title: Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution.
abstract: We probe the urea-denaturation mechanism using molecular dynamics simulations of an elementary "folding" event, namely, the formation of end-to-end contact in the linear hydrocarbon chain (HC) CH(3)(CH(2))(18)CH(3). Electrostatic effects are examined using a model HC in which one end of the chain is positively charged (+0.2e) and the other contains a negative charge (-0.2e). For these systems multiple transitions between "folded" (conformations in which the chain ends are in contact) and "unfolded" (end-to-end contact is broken) can be observed during 4 ns molecular dynamics simulations. In water and 6 M aqueous urea solution HC and the charged HC fluctuate between collapsed globular conformations and a set of expanded structures. The collapsed conformation adopted by the HC in water is slightly destablized in 6 M urea. In contrast, the end-to-end contact is disrupted in the charged HC only in aqueous urea solution. Despite the presence of a large hydrophobic patch, on length scales on the order of approximately 8-10 A "denaturation" (transition to the expanded unfolded state) occurs by a direct interaction of urea with charges on the chain ends. The contiguous patch of hydrophobic moieties leads to "mild dewetting", which becomes more pronounced in the charged HC in 6 M aqueous urea solution. Our simulations establish that the urea denaturation mechanism is most likely electrostatic in origin.
authors.affiliation: Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, USA. RMountain@nist.gov
authors.forename: Raymond D
authors.initials: RD
authors.lastname: Mountain
authors.forename: D
authors.initials: D
authors.lastname: Thirumalai
mesh_terms: D003198:Computer Simulation; D006838:Hydrocarbons / Q000737:chemistry*; D008956:Models, Chemical; D011489:Protein Denaturation; D012996:Solutions; D055672:Static Electricity; D014508:Urea / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D006838:Hydrocarbons; D012996:Solutions; D014867:Water; D014508:Urea