Model-Free Analysis of Protein Backbone Motion from Residual Dipolar Couplings

2002 ◽  
Vol 124 (20) ◽  
pp. 5822-5833 ◽  
Author(s):  
Wolfgang Peti ◽  
Jens Meiler ◽  
Rafael Brüschweiler ◽  
Christian Griesinger
Keyword(s):  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Protein Backbone ◽  
Model Free

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.

Model-Free Approach to the Dynamic Interpretation of Residual Dipolar Couplings in Globular Proteins

2001 ◽  
Vol 123 (25) ◽  
pp. 6098-6107 ◽  
Author(s):  
Jens Meiler ◽  
Jeanine J. Prompers ◽  
Wolfgang Peti ◽  
Christian Griesinger ◽  
Rafael Brüschweiler
Keyword(s):  
Residual Dipolar Couplings ◽  
Globular Proteins ◽  
Dipolar Couplings ◽  
Model Free ◽  
Dynamic Interpretation ◽  
Model Free Approach

Model Free Analysis of Experimental Residual Dipolar Couplings in Small Organic Compounds

2021 ◽  
Author(s):  
Felix A Roth ◽  
Volker Schmidts ◽  
Jan Rettig ◽  
Christina M. Thiele
Keyword(s):  
Organic Compounds ◽  
Residual Dipolar Couplings ◽  
Chemical Compounds ◽  
Dipolar Couplings ◽  
Model Free ◽  
Relative Arrangement

Residual dipolar couplings (RDCs) contain information on the relative arrangement and dynamics of internuclear spin vectors in chemical compounds. Classically, RDC data is analyzed by fitting to structure models, while...

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