Related ArticlesWhat contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
J Mol Biol. 2005 May 27;349(1):185-203
Authors: Best RB, Clarke J, Karplus M
Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The results reproduce the variation in core side-chain dynamics observed by NMR and highlight the relevance of anharmonic motion and transitions between local minima for explaining NMR side-chain order parameters. A method is described for calculating converged order parameters by use of replica exchange molecular dynamics in conjunction with an implicit solvent model. These simulations allow the influence of various factors, such as the flexibility of side-chains and their free volume, on the mobility to be tested by perturbing the system. Deletion mutations are found to have the largest effect on the more densely packed FNfn10. Some counterintuitive effects are seen, such as an increase in order parameters close to deletion mutation sites, but these can be rationalized in terms of direct interactions with the modified side-chains. A statistical analysis of published order parameters supports the conclusions drawn from the simulations.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Protein Pept Lett. 2011 Jan 11;
Authors: Yang D
Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. Detailed dynamics information is crucial for the understanding of protein function and biochemical and biophysical properties, which can be obtained using NMR relaxation techniques. In this review, (13)C relaxation of methine, methylene and methyl groups with and without...
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Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
J Am Chem Soc. 2010 Dec 27;
Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics...
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Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Alexandre Esadze, Da-Wei Li, Tianzhi Wang, Rafael Bru?schweiler and Junji Iwahara
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107847d/aop/images/medium/ja-2010-07847d_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja107847d
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
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12-28-2010 05:27 AM
[NMR paper] Characterization of threonine side chain dynamics in an antifreeze protein using natu
Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy.
Related Articles Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy.
J Biomol NMR. 2004 Jun;29(2):139-50
Authors: Daley ME, Sykes BD
The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance (13)C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible...
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11-24-2010 09:51 PM
[NMR paper] Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study
Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.
Related Articles Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.
J Am Chem Soc. 2003 Feb 19;125(7):1748-58
Authors: Choy WY, Shortle D, Kay LE
NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics...
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11-24-2010 09:01 PM
[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Biochemistry. 2001 Jun 5;40(22):6559-69
Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ
A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...
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11-19-2010 08:32 PM
[NMR paper] A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-cor
A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk.
Related Articles A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk.
J Mol Biol. 1998 Mar 13;276(5):939-54
Authors: Yang D, Mittermaier A, Mok YK, Kay LE
Two new NMR experiments are presented for measuring side-chain dynamics in proteins. The first method, requiring 15N, 13C,...
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11-17-2010 11:06 PM
[NMR paper] A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation da
A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data.
Related Articles A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data.
J Magn Reson. 1998 Feb;130(2):329-34
Authors: Daragan VA, Mayo KH
A simple approach to deriving motional dynamics information of protein and peptide side chains by using 13C NMR relaxation data is presented. By using linear approximation of internal rotational correlation functions, simple equations for relating side-chain conformation, bond rotational...
What contributions to protein side-chain dynamics are probed by NMR experiments? A mo
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