Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Kenichi Dedachi,Michio Iwaoka,Toshiya Minezaki,Taku Shimosato

doi:10.1155/2013/407862

Abstract

Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials <svg style="vertical-align:-2.3205pt;width:52.037498px;" id="M1" height="19.0875" version="1.1" viewBox="0 0 52.037498 19.0875" width="52.037498" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg"> <g transform="matrix(.017,-0,0,-.017,.062,16.137)"><path id="x28" d="M300 -147l-18 -23q-106 71 -159 185.5t-53 254.5v1q0 139 53 252.5t159 186.5l18 -24q-74 -62 -115.5 -173.5t-41.5 -242.5q0 -130 41.5 -242.5t115.5 -174.5z" /></g><g transform="matrix(.017,-0,0,-.017,5.944,16.137)"><path id="x1D438" d="M609 650l-19 -162l-30 -2q2 69 -14 94q-9 18 -28.5 26t-74.5 8h-88q-30 0 -37 -6.5t-12 -36.5l-41 -212h103q48 0 69 5.5t32 19t26 50.5h29l-40 -198h-30q2 58 -11.5 70.5t-85.5 12.5h-99l-30 -167q-17 -87 3 -101q18 -15 111 -15q59 0 89 7t54 27q8 7 15.5 16t16 21.5
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Highlights

In conformational analysis of short peptides, Monte Carlo (MC) and molecular dynamics (MD) simulation techniques have been widely applied [1, 2], in which a set of potential energy functions, such as ECEPP [3, 4], AMBER [5,6,7,8], CHARMM [9], OPLS [10, 11], and GROMOS [12], is employed to define the relation between the structure and the potential energy
The values of these energetic terms were maintained stable during the single amino acid potential (SAAP)-MC simulation with large fluctuation for ESAAP and ELJ, while the value of EES was almost zero, as observed previously [34]: the large dielectric constant of water would make the electrostatic interaction between the amino acid residues ignorable
The value of rY1⋅⋅⋅M5 dispersed in a range from 5 to 12 Ain the SAAP-MC simulation, while those converged at around 6 Ain the AMBER-MD simulation (Figure 3)

Summary

Introduction

In conformational analysis of short peptides, Monte Carlo (MC) and molecular dynamics (MD) simulation techniques have been widely applied [1, 2], in which a set of potential energy functions (a so-called force field), such as ECEPP [3, 4], AMBER [5,6,7,8], CHARMM [9], OPLS [10, 11], and GROMOS [12], is employed to define the relation between the structure and the potential energy. Various types of coarse-grained force fields, such as AMBER-UA [18], UNRES [19,20,21,22,23], and MARTINI [24, 25], have been developed in order to reduce time to compute the potential energy. Physicochemical implications of this unexpected similarity are not yet clear, the finding strongly suggests prominent importance of SAAP as a determinant of protein structures. This point would be supported by the previous experimental result by Dobson and coworkers [29, 30] that φ and ψ dihedral angle distributions of individual amino acid residues

Results

Discussion

Conclusion