Publication Date:
2004-09-14
Description:
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 10 to 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Ruhong -- Huang, Xuhui -- Margulis, Claudio J -- Berne, Bruce J -- GM4330/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Sep 10;305(5690):1605-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA. ruhongz@us.ibm.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15361621" target="_blank"〉PubMed〈/a〉
Keywords:
Computer Simulation
;
*Dioxygenases
;
Hydrophobic and Hydrophilic Interactions
;
Kinetics
;
Models, Molecular
;
Oxygenases/*chemistry
;
Protein Conformation
;
*Protein Folding
;
*Protein Structure, Tertiary
;
Static Electricity
;
Surface Properties
;
Water/*chemistry
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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