Combined 1H-NMR and molecular dynamics studies on conformational behavior of a model heptapeptide, GRGDSPC.
Among various strategies, the de novo design and in silico approaches are being used to develop the short peptides, models of modified peptides, and mimetics as clinically useful drugs with improved stability and bioavailability. The resulting models will help to isolate the factors behind the folded structure formation and contribute useful information about de novo peptide design. The combined (1)H-NMR spectroscopic and molecular dynamics methods were used to investigate the conformational behavior of an Arg-Gly-Asp (RGD)-containing peptide, GRGDSPC, the cell-binding heptapeptide of extracellular matrix protein, fibronectin. The formation of two fused weak β-turns of type II (HB, 4→1) and type II' (HB, 7→4) from simulation studies has been consistent with NMR data. The sustainable 'S'-shaped molecular structure (which remained unchanged during the entire simulation) and the conformational transitions due to interconversions between multiple turns initiated at Asp(4), Ser(5), and Cys(7) imply that the peptide is flexible in nature. Thus, the model of 'S'-shaped structure with flexible multiple turns for GRGDSPC peptide may provide the structural rationale for antagonistic properties of this heptapeptide toward the treatment of integrin-mediated cellular abnormal behaviors such as thrombosis and metastasis.
Department of Physiology, MediCiti Institute of Medical Sciences, Ghanpur, Medchal Mandal, R. R. District, Hyderabad, 501401, A. P., India.
Ashok K
AK
Kulkarni
Rajendra P
RP
Ojha
D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D066244:Proton Magnetic Resonance Spectroscopy; D013696:Temperature
C112077:Gly-Arg-Gly-Asp-Ser-Pro-Cys; D009842:Oligopeptides
1H-NMR; Arg-Gly-Asp; distance geometry; restrained molecular dynamics; β-turn; γ-turn