2LJ5

Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 321 
  • Conformers Submitted: 301 
  • Selection Criteria: structures with acceptable covalent geometry 

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Literature

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.

Montalvao, R.W.De Simone, A.Vendruscolo, M.

(2012) J Biomol NMR 53: 281-292

  • DOI: 10.1007/s10858-012-9644-3
  • Primary Citation of Related Structures:  
    2LJ5

  • PubMed Abstract: 
  • Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs an ...

    Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA76Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2RPS27AUBA80UBCEP1UBBUBC
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 321 
  • Conformers Submitted: 301 
  • Selection Criteria: structures with acceptable covalent geometry 
  • OLDERADO: 2LJ5 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Database references