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Science 10 September 2004:
Vol. 305. no. 5690, pp. 1605 - 1609
DOI: 10.1126/science.1101176
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Reports

Hydrophobic Collapse in Multidomain Protein Folding

Ruhong Zhou,1,2* Xuhui Huang,2 Claudio J. Margulis,2 Bruce J. Berne1,2*

We performed molecular dynamics simulations of the collapse of a two-domain protein, the BphC enzyme, into a globular structure to examine how water molecules mediate hydrophobic collapse of proteins. In the interdomain region, liquid water persists with a density 10to 15% lower than in the bulk, even at small domain separations. Water depletion and hydrophobic collapse occur on a nanosecond time scale, which is two orders of magnitude slower than that found in the collapse of idealized paraffin-like plates. When the electrostatic protein-water forces are turned off, a dewetting transition occurs in the interdomain region and the collapse speeds up by more than an order of magnitude. When attractive van der Waals forces are turned off as well, the dewetting in the interdomain region is more profound, and the collapse is even faster.

1 Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.
2 Department of Chemistry, Columbia University, New York, NY 10027, USA.

* To whom correspondence should be addressed. E-mail: ruhongz{at}us.ibm.com (R.Z.); berne{at}chem.columbia.edu (B.J.B.)

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