The generalized derivation of classical McGhee - von Hippel equation for the first time was performed by means of statistical-mechanical transfer matrix formalism. The equation is applicable for study of non-cooperative and non-specific binding of ligands of various types to a lattice biopolymer.
biopolymer, ligand, association constant, partition function, transfer matrix
1. McGhee J.D., von Hippel P.H. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol., 1974, vol. 86, pp. 469-489.
2. Nechipurenko Yu.D. Analiz svyazyvaniya ligandov s nukleinovymi kislotami. Biofizika, 2014, t. 59, c. 12-36. [Nechipurenko Yu.D. Analysis of the binding of ligands to nucleic acids. Biophysics, 2014, vol. 59, pp. 12-36 (In Russ.)]
3. Woodbury C.P. Jr. Matrix polynomial extension of the sequence-generating function method for macromolecular binding. J. Chem. Phys., 1990, vol. 92, pp. 5127-5135.
4. Beshnova D.A., Bereznyak E.G., Shestopalova A.V., Evstigneev M.P. A novel computational approach ‘BP-STOCH’ to study ligand binding to finite lattice. Biopolymers, 2011, vol. 95, pp. 208-216.
5. Teif V.B. General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage λ. Nucleic Acids Res., 2007, vol. 35, Art. No. e80.
6. Poland D., Scheraga H.A. Theory of helix-coil transitions in biopolymers. New York: Academic Press, 1970. 797 p.
7. Tsuchiya T., Szabo A. Cooperative binding of n-mers with steric hindrance to finite and infinite one-dimensional lattices. Biopolymers, 1982, vol. 21, pp. 979-994.
8. Buchelnikov A.S., Evstigneev V.P., Evstigneev M.P. General statistical-thermodynamical treatment of one-dimensional multicomponent molecular hetero-assembly in solution. Chem. Phys., 2013, vol. 421, pp. 77-83.
