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

Authors


  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: Ashok Kulkarni; e-mail: kulashok_kar_biophy@yahoo.co.in or ashok_physol@mims.edu.in

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. 1H-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[1] and Arg[2], and its tendency to inter-convert between γ-and inverse γ-turn conformations imply that the peptide is flexible in nature. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 460–471, 2013.

Ancillary