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http://hdl.handle.net/2074/849
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| Title: | Do water molecules mediate protein-DNA recognition? |
| Authors: | Reddy, Ch. Koti
Das, Achintya
Jayaram, B |
| Keywords: | hydrogen bonds
extended side-chains
electrostatic screening
water-mediated recognition
packing density |
| Issue Date: | 2001 |
| Citation: | Journal of Molecular Biology, 314(3), 619-632 |
| Abstract: | A comprehensive analysis of interfacial water molecules in the structures of 109 unique protein-DNA complexes is presented together with a new view on their role in protein-DNA recognition. Location of interfacial water molecules as reported in the crystal structures and as emerging from a series of molecular dynamics studies on protein-DNA complexes with explicit solvent and counterions, was analyzed based on their acceptor, donor hydrogen bond relationships with the atoms and residues of the macromolecules, electrostatic field calculations and packing density considerations. Water molecules for the purpose of this study have been categorized into four classes: viz. (I) those that contact both the protein and the DNA simultaneously and thus mediate recognition directly; (II) those that contact either the protein or the DNA exclusively via hydrogen bonds solvating each solute separately; (III) those that contact the hydrophobic groups in either the protein or the DNA; and, lastly (IV) ... |
| URI: | http://eprint.iitd.ac.in/dspace/handle/2074/849 |
| Appears in Collections: | Chemistry
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| reddywat2001.pdf | | 2561Kb | Adobe PDF | View/Open |
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