[NMR paper] General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
Related ArticlesGeneral Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
Biochem Biophys Res Commun. 2015 Jan 16;
Authors: Liu Q, Shi C, Yu L, Zhang L, Xiong Y, Tian C
Abstract
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extened simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner.
PMID: 25600810 [PubMed - as supplied by publisher]
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations
Publication date: Available online 16 January 2015
Source:Biochemical and Biophysical Research Communications</br>
Author(s): Qing Liu , Chaowei Shi , Lu Yu , Longhua Zhang , Ying Xiong , Changlin Tian</br>
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and...
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01-17-2015 04:14 PM
Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
Abstract
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not...
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11-21-2014 09:04 PM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
J Phys Chem B. 2014 Oct 28;
Authors: Allnér O, Foloppe N, Nilsson L
Abstract
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...
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10-29-2014 03:51 PM
Time-averaged order parameter restraints in molecular dynamics simulations
Time-averaged order parameter restraints in molecular dynamics simulations
Abstract
A method is described that allows experimental \(S^2\) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated...
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10-14-2014 09:48 PM
[NMR paper] Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Related Articles Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Biochim Biophys Acta. 2013 Dec 26;
Authors: Bernini A, De Angelis LH, Morandi E, Spiga O, Santucci A, Assfalg M, Molinari H, Pillozzi S, Arcangeli A, Niccolai N
Abstract
Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces....
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01-01-2014 03:05 PM
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies
Publication date: Available online 27 December 2013
Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics</br>
Author(s): Andrea Bernini , Lucia Henrici De Angelis , Edoardo Morandi , Ottavia Spiga , Annalisa Santucci , Michael Assfalg , Henriette Molinari , Serena Pillozzi , Annarosa Arcangeli , Neri Niccolai</br>
Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces....
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12-27-2013 11:54 AM
[NMR paper] Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.
Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.
Related Articles Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.
Biochemistry. 2005 Jul 19;44(28):9673-9
Authors: Gitti RK, Wright NT, Margolis JW, Varney KM, Weber DJ, Margolis FL
Nuclear magnetic resonance (NMR) (15)N relaxation measurements of the olfactory marker protein (OMP) including longitudinal relaxation (T(1)), transverse relaxation (T(2)), and (15)N-{(1)H} NOE data were collected at low...
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12-01-2010 06:56 PM
[NMR paper] Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone
Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions.
Related Articles Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions.
Angew Chem Int Ed Engl. 2005 May 30;44(22):3394-9
Authors: Lange OF, Grubmüller H, de Groot BL
General Order Parameter based Correlation Analysis of Protein Backbone Motions between Experimental NMR Relaxation Measurements and Molecular Dynamics Simulations.
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