Algorithms and Analytic Solutions Using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR

2010 ◽  
pp. 355-372 ◽  
Author(s):  
Anna Yershova ◽  
Chittaranjan Tripathy ◽  
Pei Zhou ◽  
Bruce Randall Donald
Keyword(s):  
High Resolution ◽  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Analytic Solutions ◽  
Dipolar Couplings ◽  
Protein Backbone ◽  
Backbone Structure

scholarly journals DYNAFOLD: A DYNAMIC PROGRAMMING APPROACH TO PROTEIN BACKBONE STRUCTURE DETERMINATION FROM MINIMAL SETS OF RESIDUAL DIPOLAR COUPLINGS

2014 ◽  
Vol 12 (01) ◽  
pp. 1450002 ◽  
Author(s):  
RISHI MUKHOPADHYAY ◽  
STEPHANIE IRAUSQUIN ◽  
CHRISTOPHER SCHMIDT ◽  
HOMAYOUN VALAFAR
Keyword(s):  
Dynamic Programming ◽  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Dynamic Programming Algorithm ◽  
Synthetic Data ◽  
Dipolar Couplings ◽  
Programming Algorithm ◽  
Programming Approach ◽  
Protein Backbone ◽  
Minimal Sets

Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N – H , C α– H α, and C – N vectors of 1BRF, 1F53, 110M, and 3LAY proteins, with up to ±1 Hz error in three alignment media, and was able to produce structures with less than 1.9 Å of the original structures. DynaFold was then tested using experimental data, obtained from the Biological Magnetic Resonance Bank, for proteins PDBID:1P7E and 1D3Z using RDC data from two alignment media. This exercise yielded structures within 1.0 Å of their respective published structures in segments with high data density, and less than 1.9 Å over the entire protein. The same sets of RDC data were also used in comparisons with traditional methods for analysis of RDCs, which failed to match the accuracy of DynaFold's approach to structure determination.

Determination of Protein Backbone Structure Using Only Residual Dipolar Couplings

2001 ◽  
Vol 123 (7) ◽  
pp. 1541-1542 ◽  
Author(s):  
Jean-Christophe Hus ◽  
Dominique Marion ◽  
Martin Blackledge
Keyword(s):  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Protein Backbone ◽  
Backbone Structure

Simultaneous Determination of Protein Backbone Structure and Dynamics from Residual Dipolar Couplings

2006 ◽  
Vol 128 (47) ◽  
pp. 15100-15101 ◽  
Author(s):  
Guillaume Bouvignies ◽  
Phineus Markwick ◽  
Rafael Brüschweiler ◽  
Martin Blackledge
Keyword(s):  
Simultaneous Determination ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Protein Backbone ◽  
Structure And Dynamics ◽  
Backbone Structure
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