The SAAP Force Field.A.Simple Approach to a New All-Atom Protein Force Field by Using Single Amino Acid Potential (SAAP) Functions in Various Solvents

摘要

A simple stategy to compose a new all-atom protein force field (named as the SAAP force field),which dutilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM)is presented We considered that the total energy function of a protein force field (E~TOTAL) is divided into three components a single damino acid potential term (E~SAAP) an interamino acid nonbonded interaction term (E~INTER) and a miscellaneous term (E~OTHERS) which is ignored (or considered to be constant) at the current version of hte forde fiedl The E~INTER term consists of electrostatic interactions(E~ES) and van der Wasls interactions (E~LJ).Despite simplicity the SAAP force field implicitly involves the correlation among individeual terms of the Lifson's potential function within a single amino acid duit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium Application of the SAAP force field to the Monte Carlo simulation of For-Ala_2-NH_2 in vacuo reasonabley reproduced the results of the extensive cinformation aearch by ab initio molecular orbital calculation In addition the preliminary Monte Carlo simulations for For-Gly_10-NH_2 and For-Ala_10-Nh_2 showed reversible transitions from the extended to the pseudosecondary structures in water (D= 78.39) as well as in ether (D=4.336).The result suppested that the new approach is efficient for fast modeling of protein structures in various environmments Decomposition analysis of the total energy function (E~total) by using the SAAP force field suggested that conformational propensities of single amion acids (i.e theE~SAAP term) may play definitive roles on the topologies of protein secondary structures.