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Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties
Author(s) -
Pappu Rohit V.,
Schneller William J.,
Weaver David L.
Publication year - 1996
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199606)17:8<1033::aid-jcc12>3.0.co;2-f
Subject(s) - multipole expansion , molecular dynamics , representation (politics) , chain (unit) , myoglobin , steric effects , chemistry , computational chemistry , electrostatics , helix (gastropod) , side chain , crystallography , statistical physics , physics , algorithm , computer science , quantum mechanics , stereochemistry , politics , political science , law , ecology , organic chemistry , snail , biology , polymer
A method for describing a polypeptide chain based on an electrostatic multipole representation is introduced. The main features of the description are outlined. Appropriate energy functions for nonbonded interactions are developed. The full atomic representation may be retrieved from the electrostatic multipole representation at any point in a calculation. The multipole description and the energy functions are tested by calculation of steric maps for different amino acid side‐chain groups. The ability to calculate energetically stable structures is demonstrated by energy conformation maps and the results of energy calculations in optimal secondary structural elements. Results from dynamics simulations of helical chains of polyglycine, polyalanine, polyvaline, and a 21‐residue helix obtained from the crystal structure of sperm whale myoglobin are included to demonstrate the efficiency of the algorithm. It is demonstrated that this description of the polypeptide chain is both simple and complete and will allow for the rapid simulation of chain dynamics without loss of essential information about the chain. © 1996 by John Wiley & Sons, Inc.