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Molecular dynamics simulations of a winter flounder “antifreeze” polypeptide in aqueous solution
Author(s) -
McDonald Shawn M.,
Brady John W.,
Clancy Paulette
Publication year - 1993
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360331002
Subject(s) - chemistry , hydrogen bond , aqueous solution , molecular dynamics , side chain , solvent , salt bridge , molecule , crystallography , salt (chemistry) , helix (gastropod) , computational chemistry , mutant , organic chemistry , biochemistry , polymer , ecology , biology , snail , gene
A winter flounder antifreeze polypeptide (HPLC‐6) has been studied in vacuo and in aqueous solution using molecular dynamics computer simulation techniques. The helical conformation of this polypeptide was found to be stable both in vacuum and in solution. The major stabilizing interactions were found to be the main‐chain hydrogen bonds, a salt‐bridge interaction, and solute–solvent hydrogen bonds. A significant bending in the middle of the polypeptide chain was observed both in vacuo and in solvent at 300 K. Possible causes of the bending are discussed. From simulations of mutant polypeptide molecules in vacuo, it is concluded that the bend in the native polypeptide was caused by side chain to backbone hydrogen bond competition involving the Thr 24 side chain and facilitated by strains on the helix resulting from the Lys 18‐Glu 22 salt bridge. © 1993 John Wiley & Sons, Inc.