title: Distinctions in early stage unwinding mechanisms of zwitterionic, capped, and neutral forms of different α-helical homopolymeric peptides.
abstract: Molecular dynamics simulations of α-helical polyalanine, polyleucine, polylysine, and poly(glutamic acid) with different forms of terminal groups in water at 300 K showed sharp distinctions in their unwinding mechanisms. Zwitterionic, capped, and neutral forms of polyalanine, polyleucine, and polylysine have been explored to elucidate their unwinding mechanism at very early stage, e.g., initial time window. Role of water in the unwinding mechanisms of the various helices has been envisaged. Also, it is evident from our calculations that the short- and long-range nonbonded interactions among the side chains is an important factor determining the unwinding mechanisms of the various homopolymeric α-helices. These findings can be helpful in constructing predictive models for understanding of the unwinding of α-helical proteins and peptides.
authors.affiliation: Physical Chemistry Division, National Chemical Laboratory , Pune 411008, India.
authors.forename: Prithvi Raj
authors.initials: PR
authors.lastname: Pandey
authors.forename: Sudip
authors.initials: S
authors.lastname: Roy
mesh_terms: D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides; D011108:Polymers