Poster abstracts

Poster number 38 submitted by Ali Hassanali

Molecular mechanisms in the repair of the cyclobutane pyrimidine dimer

Ali Hassanali (Biophysics, The Ohio State University), Dongping Zhong (Physics, Chemistry and Biochemistry, The Ohio State University), Sherwin J Singer (Chemistry and Biophysics, The Ohio State University)

Abstract:
Exposure to far UV radiation induces DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). This is the most prevalent mechanism for UV-induced mutations, and has been implicated as a first step in the generation of tumors. CPDs can be repaired by the enzyme photolyase, in which the absorption of a blue light photon initiates a sequence of photochemical events leading to the injection of an electron at the site of the CPD lesion in DNA. In this work we investigate the molecular mechanism of the repair of the cyclobutane dimer radical anion in aqueous solution using ab initio MD simulations. Umbrella sampling is used to determine a two-dimensional free energy surface as a function of the C5-C5´ and C6-C6´ distances. The neutral dimer is unable to surmount a large free energy barrier for repair. Upon addition of an electron, there exist two populations of trajectories: one whose C5-C5´ split spontaneously and another that remains intact. Our simulations are the first to show the important role of water motions in controlling the splitting of the C5-C5´ and C6-C6´ bonds. Transition state theory predicts that the splitting of the C6-C6´ bond is complete on a picosecond timescale. The free energy surface suggests that the splitting of the two bonds is asynchronously concerted. Our work is the first to explicitly include the electronic degrees of freedom for both the cyclobutane dimer and the surrounding water pocket. The simulations show that at least 30% of the electron density is delocalized onto the surrounding solvent during the splitting process. Simulations on the neutral surface show that back electron transfer from the dimer is critical for the completion of splitting: splitting of the C5-C5´ and C6-C6´ bonds can be reversed or enhanced depending on when electron return occurs. The simulations show that equilibrium fluctuations of amino acids in the active site will play a crucial role in the repair process.

References:
Y.-T. Kao, C. Saxena, L. Wang, A. Sancar, and D. Zhong, Proc. Nat. Acad. Sci. U.S.A., 102(45), 16128–16132 (2005).

F. Masson, T. Laino, U. Rothlisberger, and J. Hutter, ChemPhysChem, 10(2), 400–410
(2009).

A. A. Hassanali, D. Zhong and S. J Singer, \

Keywords: Ab Initio, Free Energy, DNA repair