Springe direkt zu Inhalt

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation

M. Christen, B. Keller, W. F. van Gunsteren – 2007

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 ϕ 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 ϕ are kept restrained by the built-up local-elevation potential energies.

Title
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation
Author
M. Christen, B. Keller, W. F. van Gunsteren
Date
2007
Identifier
DOI 10.1007/s10858-007-9194-2
Source(s)
Citation
J. Biomol. NMR, 39 (2007), p. 265-273