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 previous studies of correlated motions. These sites are identified on the basis of an effective reorientational number, neff . 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 neff values indicate that longer-range motions play a more prominent role in apo calbindin than they do in ubiquitin.
Content Type Journal Article
Pages 1-12
DOI 10.1007/s10858-011-9504-6
Authors
Eric Johnson, Department of Chemistry and Physical Sciences, College of Mount St. Joseph, Cincinnati, OH 45233, USA
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.
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...
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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
