The role of water in protein-DNA recognition.
Is it by design or by default that water molecules are observed at the interfaces of some protein-DNA complexes? Both experimental and theoretical studies on the thermodynamics of protein-DNA binding overwhelmingly support the extended hydrophobic view that water release from interfaces favors binding. Structural and energy analyses indicate that the waters that remain at the interfaces of protein-DNA complexes ensure liquid-state packing densities, screen the electrostatic repulsions between like charges (which seems to be by design), and in a few cases act as linkers between complementary charges on the biomolecules (which may well be by default). This review presents a survey of the current literature on water in protein-DNA complexes and a critique of various interpretations of the data in the context of the role of water in protein-DNA binding and principles of protein-DNA recognition in general.
Jayaram
B
B
Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India. bjayaram@chemistry.iitd.ac.in
Jain
Tarun
T
D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D004268:DNA-Binding Proteins; D012997:Solvents; D014867:Water