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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

DNA-Protein Recognition in the Presence of Solvent

It is well known that the presence of solvent influences the structure & energetics of DNA as well as proteins. Especially, the presence of water made a significant contribution in mediating the interaction between the DNA bases and amino acids. This was confirmed by the experimental studies [1-2] on the complex between Trp repressor and DNA, provided evidence that DNA-Protein interaction can be mediated by water. Hence, to further nitialise it through the molecular level understanding of water mediated DNA-Protein recognition, an attempt has been made about how the presence of solvent influences the recognition between them in terms of its stability. For this purpose, The DNA bases, amino acids and Water complex have been modelled. The stabilities of the DNA-protein and water (n=1,2) complex has been calculated using HF and DFT theory. Initially, a comparision has been made with hydrophilic and hydrophobic amino acids. For example The Guanine-Lysine (hydrophilic)-water (GuaLysw1) and Guanine-Trptophan (Hydrophobic) -Water (GuaTrpow1) complex energy has been computed (as shown Figure). It has been found that the Guanine - Trptophan recognition is mediated by the presence of water molecule. Also, Water adds further stability to the DNA-Protein interactions. The Details will be discussed in the presentation.

References and Footnotes

  1. Z. Otwinowski, R.W. Schevitz, R.G. Zhang, C.L. Lawson, A. Joachimiak, R.Q. Marmorstein, B.F. Luisi, P.B. Sigler, Nature 335 (1988) 321.
  2. C.L. Lawson, J. Carey, Nature 366 (1993) 178.

D. Sivanesan and W. J. Welsh

Department of Chemistry, 315 Benton Hall, 8001, Natural Bridge Road, University of Missouri, St. Louis, MO 63121
Phone: 314-516-6882; Fax : 314-516-5342; E-mail: siva@ozone.umsl.edu