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Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water and Aqueous Urea Solution



Raymond D. Mountain, D Thirumalai


We probe 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)CH3-(CH2)18-CH3. Electrostaticeffects are examined using a model HC in which one end of the chain is positively charged and the other contains a negative charge. 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 4ns molecular dynamics simulations. In water and 6M aqueous urea solution HC and the charged HC fluctuate between collapsed globular conformations and a set of expanded structures. The collapsed on formation adopted by the HC in water is slightly destablized in 6M urea. In contrast, the end-to-end contact is disrupted in the charge HC only in aqueous urea solution. Despite the presence of a large hydrophobic patch on length scales on the order of {approximately} (8 - 10) 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 dewetting which becomespronounced in the charged HC in 6M aqueous urea solution. Our simulations firmly establish that the urea denaturation mechanism is electrostatic in origin.
Journal of the American Chemical Society


chain folding, electrostatic mechanism, hyddrophobic interaction, hydrogen bonding, molecular dynamics, urea-water solution


Mountain, R. and Thirumalai, D. (2003), Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water and Aqueous Urea Solution, Journal of the American Chemical Society (Accessed July 24, 2024)


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Created February 1, 2003, Updated February 17, 2017