Solvent-temperature perturbations of ionizable groups as a tool for the investigation of the active site of enzymes

On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+

The structurally diverse polysaccharide lyase enzymes are distributed from plants to animals but share common catalytic mechanisms. One, heparinase I (F. heparinum), is employed in the production of the major anticoagulant drug, low molecular weight heparin, and is a mainstay of cell surface proteoglycan analysis. We demonstrate that heparinase I specificity and efficiency depend on the cationic form of the substrate. Ca(2+)-heparin, in which α-L-iduronate-2-O-sulfate residues adopt (1)C4 conformation preferentially, is a substrate, while Na(+)-heparin is an inhibitor. His and Tyr residues are identified in the catalytic step and a model based on molecular dynamics and docking is proposed, in which deprotonated His203 initiates β-elimination by abstracting the C5 proton of the α-L-iduonate-2-O-sulfate residue in the substrate, and protonated Tyr357 provides the donor to the hexosamine leaving group.

A steady-state kinetic analysis of the reaction between arginine esterase E-I from Bitis gabonica venom and synthetic arginine substrates and the influence of pH, temperature and solvent deuterium isotope

1. Using synthetic arginines as substrates, steady-state kinetic studies showed a deviation from Michaelis-Menten kinetics for esterase E-I purified from the venom of Bitis gabonica. Graphical analysis indicated a rate equation of at least a degree of 3:3. 2. pH variation of the kinetic parameters indicated the involvement of groups with pK values of approximately 7 and approximately 9 which had to be in the ionic form for activity. 3. Solvent isotope studies suggested transition states where proton transfer or reorganization was the rate-limiting step of proteolytic catalysis. A single protogenic site was postulated. 4. Temperature effects on the enzymic reaction showed a significant reduction in entropy loss upon formation of the transition state with both esters and extended tail polypeptide-anilides in comparison with the activation entropy for benzoyl-L-arginine p-nitroanilide.

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 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.

Cryoenzymologic studies on arginine kinase: solvent, temperature and pH effects on the overall reaction

The overall reaction catalyzed by the phosphotransferase arginine kinase was studied at normal and subzero temperatures. Ethylene glycol was used as the antifreeze and its effects on the Km values of substances, kcat and pH profiles were investigated in detail. a) The Km values for the substrate (2 mM for ATP and 0.6 mM for arginine) were little affected by the solvent composition or temperature of the reaction mixture. b) At concentration of ethylene glycol higher than 40% there was a sharp drop of enzyme activity. c) Ethylene glycol induces a large shift in the enzymic pK D) At -5 degrees C in 40% of solvent there was a break in the Arrhenius plot suggesting a change of the rate-limiting step. The relevance of these results to the reaction pathway of arginine kinase is discussed. In addition, controlled perturbations induced by cosolvent and temperature appear as useful tools for further kinetic investigations.

Redox potentials in hydro-organic media at normal and subzero temperatures. Ferro-ferricyanide and cytochrome c as models

Redox potentials of ferro-ferricyanide and cytochrome c were measured in water/ethylene glycol and water/dimethylsulfoxide (volume ratio from 100/0 to 50/50) between 25 and -25 degrees C. For both systems, the midpoint potential decreases in the presence of organic solvents and increases by cooling. The magnitude of these variations is larger in dimethylsulfoxide than in ethylene glycol; moreover in the same solvent mixture it is larger with ferro-ferricyanide than with cytochrome c, so that the difference between the redox potentials of these two systems can be strongly affected and even reversed. While in pure water (cacodylate buffer pH 7.0, NaCl 0.1 M) they are respectively +388 and +265 mV, in 50% dimethylsulfoxide at 25 degrees C they decrease to +112 and +208 mV. Reduction of cytochrome c by ferro-ferricyanide, in this mixture, is then expected and was indeed observed. On the other hand, as (deltaE/deltaT)T, (E being the redox potential) is higher for ferro-ferricyanide than for cytochrome c, the oxidative power of the former for the latter is expected to increase as temperature decreases. This effect was observed in 50% ethylene glycol at -16 degrees C. Organic solvents and large temperature variations appear then as powerful perturbants of redox reactions. Their effects should be taken into account in studies of redox reactions carried out in cooled hydro-organic media.

Ionization dependence of camphor binding and spin conversion of the complex between cytochrome P-450 and camphor. Kinetic and static studies at sub-zero temperatures

The kinetic rate constants of formation and dissociation of the cytochrome-P-450 - camphor complex (Fe3+-RH) have been obtained by low-temperature (+ 5 degrees C to -20 degrees C) stopped-flow experiments. Simiarly the high-spin/low-spin equilibrium of this complex has been studied as a function of temperature and protonic activity. Both the camphor-binding mechanism and the high-spin/low-spin thermodynamic parameters of Fe3+-RH depend on the protonic activity of the medium in the physiological pH range. The binding rate constants are shown to depend on the ionization of a residue of the protein, probably a histidine. Linear enthalpy-entropy compensation is observed for the camphor binding as well as for the spin-state transition. A camphor-binding-induced change of the electrostatic potential is discussed.

Crystal structure of elastase-substrate complex at -- 55 degrees C

The structure of a specific acyl-enzyme intermediate in the elastase-catalysed hydrolysis of N-carbobenzoxy-L-alanyl-p-nitrophenol ester has been determined by X-ray diffraction at 3.5 A resolution. The acyl-enzyme was stabilised by cooling the crystal to --55 degrees C during substrate addition and data collection.