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)
✍ Scribed by Zhi-Ping Liu; Lila M. Gierasch
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 1992
- Tongue
- English
- Weight
- 1014 KB
- Volume
- 32
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
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 y turn with Pro in position i + 1 and a y 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 y-turn structure with the @-branched Val residue in position i + 1, and this hydrogen bond is retained in the different conformational families. * DISCOVER, with the molecular modeling program IN-SIGHTII, are commercially available from Biosym Technologies,