Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings

2009 ◽  
Vol 131 (49) ◽  
pp. 17908-17918 ◽  
Author(s):  
Gabrielle Nodet ◽  
Loïc Salmon ◽  
Valéry Ozenne ◽  
Sebastian Meier ◽  
Malene Ringkjøbing Jensen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Residual Dipolar Couplings ◽  
Quantitative Description ◽  
Dipolar Couplings ◽  
Conformational Sampling ◽  
Unfolded Proteins ◽  
Nmr Residual Dipolar Couplings

Theoretical framework for NMR residual dipolar couplings in unfolded proteins

2007 ◽  
Vol 39 (1) ◽  
pp. 1-16 ◽  
Author(s):  
O. I. Obolensky ◽  
Kai Schlepckow ◽  
Harald Schwalbe ◽  
A. V. Solov’yov
Keyword(s):  
Residual Dipolar Couplings ◽  
Theoretical Framework ◽  
Dipolar Couplings ◽  
Unfolded Proteins ◽  
Nmr Residual Dipolar Couplings

Direct Prediction of NMR Residual Dipolar Couplings from the Primary Sequence of Unfolded Proteins

2012 ◽  
Vol 52 (2) ◽  
pp. 687-690 ◽  
Author(s):  
Jie-rong Huang ◽  
Valéry Ozenne ◽  
Malene Ringkjøbing Jensen ◽  
Martin Blackledge
Keyword(s):  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Primary Sequence ◽  
Unfolded Proteins ◽  
Nmr Residual Dipolar Couplings

Residual dipolar couplings measured in unfolded proteins are sensitive to amino-acid-specific geometries as well as local conformational sampling

2012 ◽  
Vol 40 (5) ◽  
pp. 989-994 ◽  
Author(s):  
Jie-rong Huang ◽  
Martin Gentner ◽  
Navratna Vajpai ◽  
Stephan Grzesiek ◽  
Martin Blackledge
Keyword(s):  
Amino Acid ◽  
Residual Dipolar Couplings ◽  
Intrinsically Disordered Proteins ◽  
Dipolar Couplings ◽  
Disordered Proteins ◽  
Conformational Sampling ◽  
Intrinsically Disordered ◽  
Potential Energy Landscape ◽  
Order Of Magnitude ◽  
Folded Structures

Many functional proteins do not have well defined folded structures. In recent years, both experimental and computational approaches have been developed to study the conformational behaviour of this type of protein. It has been shown previously that experimental RDCs (residual dipolar couplings) can be used to study the backbone sampling of disordered proteins in some detail. In these studies, the backbone structure was modelled using a common geometry for all amino acids. In the present paper, we demonstrate that experimental RDCs are also sensitive to the specific geometry of each amino acid as defined by energy-minimized internal co-ordinates. We have modified the FM (flexible-Meccano) algorithm that constructs conformational ensembles on the basis of a statistical coil model, to account for these differences. The modified algorithm inherits the advantages of the FM algorithm to efficiently sample the potential energy landscape for coil conformations. The specific geometries incorporated in the new algorithm result in a better reproduction of experimental RDCs and are generally applicable for further studies to characterize the conformational properties of intrinsically disordered proteins. In addition, the internal-co-ordinate-based algorithm is an order of magnitude more efficient, and facilitates side-chain construction, surface osmolyte simulation, spin-label distribution sampling and proline cis/trans isomer simulation.

Direct Prediction of NMR Residual Dipolar Couplings from the Primary Sequence of Unfolded Proteins

2012 ◽  
Vol 125 (2) ◽  
pp. 715-718 ◽  
Author(s):  
Jie-rong Huang ◽  
Valéry Ozenne ◽  
Malene Ringkjøbing Jensen ◽  
Martin Blackledge
Keyword(s):  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Primary Sequence ◽  
Unfolded Proteins ◽  
Nmr Residual Dipolar Couplings

Determination of the Relative Configuration of β-Amino Acid Esters Based on Residual Dipolar Couplings

2015 ◽  
Vol 2015 (31) ◽  
pp. 6801-6805 ◽  
Author(s):  
Thomas Niklas ◽  
Christian Steinmetzger ◽  
Weiping Liu ◽  
Daniel Zell ◽  
Dietmar Stalke ◽  
...  
Keyword(s):  
Amino Acid ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Amino Acid Esters ◽  
Relative Configuration ◽  
Acid Esters
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