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

Joseph M. Salvino, Peter R. Seoane, Roland E. Dolle

Research output: Contribution to journalArticle

34 Scopus citations

Abstract

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. © 1993 John Wiley & Sons, Inc.

Original languageEnglish
Pages (from-to)438-444
Number of pages7
JournalJournal of Computational Chemistry
Volume14
Issue number4
DOIs
StatePublished - Apr 1993

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