Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Coarse-Grained Model of Nucleic Acids

Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. Most coarse-grained models developed so far implemented harmonic (1, 2) or Go-like potentials (3). Here we present physics-based coarse-grained model of nucleic acids based on our recently developed method of coarse-graining (4). The model is built of six types of rigid bodies connected by virtual bonds. Bases are represented by several (three to five) centers of van der Waals and electrostatic interactions (dipolar beads), deoyribose is approximated by single van der Waals interaction center (neutral bead) and phosphate group is represented by charged van der Waals sphere (charged bead). Recently developed method of coarse-graining was used for parametrization of two-body long-range interactions between coarse-grained objects (4). Bonded part of interaction energy was determined by fitting analytical expression to potentials of mean force computed for the model system. Umbrella sampling and WHAM methods were applied to the model three-nucleotide water-solvated system. Rigid-body equations of motion were integrated with simplectic rotation matrix constraint method (5). Good numerical stability of microcanonical simulation was achieved for timesteps up to 25 fs for the model DNA duplex.

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  2. M. Maciejczyk, W. R. Rudnicki and B. Lesyng, J Biomol Struct Dyn 17, 1109-1116 (2000).
  3. E. J. Sambirski, V. Oritz, J. J. de Pablo, J Phys: Condens Matter, 21, 034105- 034118 (2009).
  4. M. Maciejczyk, A. Spasic, A. Liwo and H. A. Scheraga, J Comp Chem 31, 1644-1655 (2010).
  5. A. Kol, B. B. Laird and B. J. Leimkuhler, J Chem Phys 107, 2580-2588 (1997).

Maciej Maciejczyk1
Aleksandar Spasic2
Adam Liwo3
and Harold A. Scheraga4

1Department of Physics and Biophysics University of Warmia and Mazury Olsztyn 10718, Poland
2Department of Biochemistry and Biophysics University of Rochester Medical Center Rochester, NY 14642, USA
3Faculty of Chemistry University of Gdańsk Gdansk 80216, Poland
4Baker Laboratory of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA

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