Dewetting transitions in protein cavities.
In a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of Cox-2. With the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the PDB, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. Because such cavities need not desolvate before binding hydrophobic ligands they often exhibit very large binding affinities. This article gives evidence that drying in protein cavities is not unique to Cox-2.
Department of Chemistry, Columbia University, New York, NY 10027, USA. simpleliquid@gmail.com
Tom
T
Young
Lan
L
Hua
Xuhui
X
Huang
Robert
R
Abel
Richard
R
Friesner
B J
BJ
Berne
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D030562:Databases, Protein; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012709:Serum Albumin / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D011506:Proteins; D012709:Serum Albumin; D014867:Water