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PEDS Advance Access published online on October 24, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi068
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received August 17, 2005
Accepted September 8, 2005

Article

Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data

Oscar Hur 1* and Kevin Karplus 2

1 PO Box 2548, Sunnyvale, CA 94087-0548, USA
2 Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA

* To whom correspondence should be addressed.
Oscar Hur, E-mail: ohur1688{at}alumni.ucsd.edu


  Abstract

This paper proposes a strategy to translate experimental 1H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, {alpha}-protons, {beta}-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, {alpha}-protons, {beta}-protons in {alpha}-helices, anti-parallel {beta}-sheets and parallel {beta}-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.

Keywords: heavy atom distance; NMR; proton distance.
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