilZyMzc4IMaQU0R1GGNVb7PoNu94y1a3Ub9i1mHJn_354SO05T_r3nY4TprXHqBN4HACtjwhZ2-DfWXgFJZWUtA</recordid><startdate>19971201</startdate><enddate>19971201</enddate><creator>van Aalten, D.M.</creator><creator>Conn, D.A.</creator><creator>de Groot, B.L.</creator><creator>Berendsen, H.J.</creator><creator>Findlay, J.B.</creator><creator>Amadei, A.</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</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><scope>5PM</scope></search><sort><creationdate>19971201</creationdate><title>Protein dynamics derived from clusters of crystal structures</title><author>van Aalten, D.M. ; Conn, D.A. ; de Groot, B.L. ; Berendsen, H.J. ; Findlay, J.B. ; Amadei, A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c462t-c070c9f88f420b566d6af51da8d32f4f5821644afb87e5afcbe787cc6ed6cfd33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1997</creationdate><topic>Animals</topic><topic>Biophysical Phenomena</topic><topic>Biophysics</topic><topic>Crystallization</topic><topic>Crystallography, X-Ray</topic><topic>Models, Molecular</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>van Aalten, D.M.</creatorcontrib><creatorcontrib>Conn, D.A.</creatorcontrib><creatorcontrib>de Groot, B.L.</creatorcontrib><creatorcontrib>Berendsen, H.J.</creatorcontrib><creatorcontrib>Findlay, J.B.</creatorcontrib><creatorcontrib>Amadei, A.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</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><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biophysical journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>van Aalten, D.M.</au><au>Conn, D.A.</au><au>de Groot, B.L.</au><au>Berendsen, H.J.</au><au>Findlay, J.B.</au><au>Amadei, A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Protein dynamics derived from clusters of crystal structures</atitle><jtitle>Biophysical journal</jtitle><addtitle>Biophys J</addtitle><date>1997-12-01</date><risdate>1997</risdate><volume>73</volume><issue>6</issue><spage>2891</spage><epage>2896</epage><pages>2891-2896</pages><issn>0006-3495</issn><eissn>1542-0086</eissn><abstract>A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. 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| ispartof | Biophysical journal, 1997-12, Vol.73 (6), p.2891-2896 |
| issn | 0006-3495 1542-0086 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1181194 |
| source | PubMed Central Free |
| subjects | Animals Biophysical Phenomena Biophysics Crystallization Crystallography, X-Ray Models, Molecular Protein Conformation Proteins - chemistry Thermodynamics |
| title | Protein dynamics derived from clusters of crystal structures |
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