Premium
Examination of the Effect of N‐terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine–based Short Peptides: A Molecular Dynamics Study
Author(s) -
Goyal Bhupesh,
Srivastava Kinshuk Raj,
Durani Susheel
Publication year - 2016
Publication title -
chemistryselect
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.437
H-Index - 34
ISSN - 2365-6549
DOI - 10.1002/slct.201601381
Subject(s) - side chain , cationic polymerization , chemistry , alanine , lysine , stereochemistry , molecular dynamics , helix (gastropod) , peptide , amino acid , glutamic acid , crystallography , biochemistry , computational chemistry , organic chemistry , polymer , ecology , snail , biology
The effect of N‐terminal diproline segment and charged side chains on the stabilization of helical conformation in alanine‐based short peptides are examined using molecular dynamics (MD) simulations. The cationic peptides, Ac–Pro 1 –Pro 2 –Ala 3 –Lys 4 –Ala 5 –Lys 6 –Ala 7 –Lys 8 –Ala 9 –NH 2 ( Ia ) and Ac– D Pro 1 –Pro 2 –Ala 3 –Lys 4 –Ala 5 –Lys 6 –Ala 7 –Lys 8 –Ala 9 –NH 2 ( IIa ) are examined for the role of lysine side chains on the inducement of helical conformation in alanine‐based short peptides. To examine the influence of lysine and glutamic acid in the i , i + 4 arrangement on the stabilization of helical conformation, cationic peptides, Ia and IIa , are modified as ion‐pair peptides, Ac–Pro 1 –Pro 2 –Glu 3 –Glu 4 –Ala 5 –Ala 6 –Lys 7 –Lys 8 –Ala 9 –NH 2 ( Ib ) and Ac– D Pro 1 –Pro 2 –Glu 3 –Glu 4 –Ala 5 –Ala 6 –Lys 7 –Lys 8 –Ala 9 –NH 2 ( IIb ), respectively. MD simulations manifest enhanced occupancies in the α basin of ϕ , ψ space for ion‐pair peptides as compare to cationic peptides. The radial distribution function (RDF) analysis highlight that large side chain substituents of lysine and glutamic acid assist in helix formation by blocking water molecules from solvating backbone CO and NH groups.