title: 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.affiliation: Department of Physiology, Mediciti Institute of Medical Sciences, Hyderabad, 501401, Andhra Pradesh, India.  kulashok_kar_biophy@yahoo.co.in
authors.forename: Ashok K
authors.initials: AK
authors.lastname: Kulkarni
authors.forename: Rajendra P
authors.initials: RP
authors.lastname: Ojha
mesh_terms: D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D066244:Proton Magnetic Resonance Spectroscopy