title: Ultrafast interfacial solvation dynamics in specific protein DNA recognition.
abstract: An overwhelming number of structural and functional studies on specific protein-DNA complexes reveal the existence of water molecules at the interaction interface. What role does the interfacial water molecules play in determining the specificity of association is thus a critical question. Herein, we have explored the dynamical role of minor groove water molecules and DNA side chain flexibility in lambda repressor-operator DNA interaction using well-characterized DNA minor groove binder dye, Hoechst 33258. The most striking finding of our studies reveals that the solvation time scale corresponding to the minor groove water molecules (∼50 ps) and DNA side chain flexibility (∼10 ns) remain unaltered even in protein-DNA complex in comparison to unbound operator DNA. The temperature dependent study further reveals the slower exchange of minor grove water molecules with bulk water in DNA-protein complex in comparison to the unbound DNA. Detailed structural studies including circular dichroism (CD) and Förster resonance energy transfer (FRET) have also been performed to elucidate the interaction between protein and DNA.
authors: Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors: Subrata
authors: S
authors: Batabyal
authors: Tanumoy
authors: T
authors: Mondol
authors: Susobhan
authors: S
authors: Choudhury
authors: Abhishek
authors: A
authors: Mazumder
authors: Samir Kumar
authors: SK
authors: Pal
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000302:isolation & purification*; D004926:Escherichia coli; D031541:Fluorescence Resonance Energy Transfer; D046912:Multiprotein Complexes / Q000737:chemistry / Q000302:isolation & purification*; D012097:Repressor Proteins / Q000737:chemistry / Q000302:isolation & purification*; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry / Q000302:isolation & purification*; D014867:Water / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D012097:Repressor Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D014867:Water; D004247:DNA
keywords: DNA minor groove water dynamics; Operator DNA; Protein DNA interface; Resonance energy transfer; Specific protein DNA interaction