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Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations

✍ Scribed by Joseph M. Salvino; Peter R. Seoane; Roland E. Dolle

Publisher
John Wiley and Sons
Year
1993
Tongue
English
Weight
554 KB
Volume
14
Category
Article
ISSN
0192-8651

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✦ Synopsis

Conformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD-determined conformations are in the same energy range as the NMR-determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands.

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