V. A. Tverdislov

Interactions of helical structures as a molecular basis of intra- and intercellular interactions

Two types of formation of super spirals by spiral counter- and co-intertwining of spiral molecular strings were identified using chiral biomimetics. An earlier statement on the formation of hierarchies of super-spiral structures with an alternating chirality sign in molecular homochiral systems was experimentally proven. By developing the Euler model, estimates of forces and velocities in systems of interacting spiral structures that quantitatively correspond to the characteristic times and dimensions of intracellular and inter-cellular interactions were theoretically obtained. It was shown that the phase of structure formation in the cell is not limiting and the time of formation of intracellular structures is determined by the time that is necessary for the cell to choose a functional program.

Self assembly of supramolecular homochiral structures in solutions of chiral biomimetics

The phenomenon of the formation of homochiral sets of supramolecular vortices in xerogels with a low concentration of chiral biomimetics of trifluoroacetylated amino alcohols that are metrically similar to certain macromolecular and macroscopic helical biological structures was discovered and described. Each vortex, with a characteristic scale of ∼ 1 mm, corresponds approximately to the rotational symmetry Sn groups depending on the number of strings that have a common anchorage or are formed from a single nucleation and experience a mutual agreed deviation. It is essential that the direction of deviation is changed to the opposite one with the change of the chirality of the enantiomer and does not depend on the solvent type. Both weakening and strengthening of this trend were observed in the mixtures of various chiral compounds. The result is an important confirmation of the synergetic rule that was proposed by authors. According to this rule, the sign of the chirality of a supramolecular helix is changed to the opposite with a change in the chirality sign of the basic monomers from which it is formed. This regularity has a fundamental character and is executed as a trend in the hierarchies of DNA, protein, and polysaccharide macromolecular structures.

Self-organization as the driving force for the evolution of the biosphere

Synergic parallels between the mechanisms of the spatio-temporal evolution of physic-chemical and biological systems are considered. The evolution of the biosphere is treated as self-organization in the hierarchy of the active media, which is its driving force. The superposition of selection, vertical and horizontal gene transfer, as well as the processes of divergence and convergence of species, constitutes the synergetic out-line of biological evolution.

Ionic and chiral asymmetries as physical factors of biogenesis and ontogenesis

AbstractsThe proposed approach to the evolution of the universe and life on Earth is based on general physical principles that lead to the assertion that their rise was made possible through the chain of emergence and collapse of symmetries in the states of dynamic systems. The hypothesis is proposed and substantiated that the phylogenetic law of Haeckel (each species in its ontological development repeats its evolutionary history) might be extended so that it would include two processes that are comparable from the point of view of biophysics: the emergence of the discrete predecessors of the cell in the ancient Ocean and initial stages of embryogenesis. A new proposition is made and grounded that formation of the two fundamental biological asymmetries (cellular-ionic and molecular-chiral) are similar and constitute coupled bifurcations that gave rise to life on the Earth and the individual life of multicellular organisms. This work aims to resolve the principal contradiction between the notions of the essentially thermodynamic non-equilibrium nature of all living cells and conventional equilibrium models of their origination. The authors and their colleagues give the first experimental evidence that the original deviation of the predecessors of living cells from the state of thermodynamic equilibrium may be directly related to the spontaneous generation of the two fundamental biological asymmetries (ionic and molecular) in the ocean’s thin surface layer. The ionic asymmetry predefined the ability of discrete protocells to react to external stimuli, which was a necessary condition of their inclusion into the process of biological evolution, whereas the chiral asymmetry predetermined the unique molecular stereospecificity of carbon compounds in the processes of biosynthesis and metabolism. Concerning amino acids, chiral asymmetry may also be extended to embrace participation of their D-isomers in the regulation of the most important stages of ontogenesis, while earlier it was deemed only as an underpinning of the principle of the “chiral purity of the biosphere,” within which solely the inclusion of amino acid L-isomers in the ribosomal synthesis of proteins. The enantiomers of biologically important chiral substances are able to not only play a key role in complementary interaction but also serve as a logical element for switching information and not only at the level of simple coding of the “yes/no” type but also at the level of conversion of “sensible” signals.

Chirality as a problem of biochemical physics

Molecular chiral asymmetry, created in the biosphere during biological evolution, is unambiguously realized in today’s world at the genetic level and in biosynthesis. According to our hypothesis, origination of molecular chiral asymmetry is associated with fractionation of enantiomers of chiral compounds that abiogenously evolved at the ocean-atmosphere nonequilibrium boundary during origination of the predecessors of living cells.

The principle of parametric fractionation (separation) of substances in biological systems and technology

The parametric fractionation (separation) of substances is based on simultaneous exposure of a heterogeneous system with the phases (solid and liquid or liquid and gaseous) including components subject to be separated to the influence of two periodic fields of different nature. One field, “parameter” (for instance, temperature, pH) causes periodical redistribution of the components between phases, and the other field (for instance, mechanical forces, surface tension, electric field) effects synchronous shift of the components of one phase with respect to the other. As a result a counter flow of components to be separated formed against the gradient of their chemical or electrochemical potentials. This method underlain by the general principle of synchronous detection by no means is connected with definite mixtures or sorbents, it operates spontaneously in the inanimate and animate natural systems and can be applied to quite unexpected technologies.

Formation of Chiral Structures in UV-Initiated Formose Reaction

It has been found that the UV-initiated formose reaction in an extremely concentrated aqueous solution of formaldehyde gives sugars and other biologically significant chiral compounds with sp3-hybridized carbon atom. The reaction leads to an optically active condensed phase, which is a result of the spontaneous spatial separation of enantiomers in the racemate into the antipodes, similarly to the separation of enantiomers of different chirality sign in the famous Pasteur experiments. In our opinion, such a scenario is as close as possible to the actually realized de novo scenario of synthesis of chiral prebiotic molecules and matrices.

A periodic system of chiral structures in molecular biology

A systemic regularity of molecular biology is considered: the tendency towards alternating of the sense of chirality of intramolecular structural levels of DNA and proteins, namely, D–L–D–L for DNA and L–D–L–D for proteins, is observable starting from the level of asymmetric carbon in deoxyribose and amino acids. Helicity is a special case of chirality. In intermolecular interactions, the sense of chirality of the highest intramolecular structural level directly involved in the interaction prevails in each of the participants. The interaction of molecules of the same nature (protein–protein, DNA–RNA, tRNA–mRNA, and ribozymes) mainly occurs in the case of the same sense of chirality, either L–L or D–D, and for molecules of different types (DNA–protein, tRNA–amino acids, and enzyme–substrate), in the case of different senses of chirality, either D–L or L–D. An alternating sense of the chiral hierarchy of conjugated levels of macromolecular structures in proteins and nucleic acids is of general biological importance: it determines the discreteness of levels, serves as a tool of folding, and provides a structural basis for “preferred collective” (or “macroscopic mechanical”) degrees of freedom in the design of macromolecular machines, as well as being one of the mechanisms of blockwise/saltatory development of the evolutionary process. A new fundamental concept is proposed: the homochirality of primary structures of DNA and proteins determines the amount of the entropic component of the free energy, which is used in the processes of folding and molecular rearrangements.

Structure formation in low-concentrated solutions of cholesterol and ergosterol

The conformational behavior of biologically important chiral molecules of cholesterol and ergosterol was studied via the method of molecular dynamics. The formation of strings and their absence was experimentally observed in methanol solutions of cholesterol and ergosterol, respectively. It was shown that the intermolecular dynamics of the molecule significantly affects the possibility of structure formation. We proposed an alternative explanation of the functional significance of cholesterol, which is apparently associated with the formation of commutation structures outside the membrane, and the biological feasibility of the presence of ergosterol in the non-commuting cells of fungi and cholesterol in the commuting cells of macroorganisms.

An autowave model of vesicle formation on the ocean surface

According to the hypothesis of the origin of life on Earth proposed by the coauthors of this publication [4–6], when an aerosol particle that was generated by bursts of air bubbles on the surface of an ancient ocean and was covered by a monolayer of amphiphile fell back on the surface it was transformed into a vesicle covered by a bilayer of amphiphilic molecules. The vesicle is considered as a cell prototype because it is in a thermodynamically nonequilibrium state caused by asymmetry of the distributions of ions and chiral components. In this work, the ocean surface layer is considered as an active medium that can be described by the Fitzhugh-Nagumo equations. A computational experiment showed that a stable vesicle covered by a bilayer of amphiphilic molecules can be formed under such conditions and that it submerges.