We describe an efficient method to calculate analytically the solvent accessible surface areas and their gradients in proteins for empirical force field calculations on serial and parallel computers. In an application to the small three helix bundle protein E r-10, energy minimizations and Monte Carlo simulations were performed with the empirical ECEPP/2 force field, which was extended by a protein solvent interaction term. We show that the NMR structure is stable when refined with the force field including the protein solvent interaction term, but large structural deviations are observed in energy minimization in vacuo. When we started from random structures with preformed helices and maintained the helical segments by dihedral angle constraints, the final structures with the lowest energies resembled the native form. The root-mean-square deviations for the backbone atoms of the three helices compared to the experimentally determined structure was 3 Å to 4 Å.
- Keywords Protein folding, accesible surface areas, Monte Carlo simulations, FANTOM, parallel computers, three-helix bundle
ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry
- Organic Chemistry
- Inorganic Chemistry
- Computational Theory and Mathematics