Conformational flexibility and loss of structural rigidity for a model hexapeptide, GRGDTP: 1H-NMR and molecular dynamics studies.

Abstract

The NMR and molecular dynamics methods are used to study the conformations of a hexapeptide, GRGDTP, which has been shown to be accessible to various types of cell-adhesion based cellular behaviors such as cell-to-matrix interactions, cell differentiation, immunogenicity development, gene expression, angiogenesis, metastasis, sex determination and gamete fusion. (1)H-NMR results indicate the existence of weak 5→2 hydrogen bonded β-turn type-III. Molecular simulation studies using a mixed protocol of distance geometry, constrained minimization, restrained molecular dynamics followed by energy minimization resulted additional conformations that include about 64% of population of inverse γ-turn (HB, 3→1) and about 35% population of γ-turn (HB, 4→2). The inter-proton distances observed in γ-and inverse γ-turns are also consistent with the NMR constraints. The variable internal hydrogen bonding due to γ-turns initiated at Gly and Arg, and its tendency to inter-convert between γ-and inverse γ-turn conformations imply that the peptide is flexible in nature.

• Authors: Ashok K Kulkarni, Rajendra P Ojha
• Journal: Biopolymers (Biopolymers) Vol. 99 Issue 7 Pg. 460-71 (Jul 2013) ISSN: 1097-0282 [Electronic] United States
• PMID: 23616214 (Publication Type: Journal Article)
• Copyright: Copyright © 2013 Wiley Periodicals, Inc.

Topics

• Hydrogen Bonding
• Magnetic Resonance Spectroscopy
• Models, Molecular
• Molecular Dynamics Simulation
• Protein Conformation
• Proton Magnetic Resonance Spectroscopy