Formation of stable crystalline enzyme-substrate intermediates at sub-zero temperatures

Thermal segment microwell plate control for automated liquid handling setups

Automated high-throughput liquid handling operations in biolabs necessitate miniaturised and automatised equipment for effective space utilisation and system integration. This paper presents a thermal segment microwell plate control unit designed for enhanced microwell-based experimentation in liquid handling setups. The development of this device stems from the need to move towards geometry standardization and system integration of automated lab equipment. It incorporates features based on Smart Sensor and Sensor 4.0 concepts. An enzymatic activity assay is implemented with the developed device on a liquid handling station, allowing fast characterisation via a high-throughput approach. The device outperforms other comparable devices in certain metrics based on automated liquid handling requirements and addresses the needs of future biolabs in automation, especially in high-throughput screening.

Cryogenic activity and stability of benzaldehyde lyase enzyme in lipidic mesophases-nanoconfined water

Phytantriol-based lipidic mesophases (LMs) are introduced as a platform for cryoenzymology, which relies on the presence of liquid water in LMs at subzero temperatures. After incorporation into LMs, the model enzyme Benzaldehyde lyase (BAL) shows high cryogenic stability and activity. In contrast, BAL in bulk solution undergoes significant secondary structural transitions caused by low temperatures (cold denaturation), demonstrating the potential of this approach to enable in meso cryoenzymology.

Modification of Unicryl composition for rapid polymerization at low temperature without alteration of immunocytochemical sensitivity

We introduced a slight modification of Unicryl for fast polymerization at low temperature (in the range-20 degree C to-35 degree C) without modification of both physical properties and immunocytochemical yield. An UV initiator benzoin ethyl ether (BEE) is added at 0.05% concentration in neat resin during infiltration and final polymerization at-35 degree C. Immunogold labeling of amylase of mouse pancreas embedded in standard conditions recommended by the manufacturer or with our modification were compared by counting colloidal gold particles over zymogen granules using MACS, a specialized software dedicated to this operation. We noticed that addition of 0.05% BEE in Unicryl reduces the curing time to 16 h, which can be extended up to a maximum of 48 h at-35 degree C without noticeable modification of ultrastructural morphology, physical properties and immunocytochemical yield.

Learning about truth and biases through experience: section surface corrugation, protein denaturation, and staining

By developing and investigating the use of thin resin sections for electron microscopy, we discovered that many of the current biases became invalid: 1) No evidence could be produced that the involved organic liquids produce the protein denaturation responsible for loss of antigenicity and lowered resolution. For immunolabeling, "water-soluble" resins are not per se to be preferred over less polar and more hydrophobic ones. 2) The relief formed by the corrugated section surface enables access to the antigenic sites. The depth of relief is determined by the strength of copolymerization and depends on temperature, the chemical nature of resin and biological matter, and, thus, also on surface modification through fixatives. The stronger the relief, the better the immunolabeling and the less the image resolution. Strong copolymerization favors flatter relief, but also a hiding of antigenic sites by thin layers of resin. 3) Heavy metal stain remains the main culprit for low resolution of sections when compared to results obtained with other preparation methods.

Time-resolved X-ray diffraction studies of enzymes under cryoconditions

Cryoenzymological techniques provide a means of initiating enzymatic reactions in crystals homogeneously and of prolonging the lifetimes of intermediate reaction steps. Catalytic intermediates may accumulate to sufficiently high population for X-ray crystal structure analysis by time-resolved monochromatic or Laue diffraction data collection using synchrotron radiation. Due to short exposure times, intermediates may be studied at moderately low temperatures. A combination of cryoenzymology and time-resolved crystallography has been applied to crystal structure analysis at high resolution of an acyl-enzyme intermediate of a productive reaction catalysed by porcine pancreatic elastase.

1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures

The structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 A and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dimensions in going from room temperature to low temperature is accompanied by a decrease in molecular surface area and radius of gyration. The overall structure remains similar to that at room temperature. The attainable resolution appears to be improved due to the decrease in the fall off of intensities with resolution [reduction of the temperature factor]. This decreases the uncertainty in the atomic positions and allows the localization of more protein atoms and solvent molecules in the low temperature map. The largest differences between the two models occur at residues with higher than average temperature factors. Several features can be localized in the solvent region of the 120 K map that are not seen in the 295 K map. These include several more water molecules as well as an interstitial sulfate ion and two interstitial benzamidine molecules.

Temperature control in Lowicryl K4M and glycol methacrylate during polymerization: is there a low-temperature embedding method?

An apparatus for embedding tissues at resin temperatures down to 228 K is described. By placing thermocouples in the resin the temperature has been monitored during embedding at low temperature with glycol methacrylate (GMA) and Lowicryl K4M. Even in this apparatus with a liquid cooling bath the heat of polymerization is not dissipated and the resin temperature rises. This rise is directly proportional to the resin temperature at the onset of polymerization and is higher in Lowicryl K4M than GMA. The initial resin temperature also affects the time taken for polymerization. The time to the onset of the peak and its duration are both increased as the temperature is lowered. This effect is more pronounced with GMA than Lowicryl K4M and polymerization of GMA is inhibited at the lowest temperature used. When Lowicryl K4M, polymerized at low temperature, is warmed up to ambient a further exothermic reaction occurs, which causes the resin temperature to rise well above ambient. Both this temperature peak and that during polymerization are reduced, but not totally eliminated, by reducing the resin volume. Air-cooled systems are inefficient compared with the low-temperature apparatus used here and the resin temperature rise is consequently greater and, even with small resin volumes, it can be very high. It is therefore unlikely for published methods that the temperature specified has been maintained in the resin during polymerization. The implications of these findings are discussed in relation to enzyme and antigen survival. Recommendations include use of very small volumes of resin, refrigerated liquid-bath rather than air-cooled systems and contact with a heat sink when specimens are warmed up to ambient temperature. Examples of enzyme reaction, antigen survival and structural preservation obtained with the method are presented.

Cryoenzymology of trypsin. A detailed kinetic study of the trypsin-catalysed hydrolysis of N-alpha-benzyloxycarbonyl-L-lysine p-nitrophenyl ester at low temperatures

A detailed study of the kinetics of the trypsin (EC 3.4.21.4)-catalysed hydrolysis of N-alpha-benzyloxycarbonyl-L-lysine p-nitrophenyl ester in cryosolvents at 0 degrees C and below was undertaken. The pH-dependences of kcat, Km, k+2, k+3 and Ks were determined under cryoenzymological conditions and are compared with previous results [Antonini & Ascenzi (1981) J. Biol. Chem. 256, 12449-12455] obtained in fully aqueous media at ambient temperatures. Below pH 5.0 the kinetics, and presumably the mechanism of catalysis, are not significantly perturbed under cryoenzymological conditions. However, it is shown that below pH 5.0 both Km and Ks are decreased under these conditions but that both are increased at pH 6.7 relative to the results obtained in fully aqueous media at ambient temperatures. The effects of the cryoenzymological conditions on the individual catalytic parameters are discussed. The acylation rate constant, k+2, is essentially constant at pH 4.2 and 5.0 but decreases at lower pH values with an apparent pKa of approx. 4.0. In view of the low enthalpy of ionization associated with this pKa it is suggested that this group is the carboxy group of aspartic acid-189, which binds the positively charged lysine side chain of the substrate. The mechanistic implications of the results for the acylation step are discussed. It is also shown that only at low pH values can significant amounts of acylated trypsin be accumulated.

Developments in low-temperature biochemistry and biology

Though under most circumstances harmful changes are induced in cellular structures by subzero temperatures, conditions can be found under which such damage is avoided. Thus, in solution, biochemical reactions can be slowed and more easily analysed and many enzyme-substrate complexes can be stabilized and structurally analysed; in crystals, 'stop-action' pictures unveil the stereochemical changes along reaction pathways. The progressive 'solidification' of non-covalent bonds involved in protein structures should permit investigation of their dynamics. Studies at high pressures open the way to new investigations on 'activated' enzyme-substrate complexes and might permit the refinement of current concepts to a considerable degree, as a preliminary but decisive step towards a full description of enzyme mechanisms. The conditions of medium allowing such cryobiochemical studies fail to protect cellular structures against cold. Investigations of plasma membrane behaviour are now under way to determine processes leading to cryosensitivity or cryotolerance of cells.

Solvent effects and polar interactions in the structural stability and dynamics of globular proteins

Using detailed hydrogen bonding, surface exposure, internal environment, and solvent interaction calculations on several proteins, in conjunction wit data from quantum mechanical hydrogen-bonding studies, various contributions to the free energy of globular estimated and their likely relative significance discussed. A picture emerges of globular proteins as extremely well-fitting jigsaw-puzzles, in which no single driving force dominates the marginal stability of the native conformation. Rather, the folded structure is seen as the result of a complex global maximization of several strongly-interacting driving forces. In particular, the necessity to maintain very efficient internal hydrogen-bonding, and the role of the solvent as a hydrogen-bond sink, are stressed as strong constraints on the (incomplete) maximization of hydrophobic effects. The possible significance of internal dipole-induced dipole interactions is discussed tentatively. Although quantitative estimates of the various contributions remain uncertain, consideration of effective force constants suggests that polar, including solvent, interactions may largely determine the overall curvatures of the native conformation's potential well, and be important in controlling the flexibility of local regions which are important for the exact positioning of groups during enzyme catalysis, as well as the molecule's overall dynamics. In contrast, hydrophobic interactions change less for small geometrical perturbations, and seem more relevant to directing the folding protein. along a path to a region in configurational space where the polar interactions can switch on for the final "docking".

The crystal structure of tortoise egg-white lysozyme at 6 A resolution

Lysozyme extracted from the egg-white of tortoise, the first example of a reptilian lysozyme to have been purified, has been crystallized and its tertiary structure determined at low resolution by X-ray analysis. This structure is shown to be closely homologous to that of hen egg-white lysozyme. The crystals of tortoise egg-white lysozyme contain a large proportion of liquid and the X-ray map shows that this forms large channels through the crystals into which the active sites of the enzyme molecules open. This indicates that tortois lysozyme crystals may be suitable for low-temperature studies of true enzyme substrate complexes.

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.

Detection and accumulation of tetrahedral intermediates in elastase catalysis

Tetrahedral intermediates in the reaction of elastase with specific di- and tripeptide p-nitroanilide substrates have been detected, accumulated, and stabilized at high pH by using subzero temperatures and fluid aqueous/organic cryosolvents. The tetrahedral adducts are characterized by spectra with lambda max of 359 +/- 2 nm, compared with thata of 380 nm for p-nitroaniline and 315-320 nm for the substrates. The maximal concentration of intermediate that could be accumulated varied with the different substrates from 40 to 100% of the active enzyme present. The pH dependence of the reactions indicated that formation of the tetrahedral intermediates was rate-limiting at low pH (pK* = 7.0 at -39 degrees C) and that collapse to the acylenzymes was rate-determining at high pH. When corrected for the effect of temperature and cosolvent, the rate of intermediate formation was in good agreement with that measured at 25 degrees C in aqueous solution by stopped-flow techniques.

Supercooled water as medium for enzyme reactions at subzero temperatures

A water-in-oil emulsion technique was employed to investigate enzyme-catalyzed reactions at sub-zero temperatures in the supercooled liquid state. The results obtained with a monooxygenase (bacterial cytochrome P-450) clearly indicate the potentialities as well as the technical problems of the procedure which might be successfully used to investigate enzyme systems sensitive to cosolvents.

Conversion of the active-site cysteine residue of papain into a dehydro-serine, a serine and a glycine residue

Photolysis of papain which had been inhibited with 2-bromo-2',4'-dimethoxyacetophenone regenerated papain, but also formed [deltaSer25]-papain (i.e. papain in which the active-site cysteine residue 25 was replaced by dehydroserine) via the intermediate dehydrocysteine analogue, [deltaCys25]-papain. Reduction with sodium borohydride gave [Ser25]papain. Both [Ser25]papain and [deltaSer25]-papain had binding properties similar to those of papain, but were devoid of enzymic activity. Their fluorescence properties were also investigated. Incubation of [deltaSer25]papain at pH 9.0 gave [Gly25]papain.

Papain-catalyzed reactions at subzero temperatures

As a first step in the investigation of papain catalysis using subzero temperatures to detect, accumulate, and characterize enzyme-substrate intermediates, we have studied some potential cryosolvents and carried out preliminary intermediate trapping experiments. The effects of subzero temperatures and aqueous dimethyl sulfoxide solutions on the papain-catalyzed hydrolysis of Nalpha-carbobenzoxy-L-lysine p-nitrophenyl ester have been investigated in detail. At 0 degrees C, the value of kcat decreases with increasing dimethyl sulfoxide concentration, decreasing in proportion to the decreased water concentration; however, the value of Km increases exponentially. The effect on Km can be accounted for by a combination of both dielectric and competitive inhibition effects. The Arrhenius plot for the deacylation reaction in 7.65 M (60% v/v) dimethyl sulfoxide is linear over the temperature range 0 to -45 degrees C and extrapolates to a calculated value of kcat at 25 degrees C in excellent agreement with that obtained in the absence of organic solvent. The pH-rate profile is not substantially perturbed by the presence of 7.65 M dimethyl sulfoxide. At -45 degrees C and below, turnover occurs extremely slowly, and is essentially negligible, although acylation is still quite rapid. Consequently, the acyl enzyme, Na-carbobenzoxy-L-lysyl-papain, can be readily accumulated and trapped at temperatures below -50 degrees C. At these low temperatures, under conditions of excess substrate, the amount of p-nitrophenol liberated in the acylation reaction is equivalent to the active-site normality of the enzyme, indicating a 1:1 stoichiometry in formation of the acyl enzyme. The effect of dimethyl sulfoxide up to 7.65 M, on the intrinsic ultraviolet, fluorescence, and circular dichroic properties of the enzyme shows no evidence of any solvent-induced structural changes. All experimental observations are consistent with the conclusion that 7.65 M dimethyl sulfoxide and subzero temperatures have no deleterious effects on papain-catalyzed reactions. A related series of experiments indicate that aqueous ethanol cryosolvents up to 13.7 M (80% v/v) are also suitable. Preliminary experiments at subzero temperatures using Na-carbobenzoxy-L-lysine methyl ester suggest the existence of three enzyme-substrate intermediates which can be detected and accumulated.

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.