Ensemble-based interpretations of NMR structural data to describe protein internal dynamics.
Molecules. 2013;18(9):10548-67
Authors: F Ángyán A, Gáspári Z
Abstract
NMR spectroscopy is the leading technique to characterize protein internal dynamics at the atomic level and on multiple time scales. However, the structural interpretation of the observables obtained by various measurements is not always straightforward and in many cases dynamics-related parameters are only used to "decorate" static structural models without offering explicit description of conformational heterogeneity. To overcome such limitations, several computational techniques have been developed to generate ensemble-based representations of protein structure and dynamics with the use of NMR-derived data. An important common aspect of the methods is that NMR observables and derived parameters are interpreted as properties of the ensemble instead of individual conformers. The resulting ensembles reflect the experimentally determined internal mobility of proteins at a given time scale and can be used to understand the role of internal motions in biological processes at atomic detail. In this review we provide an overview of the calculation methods currently available and examples of biological insights obtained by the ensemble-based models of the proteins investigated.
[NMR paper] Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.
Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.
Related Articles Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.
J Biomol NMR. 2013 Mar 14;
Authors: Eichenberger AP, van Gunsteren WF, Smith LJ
Abstract
Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the...
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An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins
An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins
February 2012
Publication year: 2012
Source:Biochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1818, Issue 2</br>
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Solid-state NMR (SSNMR) is an invaluable tool for determining orientations of membrane proteins and peptides in lipid bilayers. Such orientational descriptions provide essential information about membrane protein functions. However, when a semi-static single conformer model is used to interpret various SSNMR observables, important dynamics information can...
[NMR paper] Influence of internal dynamics on accuracy of protein NMR structures: derivation of r
Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.
Related Articles Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.
J Mol Biol. 1999 Jan 15;285(2):727-40
Authors: Schneider TR, Brünger AT, Nilges M
In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a...
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[NMR paper] NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding reg
NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family.
Related Articles NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family.
...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
Related Articles CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
BMC Struct Biol. 2010 Oct 29;10(1):39
Authors: Angyan AF, Szappanos B, Perczel A, Gaspari Z
ABSTRACT: BACKGROUND: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data -
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - 7thSpace Interactive (press release)
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
7thSpace Interactive (press release)
These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill ...
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10-29-2010 09:32 PM
[NMR paper] An approach to protein homology modelling based on an ensemble of NMR structures: app
An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Related Articles An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Protein Eng. 1995 Jul;8(7):615-25
Authors: Adzhubei AA, Laughton CA, Neidle S
A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of...
Ensemble-based interpretations of NMR structural data to describe protein internal dynamics.
Linear Mode
