title: Role of hydrophobic interactions and salt-bridges in beta-hairpin folding.
abstract: Beta-hairpins are the simplest form of beta-sheets which, due to the presence of long-range interactions, can be considered as tertiary structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a beta-hairpin peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide. Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.
authors.affiliation: Distributed Information Centre, Centre for Biotechnology, Anna University, 600025 Chennai , India.
authors.forename: Aswin Sai Narain
authors.initials: AS
authors.lastname: Seshasayee
authors.forename: Krishnan
authors.initials: K
authors.lastname: Raghunathan
authors.forename: Karthikeyan
authors.initials: K
authors.lastname: Sivaraman
authors.forename: Gautam
authors.initials: G
authors.lastname: Pennathur
mesh_terms: D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D009038:Motion; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D011506:Proteins