2KN5

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 50 
  • Selection Criteria: all calculated structures submitted 

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Literature

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland, G.D.Lakomek, N.A.Griesinger, C.Meiler, J.Kortemme, T.

(2009) PLoS Comput Biol 5: e1000393-e1000393

  • DOI: 10.1371/journal.pcbi.1000393
  • Primary Citation of Related Structures:  
    2KN5

  • PubMed Abstract: 
  • 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 c ...

    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.


    Organizational Affiliation

    Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA76Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1UBA52UBCEP2UBBUBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 50 
  • Selection Criteria: all calculated structures submitted 
  • OLDERADO: 2KN5 Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-08-14 
  • Released Date: 2009-11-17 
  • Deposition Author(s): Friedland, G.D.

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance