Improved treatment of cyclic ?-amino acids and successful prediction of ?-peptide secondary structure using a modified force field: AMBER*C
✍ Scribed by Christianson, Laurie A.; Lucero, Melissa J.; Appella, Daniel H.; Klein, Daniel A.; Gellman, Samuel H.
- Publisher
- John Wiley and Sons
- Year
- 2000
- Tongue
- English
- Weight
- 288 KB
- Volume
- 21
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
We added parameters to the AMBER * force field to model cyclic β-amino acid derivatives more 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 trans-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 β-amino acid homo-oligomers.