Laboratory of computational structural biology

Head Leonid Gorb, Dr.Sc. Phone: (380-44) 526-11-09; Fax: (380-44) 526-07-59; E-mail: leonid.gorb@gmail.com

Research Areas:

The study of the Laboratory are focused on the application of the methods of computational biology to the predictions of DNA properties, its components and enzymes-DNA complexes; another direction concerns the study of mechanisms that govern the fidelity of DNA synthesis.

Current Research Activities:

• Application of the state of the art methods of quantum chemistry to study tautomerization mechanisms of DNA bases;
• Application of docking and molecular dynamics methods (both classical and ab initio) to study physical and chemical properties of nucleoside-tri-phosphates and their correct and incorrect interaction with active sites of DNA-polymerase.

Selected publications:

1. Michalkova A.; Kosenkov D.; Gorb L., Leszczynski J. Thermodynamics and kinetics of intramolecular water assisted proton transfer in Na+-1-methylcytosine water complexes // J. Phys. Chem.-2008.-Vol. 112, N 29.-P. 8624-8633.
2. Close D.M., Crespo-Hernandez C.E.,Gorb L., Leszczynski J. Ionization energy thresholds of microhydrated adenine and its tautomers // J. Phys. Chem.-2008.- Vol.112, N 49.-P.12702-12706.
3. Palamarchuk G.V., Shishkin O.V., Gorb L., Leszczynski J. Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides on DNA conformations // J. Biomol.Struct. and Dynam.-2009.-Vol.26, N 5.-P. 653-661.
4. Kosenkov D., Kholod Y., Gorb L., Shishkin O., Hovorun D. M., Mons M., Leszczynski J. Ab initio kinetic simulation of gas-phase experiments : tautomerization of cytosine and guanine//J. Phys. Chem. B.-2009.-Vol.113, N 17.-P. 6140-6150.
5. Shishkin O., Gorb L., Leszczynski J. Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study // Struct. Chem.-2009.-Vol.20, N 4.-P.743-749.
6. Kosenkov D., Kholod Y., Gorb L., Shishkin O., Kuramshina G.M., Dovbeshko G. I., Leszczynski J. Effect of a pH change on the conformational stability of the modified nucleotide queuosine monophosphate // J.Phys.Chem.-2009.-Vol.113, N 33.-P. 9386-9395.
7. Gorb L., Podolyan Y., Dziekonski P., Sokalski W.A., Leszczynski J. Double-Proton Transfer in Adenine-Thymine and Guanine-Cytosine Base Pairs. A Post-Hartree-Fock ab Initio Study // J. Am. Chem. Soc. – 2004 . – V. 126, N 32. – P. 10119-10129.
8. Hovorun D.M., Gorb L., Leszczynski J. From the Nonplanarity of the Amino Group to the Structural Nonrigidity of the Molecule: A Post-Hartree—Fock Ab Initio Study of 2-Aminoimidazole // Int. J. Quantum Chem. – 1999. – V. 75, N 3. – P. 245-253.
9. Gorb L., Leszczynski J. Intramolecular Proton Transfer in Mono- and Dihydrated Tautomers of Guanine: An ab Initio Post Hartree—Fock Study // J. Am. Chem. Soc. – 1998. – V. 120, N 20. – p. 5024-5032.