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Analysis of the conformational profile of trishomocubane amino acid dipeptide

Analysis of the conformational profile of trishomocubane amino acid dipeptide 4‐Amino‐(D3)‐trishomocubane‐4‐carboxylic acid is a constrained α‐amino acid residue that exhibits promising conformational characteristics, i.e., helical and β‐turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The Cα carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N‐terminus and a methylamide group on its C‐terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6‐31G* basis set. Trishomocubane peptide (Ac‐Tris‐NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 310, and αL helical structures. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 339–349, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biopolymers Wiley

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