Low Energy Conformations of a Three-Helix Peptide in an All-Atom Biomolecular Forcefield

摘要

Using a recently developed all-atom forcefields for biomolecular structure prediction we have analyzed an approximate free-energy surface of the 36 residue headpiece of the villin protein with stochastic optimization methods. With an initial paramterization of the solvent accessible surface area based solvation term we found configurations that were lower in energy than the NMR configuration. We then adjusted the parameters of the solvent model to stabilize the NMR structure using a decoy approach and arrived at a free energy surface that is characterized by a deep folding funnel populated by different three helix structures one of which is very similar to the NMR structure.