Improved treatment of cyclic beta-amino acids and successful prediction of beta-Peptide secondary structure using a modified force field: AMBER*C

摘要

We added parameters to the AMBER* force field to model cyclic beta-amino acid derivatives moro accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon-carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of traits 2-aminocyclohexanecarboxylic acid (trans-ACHC) and trans-2-aminocyclopentanecarboxylic acid (trans-ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen-bonding tendencies of simple diamide derivatives of trans-ACHC and trans-ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by beta-amino acid homo-oligomers. (C) 2000 John Wilely & Sons, Inc. [References: 70]