Combined use of molecular dynamics simulations and NMR to explore peptide bond isomerization and multiple intramolecular hydrogen‐bonding possibilities in a cyclic pentapeptide, cyclo (Gly‐Pro‐D‐Phe‐Gly‐Val)

Z. P. Liu, L. M. Gierasch

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

The conformational behavior of a model cyclic pentapeptide—cyclo(Gly‐L‐Pro‐D‐Phe‐Gly‐L‐Val)—has been explored through the combined use of in vacuo molecular dynamics simulations and a range of nmr experiments (preceding paper). The molecular dynamics analysis suggests that, despite the conformational constraints imposed by formation of the pentapeptide cycle, this pentapeptide undergoes conformational transitions between various hydrogen‐bonded conformations, characterized by low energy barriers. An inverse γ turn with Pro in position i+1 and a γ turn with D‐Phe in position i+1 are two alternatives occurring frequently. Like other DLDDL cyclic pentapeptides, cyclo (Gly‐Pro‐D‐Phe‐Gly‐Val) is also stabilized by an inverse γ‐turn structure with the β‐branched Val residue in position i + 1, and this hydrogen bond is retained in the different conformational families. The γ‐turn around D‐Phe3 and the inverse γ turn around Val5 are consistent with the nmr observations. 3JNH—CHα coupling constants of the all‐trans forms were calculated from one of the molecular dynamics trajectories and are comparable to nmr experimental data, suggesting that the conformational states visited during the simulation are representative of the conformational distribution in solution. In addition to the equilibrium among various hydrogen‐bonded all‐trans conformers, the observation in nmr spectra of two sets of resonances for all peptide protons indicated a slow conformational interconversion of the Gly‐Pro peptide bond between trans and cis isomers. The activation energy between these two conformers was determined experimentally by magnetization transfer and was calculated by high temperature constrained molecular dynamics simulation. Both methods yield a free energy of activation of ca. 20 kcal/mol. Furthermore, the free energy of activation is dependent on the direction of rotation of the Gly‐Pro peptide bond. © 1992 John Wiley & Sons, Inc.

Original languageEnglish (US)
Pages (from-to)1727-1739
Number of pages13
JournalBiopolymers
Volume32
Issue number12
DOIs
StatePublished - Dec 1992

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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