Quantum Mechanical Model for Conformons

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.

The bhopalator: a molecular model of the living cell based on the concepts of conformons and dissipative structures

A molecular model of the living cell has been formulated based on a new theory of enzymic catalysis which takes into account the complementary roles of free energy and genetic information. The elementary units of free energy and genetic information that are necessary and sufficient for effectuating molecular mechanisms responsible for the life of the cell are called conformons. Conformons are visualized as a collection of a small number of catalytic residues of enzymes or segments of nucleic acids that are arranged in space and time with appropriate force vectors so as to cause chemical transformations or physical changes of a substrate or a bound ligand. So defined, conformons provide a plausible molecular means to link the genetic information stored in DNA and its ultimate expression, namely networks of coupled intracellular biochemical reactions and physical processes maintained by a continuous dissipation of free energy--dissipative structures of Prigogine. The proposed model of the living cell appears to possess the potential for bridging the gap between molecular biology and the biology of multicellular systems.