A comparative theoretical study of dipeptide solvation in water

✍ Scribed by Håkan W. Hugosson; Alessandro Laio; Patrick Maurer; Ursula Rothlisberger

• Publisher: John Wiley and Sons
• Year: 2006
• Tongue: English
• Weight: 219 KB
• Volume: 27
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.20360

✦ Synopsis

Abstract

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine–alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car–Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged —NH and —CO side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd). © 2006 Wiley Periodicals, Inc. J Comput Chem 27:672–684, 2006