NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion.
J Biomol NMR. 2011 May;50(1):59-70
Authors: Johnson E
Abstract
NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in previous studies of correlated motions. These sites are identified on the basis of an effective reorientational number, n ( eff ). Not only does this parameter identify sites of short- and long-range motion, it also provides a way of evaluating the separability condition that is key to the Lipari-Szabo model-free method. When analyzed in conjunction with the Prompers-Brüschweiler separability index, the n ( eff ) values indicate that longer-range motions play a more prominent role in apo calbindin than they do in ubiquitin.
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion
Abstract NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca2+-free) state of calbindin D9k. Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in...
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04-24-2011 03:40 AM
[NMR paper] Determination of protein structures consistent with NMR order parameters.
Determination of protein structures consistent with NMR order parameters.
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J Am Chem Soc. 2004 Jul 7;126(26):8090-1
Authors: Best RB, Vendruscolo M
Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...
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11-24-2010 09:51 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics.
Temperature dependence of NMR order parameters and protein dynamics.
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J Am Chem Soc. 2003 Sep 17;125(37):11158-9
Authors: Massi F, Palmer AG
The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...
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11-24-2010 09:16 PM
[NMR paper] Correlation between 2H NMR side-chain order parameters and sequence conservation in g
Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins.
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J Am Chem Soc. 2003 Jul 30;125(30):9004-5
Authors: Mittermaier A, Davidson AR, Kay LE
Side-chain 2H NMR relaxation data have been collected for the SH3 domain from the Fyn tyrosine kinase and analyzed with respect to sequence preference and per-residue solvent accessibility. Residues that are highly preferred at a given...
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[NMR paper] Contact model for the prediction of NMR N-H order parameters in globular proteins.
Contact model for the prediction of NMR N-H order parameters in globular proteins.
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J Am Chem Soc. 2002 Oct 30;124(43):12654-5
Authors: Zhang F, Brüschweiler R
An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the...
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[NMR paper] Defining long range order in NMR structure determination from the dependence of heter
Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.
Related Articles Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.
Nat Struct Biol. 1997 Jun;4(6):443-9
Authors: Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM
Structure determination by NMR presently relies on short range restraints between atoms in close spatial proximity, principally in the...
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08-22-2010 03:31 PM
[NMR paper] Defining long range order in NMR structure determination from the dependence of heter
Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.
Related Articles Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.
Nat Struct Biol. 1997 Jun;4(6):443-9
Authors: Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM
Structure determination by NMR presently relies on short range restraints between atoms in close spatial proximity, principally in the...
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08-22-2010 03:03 PM
Script to obtain order parameters from a structure
A Python script for prediction of order paramter from a structure is available from this website.
The script is based on the following paper
F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion.
Linear Mode
