Free energy and information contents of Conformons in proteins and DNA

Sequence-specific conformational strains (SSCS) of biopolymers that carry free energy and genetic information have been called conformons, a term coined independently by two groups over two and a half decades ago [Green, D.E., Ji, S., 1972. The electromechanochemical model of mitochondrial structure and function. In: Schultz, J., Cameron, B.F. (Eds.), Molecular Basis of Electron Transport. Academic Press, New York, pp. 1–44; Volkenstein, M.V., 1972. The Conformon. J. Theor. Biol. 34, 193–195]. Conformons provide the molecular mechanisms necessary and sufficient to account for all biological processes in the living cell on the molecular level in principle — including the origin of life, enzymic catalysis, control of gene expression, oxidative phosphorylation, active transport, and muscle contraction. A clear example of SSCS is provided by SIDD (strain-induced duplex destabilization) in DNA recently reported by Benham [Benham, C.J., 1996a. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425–434; Benham, C.J., 1996b. Computation of DNA structural variability — a new predictor of DNA regulatory regions. CABIOS 12(5), 375–381]. Experimental as well as theoretical evidence indicates that conformons in proteins carry 8–16 kcal/mol of free energy and 40–200 bits of information, while those in DNA contain 500–2500 kcal/mol of free energy and 200–600 bits of information. The similarities and differences between conformons and solitons have been analyzed on the basis of the generalized Franck-Condon principle [Ji, S., 1974a. A general theory of ATP synthesis and utilization. Ann. N.Y. Acad. Sci. 227, 211–226; Ji, S., 1974b. Energy and negentropy in enzymic catalysis. Ann. N.Y. Acad. Sci. 227, 419–437]. To illustrate a practical application, the conformon theory was applied to the molecular-clamp model of DNA gyrase proposed by Berger and Wang [Berger, J.M., Wang, J.C., 1996. Recent developments in DNA topoisomerases II structure and mechanism. Curr. Opin. Struct. Biol. 6(1), 84–90], leading to the proposal of an eight-step molecular mechanism for the action of the enzyme. Finally, a set of experimentally testable predictions has been formulated on the basis of the conformon theory.