title: Experiments and comprehensive simulations of the formation of a helical turn.
abstract: We investigate the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH(2). NMR measurements indicate that this peptide has significant tendency to form a structure of a helical turn, while temperature dependent CD establishes the helix fraction at different temperatures. Molecular dynamics and milestoning simulations agree with experimental observables and suggest an atomically detailed picture for the turn formation. Using a network representation, two alternative mechanisms of folding are identified: (i) a direct co-operative mechanism from the unfolded to the folded state without intermediate formation of hydrogen bonds and (ii) an indirect mechanism with structural intermediates with two residues in a helical conformation. This picture is consistent with kinetic measurements that reveal two experimental time scales of sub-nanosecond and several nanoseconds.
authors.affiliation: Department of Chemistry, Biochemistry, and Institute of Biomedical Studies, Baylor University, Waco, Texas 76706, USA.
authors.forename: Gouri S
authors.initials: GS
authors.lastname: Jas
authors.forename: Wendy A
authors.initials: WA
authors.lastname: Hegefeld
authors.forename: Peter
authors.initials: P
authors.lastname: Májek
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Kuczera
authors.forename: Ron
authors.initials: R
authors.lastname: Elber
mesh_terms: D000465:Algorithms; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics
chemical_list: D010455:Peptides