An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide.
We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.
Freedman
Holly
H
Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
Truong
Thanh N
TN
D000409:Alanine / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008432:Mathematical Computing; D008956:Models, Chemical; D011487:Protein Conformation; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D004151:Dipeptides; D014867:Water; D000409:Alanine