Repository: Freie Universit├Ąt Berlin, Math Department

Local elevation on the dihedral angles to improve the J-values

Christen, M. and Keller, B. and van Gunsteren, W. F. (2007) Local elevation on the dihedral angles to improve the J-values. Journal of Biomolecular NMR, 39 . pp. 265-273.

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Official URL: http://dx.doi.org/10.1007/s10858-007-9194-2

Abstract

Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, (3)J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. Because multiple torsion angle values phi correspond to the same (3)J-coupling constant and high-energy barriers are separating those, restraining (3)J-coupling constants remains difficult. A method to adaptively enforce restraints using a local elevation (LE) potential energy function is presented and applied to (3)J-coupling constant restraining in an MD simulation of hen egg-white lysozyme (HEWL). The method succesfully enhances sampling of the restrained torsion angles until the 37 experimental (3)J-coupling constant values are reached, thereby also improving the agreement with the 1,630 experimental NOE atom-atom distance upper bounds. Afterwards the torsional angles phi are kept restrained by the built-up local-elevation potential energies.

Item Type:Article
Subjects:Physical Sciences > Physics > Mathematical & Theoretical Physics > Computational Physics
Physical Sciences > Chemistry > Physical Chemistry
Biological Sciences > Molecular Biology
ID Code:843
Deposited By: BioComp Admin
Deposited On:12 Mar 2010 11:30
Last Modified:27 Oct 2010 11:46

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