2007/01/10 by Manoj V. Athawale, Gaurav Goel, Tuhin Ghosh +2
Biochemistry, Genetics and Molecular Biology · Chemical Engineering · Chemistry · Materials Science · Physics and Astronomy · #Chemical physics #Chemistry #Computational chemistry #Entropic force #Entropy (arrow of time) #Folding (DSP implementation) #Hydrophobic effect #Material Dynamics and Properties #Molecular dynamics #Organic chemistry #Physical chemistry #Physics #Polymer #Protein Structure and Dynamics #Rheology and Fluid Dynamics Studies #Surface energy #Surface tension #Thermodynamics #cond-mat.soft #cond-mat.stat-mech
paper · pdf · doi:10.1073/pnas.0605139104
published as Proceedings of the National Academy of Sciences, USA 104, 733-738 (2007). [Open Access Article available at www.pnas.org] · 24 pages, 5 figures
openalex publication_date 2007/01/10 · arxiv created 2007/01/26 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer-water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, DeltaG = gamma(T)DeltaA, where the surface tension, gamma, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer-water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor-liquid interface.