TITLE:
A Stereochemically-Bent β-Hairpin: Scrutiny of Folding by Comparing a Heteropolypeptide and Cognate Oligoalanine
AUTHORS:
Kinshuk Raj Srivastava, Susheel Durani
KEYWORDS:
Protein Folding, Protein Stereochemistry, β-Hairpin, Polyalanine Model, Solvent Effects
JOURNAL NAME:
Open Journal of Physical Chemistry,
Vol.4 No.3,
July
29,
2014
ABSTRACT: A poly-L β-hairpin bent stereochemically
as a boat-shaped protein of mixed-L,D structure is scrutinized in basis of
ordering as minimum of energy specific for its sequenceand solvent. The model
suitable for the scrutiny is accomplished by design. A terminally-blocked
oligoalanine is nucleated overDPro6-Gly7 and DPro6-LAsp7 dipeptide structures as a
twelve-residue β-hairpin
and bent stereochemically as a boat-shaped fold. The structure is inverse
designed with side chains suitable to bind substrate p-nitophenyl phosphate, a
surrogate substrate of acetyl choline and CO2. The designed
sequences were proven by spectroscopy and molecular dynamics to order with
solvent effects of water and display high binding affinity for the substrate.
One of the proteins and a cognate oligoalanine are evolved with molecular
dynamics to equilibrium in a solvent bath of water. Molecular dynamics studies
establish that heteropolypeptide well ordered as β-hairpin fold and cognate
oligoalanine as an ensemble of hairpin-like folds in water. The ordering of
cognate oligoalanine as ensembles of hairpin-like folds manifests combined role
of water as strong dielectric and weak dipolar solvent of peptides. The roles
of stereochemistry and chemical details of sequence in defining polypeptides as
energy minima under specific effect of solvent are illuminated and have been
discussed.