Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

With computer simulations of >100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain was obtained by tiling space with (0.2 nm)3 cubes and projecting the atomistic water molecule positions onto this grid. With the coarse-grained field thus defined, the string method in collective variables was used to compute a minimum free-energy pathway (MFEP) for the collapsing chain. These calculations provide a proof of principle for a coarse-grained description of water solvent. Furthermore, the calculated MFEP characterizes the mechanism for the collapse of the hydrated chain by providing a path of maximum likelihood for dynamical trajectories. The reliability of the calculated MFEP was confirmed with the use of conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.

[1]  W. Kauzmann.  Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.

[2]  K. Fukui.  The path of chemical reactions - the IRC approach , 1981 .

[3]  A. K. Mishra,et al.  APPARENT MOLAL VOLUMES OF AMINO ACIDS, N‐ACETYLAMINO ACIDS, AND PEPTIDES IN AQUEOUS SOLUTIONS , 1984 .

[4]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[5]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[6]  D. Chandler,et al.  Hydrophobicity at Small and Large Length Scales , 1999 .

[7]  Gerhard Hummer,et al.  New perspectives on hydrophobic effects , 2000 .

[8]  A. Luzar,et al.  Dynamics of capillary evaporation. II. Free energy barriers , 2000 .

[9]  Peter G. Bolhuis,et al.  Transition path sampling of cavitation between molecular scale solvophobic surfaces , 2000 .

[10]  A. Luzar,et al.  Dynamics of capillary evaporation. I. Effect of morphology of hydrophobic surfaces , 2000 .

[11]  D Chandler,et al.  Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Chandler,et al.  Scaling of Hydrophobic Solvation Free Energies , 2001 .

[13]  E. Vanden-Eijnden,et al.  String method for the study of rare events , 2002, cond-mat/0205527.

[14]  Pieter Rein ten Wolde,et al.  Drying-induced hydrophobic polymer collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Berne,et al.  Dewetting-induced collapse of hydrophobic particles , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Qiang Huang,et al.  A computer simulation study of water drying at the interface of protein chains. , 2004, The Journal of chemical physics.

[17]  D. Chandler.  Interfaces and the driving force of hydrophobic assembly , 2005, Nature.

[18]  W. E,et al.  Finite temperature string method for the study of rare events. , 2002, Journal of Physical Chemistry B.

[19]  B. Berne,et al.  Drying and hydrophobic collapse of paraffin plates. , 2005, The journal of physical chemistry. B.

[20]  Ruhong Zhou,et al.  Observation of a dewetting transition in the collapse of the melittin tetramer , 2005, Nature.

[21]  G. Ciccotti,et al.  String method in collective variables: minimum free energy paths and isocommittor surfaces. , 2006, The Journal of chemical physics.

[22]  Eric Vanden-Eijnden,et al.  Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. , 2007, The Journal of chemical physics.

[23]  Thomas M Truskett,et al.  Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water , 2007, Proceedings of the National Academy of Sciences.

[24]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.