Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation.
Chemphyschem. 2013 May 23;
Authors: Guerry P, Mollica L, Blackledge M
Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides detailed understanding of the nature and extent of protein dynamics on physiologically important timescales. We present recent advances in the combination of NMR with state-of-the-art molecular simulation that are providing unique new insight into the motions on timescales from nanoseconds to milliseconds. In particular, we focus on methods based on residual dipolar couplings (RDCs) that allow for detailed mapping of the protein conformational energy landscape. A novel combination of RDCs with accelerated molecular dynamics allows for the development of ensemble representations of the underlying Boltzmann ensemble.
PMID: 23703956 [PubMed - as supplied by publisher]
[NMR paper] Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
Related Articles Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics.
Proc Natl Acad Sci U S A. 2013 Apr 9;
Authors: Granata D, Camilloni C, Vendruscolo M, Laio A
Abstract
The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The...
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[NMR paper] Mapping the population of protein conformational energy sub-States from NMR dipolar couplings.
From Mendeley Biomolecular NMR group:
Mapping the population of protein conformational energy sub-States from NMR dipolar couplings.
Angewandte Chemie (International ed. in English) (2013). Volume: 52, Issue: 11. Pages: 3181-5. Paul Guerry, Loïc Salmon, Luca Mollica, Jose-Luis Ortega Roldan, Phineus Markwick, Nico a J van Nuland, J Andrew McCammon, Martin Blackledge et al.
Molecular dynamics: A general method for the statistical mechanical description of conformational energy landscapes of proteins in solution is proposed. This method combines NMR residual dipolar couplings (RDCs),...
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[NMR paper] Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings.
Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings.
Related Articles Mapping the Population of Protein Conformational Energy Sub-States from NMR Dipolar Couplings.
Angew Chem Int Ed Engl. 2013 Feb 1;
Authors: Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NA, McCammon JA, Blackledge M
Abstract
Molecular dynamics: A general method for the statistical mechanical description of conformational energy landscapes of proteins in solution is proposed. This method combines NMR...
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
Available online 13 December 2012
Publication year: 2012
Source:Current Opinion in Structural Biology</br>
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Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational...
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Single-shot NMR measurement of protein unfolding landscapes
Single-shot NMR measurement of protein unfolding landscapes
June 2012
Publication year: 2012
Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1824, Issue 6</br>
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The transient unfolding events from the native state of a protein towards higher energy states can be closely investigated by studying the process of hydrogen exchange. Here, we present BLUU-Tramp (Biophysics Laboratory University of Udine—Temperature ramp), a new method to measure the rates for the exchange process and the underlying equilibrium thermodynamic parameters, using...
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[NMR paper] A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation:
A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Related Articles A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Proteins. 1993 Dec;17(4):375-90
Authors: Eriksson MA, Berglund H, Härd T, Nilsson L
The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using...
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08-22-2010 03:01 AM
[NMR paper] 3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-r
3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.
Related Articles 3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.
J Biomol Struct Dyn. 1992 Apr;9(5):935-49
Authors: Braatz JA, Paulsen MD, Ornstein RL
Mainly due to computational limitations, past protein molecular dynamics simulations have rarely been extended to 300 psec; we are not aware of any published results beyond 350 psec. The present...
Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation.
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