|
|
| Line 1: |
Line 1: |
| | | | |
| | ==A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family== | | ==A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family== |
| - | <StructureSection load='2kn5' size='340' side='right' caption='[[2kn5]], [[NMR_Ensembles_of_Models | 50 NMR models]]' scene=''> | + | <StructureSection load='2kn5' size='340' side='right'caption='[[2kn5]], [[NMR_Ensembles_of_Models | 50 NMR models]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2kn5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KN5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KN5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2kn5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KN5 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d3z|1d3z]], [[1xqq|1xqq]], [[2nr2|2nr2]], [[2k39|2k39]]</td></tr> | + | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d3z|1d3z]], [[1xqq|1xqq]], [[2nr2|2nr2]], [[2k39|2k39]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kn5 OCA], [http://pdbe.org/2kn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kn5 RCSB], [http://www.ebi.ac.uk/pdbsum/2kn5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kn5 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kn5 OCA], [https://pdbe.org/2kn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kn5 RCSB], [https://www.ebi.ac.uk/pdbsum/2kn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kn5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| Line 29: |
Line 29: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Ubiquitin|Ubiquitin]] | + | *[[3D structures of ubiquitin|3D structures of ubiquitin]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 35: |
Line 35: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Human]] | | [[Category: Human]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Friedland, G D]] | | [[Category: Friedland, G D]] |
| | [[Category: Backbone flexibility]] | | [[Category: Backbone flexibility]] |
| Structural highlights
2kn5 is a 1 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Related: | |
| Gene: | RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC (HUMAN) |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.,Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T PLoS Comput Biol. 2009 May;5(5):e1000393. Epub 2009 May 29. PMID:19478996[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 2009 May;5(5):e1000393. Epub 2009 May 29. PMID:19478996 doi:10.1371/journal.pcbi.1000393
|
