Related ArticlesContributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding.
J Mol Biol. 1996 Oct 25;263(2):369-82
Authors: Yang D, Kay LE
The relation between order parameters derived from NMR spin relaxation experiments and the contribution to conformational entropy from ns-ps timescale bond vector dynamics is investigated by considering a number of simple models describing bond vector motion. In a few cases both classical and quantum mechanical derivations are included to establish the validity of obtaining order parameter-entropy relations using classical mechanics only. For these cases it is found that classical and quantum mechanical derivations give very similar results so long as the square of the order parameter of the bond vector is less than approximately 0.95. For a given change in order parameter, the change in conformational entropy is sensitive to the model employed, with the absolute value of the entropy change increasing with the number of degrees of freedom in the model. The entropy-order parameter profile calculated from a 1.12 ns molecular dynamics trajectory of fully hydrated Escherichia coli ribonuclease HI is well fit using a simple expression based on a model assuming bond vector diffusion in a cone, suggesting that it may well be possible to extract meaningful entropy changes reflecting changes in ps-ns time scale motions from changes in NMR-derived order parameters. Contributions to the conformational entropy change associated with a folding-unfolding transition of an SH3 domain and calculated from changes in rapid N-HN backbone dynamics are presented.
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy
Abstract An extension to HN(CO-α/β-N,Cα-J)-TROSY (Permi and Annila in J Biomol NMR 16:221â??227, 2000) is proposed that permits the simultaneous determination of the four coupling constants 1 J Nâ?²(i)Cα(i), 2 J HN(i)Cα(i), 2 J Cα(iâ??1)Nâ?²(i), and 3 J Cα(iâ??1)HN(i) in 15N,13C-labeled proteins. Contrasting the original scheme, in which two separate subspectra exhibit the 2 J CαNâ?² coupling as inphase and antiphase splitting (IPAP), we...
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
J Am Chem Soc. 2011 Apr 4;
Authors: Ryabov Y, Schwieters CD, Clore GM
(15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...
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Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201020c
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http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ
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04-05-2011 10:37 AM
[NMR paper] NMR relaxation studies of the role of conformational entropy in protein stability and
NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding.
Related Articles NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding.
Acc Chem Res. 2001 May;34(5):379-88
Authors: Stone MJ
Recent advances in the measurement and analysis of protein NMR relaxation data have made it possible to characterize the dynamical properties of many backbone and side chain groups. With certain caveats, changes in flexibility that occur upon ligand binding, mutation, or...
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[NMR paper] Contributions to protein entropy and heat capacity from bond vector motions measured
Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation.
J Mol Biol. 1997 Oct 10;272(5):790-804
Authors: Yang D, Mok YK, Forman-Kay JD, Farrow NA, Kay LE
The backbone dynamics of both folded and unfolded states of staphylococcal nuclease (SNase) and the N-terminal...
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[NMR paper] Refinement of the NMR solution structure of a protein to remove distortions arising f
Refinement of the NMR solution structure of a protein to remove distortions arising from neglect of internal motion.
Related Articles Refinement of the NMR solution structure of a protein to remove distortions arising from neglect of internal motion.
Biochemistry. 1991 Apr 23;30(16):3807-11
Authors: Fejzo J, Krezel AM, Westler WM, Macura S, Markley JL
The effect of internal motion on the quality of a protein structure derived from nuclear magnetic resonance (NMR) cross relaxation has been investigated experimentally. Internal rotation of the...
Contributions to conformational entropy arising from bond vector fluctuations measure
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