Premium
A Method for Conformational Sampling of Loops in Proteins Based on Adiabatic Decoupling and Temperature or Force Scaling
Author(s) -
Kunz AnnaPitschna E.,
van Gunsteren Wilfred F.
Publication year - 2011
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201100305
Subject(s) - scaling , adiabatic process , molecular dynamics , decoupling (probability) , chemistry , umbrella sampling , potential of mean force , dihedral angle , root mean square , boltzmann distribution , thermodynamics , chemical physics , computational chemistry , molecular physics , physics , molecule , hydrogen bond , quantum mechanics , mathematics , geometry , organic chemistry , control engineering , engineering
A method for conformational Boltzmann sampling of loops in proteins in aqueous solution is presented that is based on adiabatic decoupling molecular dynamics (MD) simulation with temperature or force scaling. To illustrate the enhanced sampling, the loop from residues 33 to 43 in the bovine protein ribonuclease A is adiabatically decoupled from the rest of the protein and the solvent with a mass scaling factor s m =1000 and the sampling is enhanced with a scaling of the temperature using s T =2 or of the force using s V =0.667. Over 5 ns of simulation the secondary structure of the protein remains unaltered while a combined dihedral‐angle conformational cluster analysis shows an increase of conformations outside the first most populated cluster of loop conformations for adiabatic decoupling MD with temperature scaling using s T =2 or force scaling using s V =0.667 compared to the standard MD simulation. The atom‐positional root‐mean‐square fluctuations of the C α atoms of the loop show an increase in the movement of the loop as well, indicating that adiabatic decoupling MD with upscaling of the temperature or downscaling of the force is a promising method for conformational Boltzmann sampling.