Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 5: Proteins

BP 5.9: Vortrag

Montag, 23. März 2009, 16:45–17:00, ZEU 260

DNA-protein electrostatic recognition: lessons from the Protein Data Bank analysis of DNA-protein complexes — •Andrey Cherstvy — IFF, Theorie-II, FZ Jülich, 52425 Jülich, Germany

We study the details of charge distributions on DNA-binding domains of some DNA-binding proteins. This is a continuation of our research on facilitated protein diffusion on DNA and the mechanism of DNA-protein charge-charge recognition [AC et al., JPCB, 112 4741 (2008)]. We show that relatively large structural proteins of eukaryotes and prokaryotes, which involve DNA wrapping around protein cores and induce severe bends in DNA structure, do obey the theoretical model we proposed. Namely, positively charged protein residues in close proximity of DNA prefer to track the positions of individual DNA negative phosphate charges [AC, submitted to JPCB]. To show this, we have used the computational algorithm for dealing with atomic coordinates of protein amino acids and DNA phosphates available from the Protein Data Bank files for a variety of crystallized DNA-protein complexes. The specificity of amino acid distribution observed contributes to the sequence-specific DNA-protein electrostatic interactions. For the majority of DNA-protein complexes, the latter are however considered in the literature to be rather nonspecific to DNA bp sequence. For many simple/small DNA-protein complexes involving basic motifs of protein binding to DNA, we could not detect any statistical preference in distributions of positive atoms on Arginine and Lysine in DNA vicinity.