Transcription in vitro using mixtures of ethylene glycol and water

Osmotic regulation of gene action

Most reactions involved in gene translation systems are ionic-dependent and may be explained in electrostatic terms. However, a number of observations of equilibria and rate processes making up the overall reactions clearly indicate that there is still an enormous gap between the rough picture of the mechanism of ionic regulation and the detailed behavior of reactions at the molecular level that hold the key to specific mechanisms. The present paper deals with possible osmotic contributions arising from the gel state of gene systems that are complementary to, and interdependent of, electrostatic contributions. This treatment, although still oversimplified, explains many previous observations by relating them to a general osmotic mechanism and suggests experimental approaches to studying the mechanisms of gene regulation in organelle-free and intact systems.

Cryoprotectant toxicity and cryoprotectant toxicity reduction: in search of molecular mechanisms

Cryoprotectant toxicity is a fundamental obstacle to the full potential of artificial cryoprotection, yet it remains in general a poorly understood phenomenon. Unfortunately, most relevant biochemical studies to date have not met the basic criteria required for demonstrating mechanisms of toxicity. A model biochemical study of cryoprotectant toxicity was that of Baxter and Lathe, which demonstrated that alteration of a specific enzyme (fructose diphosphatase, or FDPase) was the cause of impaired glycolysis after treatment with and removal of dimethyl sulfoxide (D). FDPase alteration by D was reported to be preventable by the simultaneous presence of amides. This protection could be due to a "counteracting solute" effect similar to that employed by nature, but we find no meaningful correlation between the general protein stabilizing or destabilizing tendency of the cryoprotectant medium and its toxicity. Baxter and Lathe postulated that the effect of D arises from hydrogen bonding between D and the epsilon amino groups of surface lysine residues on FDPase, and it was found that molecules which resembled this group could block the alteration induced by D, presumably by competing with lysine residues for association with D. However, we find that the interaction between D and lysine in the presence of water is actually thermochemically repulsive, and that the presence of formamide does not affect the interaction between D and lysine, implying no useful complex formation between formamide and D. We were also unable to demonstrate that the blocking compounds consistently reduce toxicity when added to D rather than substituting for D, contrary to predictions based on complex formation between blocking compounds and D. In summary, it seems that present concepts of cryoprotectant toxicity are in need of serious revision.

Biological macromolecules as gels: functional similarities

Functional biological macromolecules arising from folding, cross-connection, and solvation of long-chain biopolymers forming three-dimensional networks can be compared to gels. Both involve identical internal competitive forces that are selectively influenced by external conditions and conspire to adjust conformations and modulate functions. In spite of important differences in size, chemical composition, polymer density, and configuration, biological macromolecules indeed manifest some of the essential physical-chemical properties of gels. This result represents presumptive evidence for common underlying mechanisms in functional molecules and gels. Thus, the present and highly perfectible model explains why and how, depending on initial conditions, a system may respond differently to an external parameter and similarly to different parameters. Moreover, the fact that any localized change in one of the competitive forces gives rise to a pressure in the system as a whole provides one explanation for the mechanism of the transmission of information.

New trends in cryoenzymology: probing the functional role of protein dynamics by single-step kinetics

Cryoenzymology was initially used to slow down enzyme-catalyzed reactions so as to stabilize intermediates for further study. During the course of this early work, it became clear that cryoenzymology could be extended to other ends and some of these are described. First, the use of a cryosolvent on its own (or together with temperature) as a perturbant has allowed a resolution of the substrate binding steps of certain enzymes (myosin, D-amino acid oxidase, peroxidase and cytochrome P450). Second, by the use of cryosolvent and temperature, coupled with the classical physico-chemical perturbants, one can selectively modulate the various steps of an enzyme pathway. This approach can lead to an understanding of the mechanism of enzyme regulation. Finally, by carrying out experiments over a wide range of temperatures (-30 degrees C- +30 degrees C) and pressure (up to several kbars) in specially constructed fast reaction equipment, one can study the thermodynamic properties of the individual rate constants describing the interconversions of reaction intermediates. Experiments with creatine kinase, cytochrome P450 and peroxidase are described. The thermodynamic parameters delta H, delta G, delta S and delta V are thus measured and when this is done under different solvent conditions one can, at least within the theories available, attempt an approach to the problem of protein dynamics.

Interactive effects of cryosolvents, ionic and macromolecular solutes on protein structures and functions

Surprisingly, cryosolvents may mimic the effects of ionic solutes on the structures and functions of macromolecular assemblages, showing additive or opposite effects depending on the respective concentrations. These interactive effects are hard to analyze precisely because they may result from so many possible contributions. However, studies on model systems clearly show the nature of the interactive effects and bring about useful information concerning the mechanism of action of cryosolvents and ions and the response of enzyme systems. Such results suggest new studies on the interaction of biopolymers and water and their possible impact on the cryobehavior of highly organized and living systems.

The effect of urea on catabolite sensitive operons in Escherichia coli K 12

Low concentrations of urea specifically inhibit the expression of catabolite sensitive genes (the lactose, galactose and maltose operons and the tryptophanase gene). This inhibition depends upon growth conditions, i.e. carbon source and temperature. The main effect of urea is exerted at the level of transcription initiation. However an additional inhibitory effect is observed on the decay and expression of the beta-galactosidase messenger. In a strain harboring the UV5 mutation in the lactose promoter, the effect at the level of transcription is relieved while the effect on the decay and the expression of the beta-galactosidase messenger remains the same. Just like the extreme physiological catabolite repression, the urea effect occurs even in a cya delta strain and is not antagonized by addition of adenosine 3'-5' cyclic monophosphate.

The study of enzyme mechanisms by a combination of cosolvent, low-temperature and high-pressure techniques

It is generally assumed that the mechanism of enzyme-catalysed reactions would be defined if all the intermediates, complexes and conformational states of each enzyme could be characterized, and the rate-constants for their inter-conversion recorded. In spite of the introduction during the last decades of methods for rapid data acquisition, which permit detection of the number and sequence of intermediates and complexes, measurement of rate-constants, identification of the types of catalysis involved, etc., at best a semi-quantitative understanding of the mechanism of enzyme-catalysis is obtained. The definition of the exact chemical nature of intermediates and complexes is missing because techniques establishing the structures are restricted to the study of transient states which are stable for periods that exceed the half-life of most of typical intermediates. In such conditions, while conformational changes are obviously an essential feature of enzyme activity, the conformational basis of such activity cannot be understood at the molecular level, and enzyme catalysis is still termed a ‘miracle’ compared to the rate-enhancements and specificity of ordinary chemical catalysts.

In vitro system for induction of delayed early RNA of bacteriophage T4

Concentrated lysates of Escherichia coli that had been infected with bacteriophage T4 in the presence of chloramphenicol show the same restriction of transcription in vitro as is found in vivo. Restricted lysates can be complemented with lysates from infected cells to induce production of delayed early RNA. Complementation takes place between the RNA polymerase of the restricted lysate and the DNA of the unrestricted lysate. We present evidence that delayed early RNA in these lysates is initiated at quasi-late (middle) promoters, and that such recognition is related to changes in the state of the template DNA.