Paper Citing VMD - Abstract
Kumar, Nigam, Kishore, Raghuvansh
Determination of an unusual secondary structural element in the immunostimulating tetrapeptide rigin in aqueous environments: insights via MD simulations, (1)H NMR and CD spectroscopic studies
JOURNAL OF PEPTIDE SCIENCE, 16:456-464, SEP 2010 2010
An immunomodulating tetrapeptide, rigin (H-Gly-Gin-Pro-Arg-OH), has been examined for its secondary structure preferences through combined use of high-temperature unrestrained MD simulations in implicitwater and 1D and 2D (1)H NMR spectroscopy. The distribution of backbone torsion angles revealed the predominance of trans conformers across the Xaa-Pro peptide bond. The results of MD simulations revealed that of the five predicted families A-E, the predominant families, family A (92 structures), family C (63 structures) and family D (31 structures), could be complemented by extensive 1D and 2D (1)H NMR parameters acquired in aqueous PBS solution. A survey of specific inter- and intraresidue NOEs substantiated the predominance of an unusual type VII beta-turn structure, defined by two torsion angles, i.e. psi(Gln) similar to 155 degrees and phi(pro) similar to -65 degrees across the Gin-Pro segment. The proposed semi-folded kinked topology precluded formation of any intramolecular interaction, i.e. hydrogen bond or electrostatic interaction. Far-UV CD spectral characteristics of rigin in aqueous PBS solution and non-aqueous structure-promoting organic solvents, TFE and IMP, revealed its strong solvent dependence. However, in aqueous PBS solution, the presence of a weak negative shoulder at similar to 234 nm could be ascribed to a small population with ordered, semi-folded topology. We propose that the plausible structural attributes may be exploited for design and rigidification of the bioactive conformation of this immunomodulator toward improved immunopharmacological properties. Copyright (c) 2010 European Peptide Society and John Wiley & Sons, Ltd.
