Structure and stability of thermophilic enzymes. Studies on thermolysin

Bacterial extracellular zinc-containing metalloproteases

Extracellular zinc-containing metalloproteases are widely distributed in the bacterial world. The most extensively studied are those which are associated with pathogenic bacteria or bacteria which have industrial significance. They are found practically wherever they are sought in both gram-negative and gram-positive microorganisms, be they aerobic or anaerobic. This ubiquity in itself implies that these enzymes serve important functions for the organisms which produce them. Because of the importance of zinc to enzymatic activity, it is not surprising that there is a pervasive amino acid sequence homology in the primary structure of this family of enzymes regardless of their source. The evidence suggests that both convergent and divergent evolutionary forces are at work. Within the large family of bacterial zinc-containing metalloendopeptidases, smaller family units are observed, such as thermolysin-like, elastase-like, and Serratia protease-like metalloproteases from various bacterial species. While this review was in the process of construction, a new function for zinc-containing metalloproteases was discovered: the neurotoxins of Clostridium tetani and Clostridium botulinum type B have been shown to be zinc metalloproteases with specificity for synaptobrevin, an integral membrane protein of small synaptic vesicles which is involved in neurotransmission. Additional understanding of the mode of action of proteases which contribute to pathogenicity could lead to the development of inhibitors, such as chelators, surrogate substrates, or antibodies, which could prevent or interrupt the disease process. Further studies of this broad family of metalloproteases will provide important additional insights into the pathogenesis and structure-function relationships of enzymes and will lead to the development of products, including "designer proteins," which might be industrially and/or therapeutically useful.

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

Bacillus neutral proteases (NPs) form a group of well-characterized homologous enzymes, that exhibit large differences in thermostability. The three-dimensional (3D) structures of several of these enzymes have been modelled on the basis of the crystal structures of the NPs of B. thermoproteolyticus (thermolysin) and B. cereus. Several new techniques have been developed to improve the model-building procedures. Also a 'model-building by mutagenesis' strategy was used, in which mutants were designed just to shed light on parts of the structures that were particularly hard to model. The NP models have been used for the prediction of site-directed mutations aimed at improving the thermostability of the enzymes. Predictions were made using several novel computational techniques, such as position-specific rotamer searching, packing quality analysis and property-profile database searches. Many stabilizing mutations were predicted and produced: improvement of hydrogen bonding, exclusion of buried water molecules, capping helices, improvement of hydrophobic interactions and entropic stabilization have been applied successfully. At elevated temperatures NPs are irreversibly inactivated as a result of autolysis. It has been shown that this denaturation process is independent of the protease activity and concentration and that the inactivation follows first-order kinetics. From this it has been conjectured that local unfolding of (surface) loops, which renders the protein susceptible to autolysis, is the rate-limiting step. Despite the particular nature of the thermal denaturation process, normal rules for protein stability can be applied to NPs. However, rather than stabilizing the whole protein against global unfolding, only a small region has to be protected against local unfolding. In contrast to proteins in general, mutational effects in proteases are not additive and their magnitude is strongly dependent on the location of the mutation. Mutations that alter the stability of the NP by a large amount are located in a relatively weak region (or more precisely, they affect a local unfolding pathway with a relatively low free energy of activation). One weak region, that is supposedly important in the early steps of NP unfolding, has been determined in the NP of B. stearothermophilus. After eliminating this weakest link a drastic increase in thermostability was observed and the search for the second-weakest link, or the second-lowest energy local unfolding pathway is now in progress. Hopefully, this approach can be used to unravel the entire early phase of unfolding.

Stabilization of Bacillus stearothermophilus neutral protease by introduction of prolines

The thermostability of neutral proteases has been shown to depend on autolysis which presumably occurs in flexible regions of the protein. In an attempt to rigidify such a region in the neutral protease of Bacillus stearothermophilus, residues in the solvent-exposed 63-69 loop were replaced by proline. The mutations caused large positive (Ser-65-->Pro, Ala-69-->Pro) or negative (Thr-63-->Pro, Tyr-66-->Pro) changes in thermostability, which were explained on the basis of molecular modelling of the mutant proteins. The data show that the introduction of prolines at carefully selected positions in the protein can be a powerful method for stabilization.

Mutations that significantly change the stability, flexibility and quaternary structure of the l-lactate dehydrogenase from Bacillus megaterium

In order to investigate the physical basis of protein stability, two mutant L-lactate dehydrogenases (LDH) and the wild-type enzyme from Bacillus megaterium were analyzed for differences in quaternary structure, global protein conformation, thermal stability, stability against guanidine hydrochloride, and polypeptide chain flexibility. One mutant enzyme, ([T29A, S39A]LDH), differing at two positions in the alpha-B helix, exhibited a 20 degrees C increase in thermostability. Hydrogen/deuterium exchange revealed a rigid structure of this enzyme at room temperature. The substitutions Ala37 to Val and Met40 to Leu destabilize the protein. This is observable in a greater susceptibility to thermal denaturation and in an unusual monomer/dimer/tetramer equilibrium in the absence of fructose 1,6-bisphosphate Fru(1,6)P2. The stability, flexibility and protein-conformation measurements were all performed in the presence of 5 mM Fru(1,6)P2, i.e. under conditions where the three investigated LDH species are stable tetramers. Tryptophan fluorescence was used to monitor the unfolding in guanidine HCl of two local structures in or very close to the beta-sheets at the protein surface. The LDHs form folding intermediates in guanidine HCl that aggregate at elevated temperatures. Pronounced differences between the three investigated enzymes are found in their ability to aggregate. The exchange of Thr29 and Ser39 for Ala leads to significantly less aggregation in guanidine HCl than is observed for wild-type LDH. Using 8-anilinonaphthalene-1-sulfonic acid, the folding intermediates were shown to be in accordance with molten-globule-like structures. We have found, by means of molecular sieve chromatography, that the [T29A, S39A]LDH with its increased thermostability has lower susceptibility to disintegrate into monomers in guanidine HCl at 25 degrees C. Despite the differences in aggregation at low guanidine HCl concentrations and temperatures above 25 degrees C, the molten-globule-like structures of the three investigated LDH species are structurally similar, as shown by molecular-sieve chromatography. Although the thermostabilities of the three LDH species are so different in aqueous buffers, their stabilities in guanidine HCl at 20 degrees C are, surprisingly, almost identical. Some comments are made as to the origin of the observed difference between thermal and guanidine HCl stabilities of the LDH. Near-ultraviolet and far-ultraviolet circular dichroism measurements, as well as differences in the amount of activation by Fru(1,6)P2, point to small global structural rearrangements caused by the mutations. Conformational changes upon Fru(1,6)P2 binding or point mutations in the alpha-B helix show that the Fru(1,6)P2-binding site and the alpha-B helix are structurally linked together.(ABSTRACT TRUNCATED AT 400 WORDS)

Effects of changing the interaction between subdomains on the thermostability of Bacillus neutral proteases

Variants of the thermolabile neutral protease (Npr) of B. subtilis (Npr-sub) and the thermostable neutral protease of B. stearothermophilus (Npr-ste) were produced by means of site-directed mutagenesis and the effects of the mutations on thermostability were determined. Mutations were designed to alter the interaction between the middle and C-terminal subdomain of these enzymes. In all Nprs a cluster of hydrophobic contacts centered around residue 315 contributes to this interaction. In thermostable Nprs (like Npr-ste) a 10 residue beta-hairpin, covering the domain interface, makes an additional contribution. The hydrophobic residue at position 315 was replaced by smaller amino acids. In addition, the beta-hairpin was deleted from Npr-ste and inserted into Npr-sub. The changes in thermostability observed after these mutations confirmed the importance of the hydrophobic cluster and of the beta-hairpin for the structural integrity of Nprs. Combined mutants showed that the effects of individual mutations affecting the interaction between the subdomains were not additive. The effects on thermostability decreased as the strength of the subdomain interaction increased. The results show that once the subdomain interface is sufficiently stabilized, additional stabilizing mutations at the same interface do not further increase thermostability. The results are interpreted on the basis of a model for the thermal inactivation of neutral proteases, in which it is assumed that inactivation results from the occurrence of local unfolding processes that render these enzymes susceptible to autolysis.

Structural organization and stability of a thermoresistant domain generated by in vivo hydrolysis of the alpha-crystallin B chain from calf lens

A protein fragment (M(r) approximately 9000) isolated from the cortex of nonpathological calf lenses has been structurally characterized. The polypeptide structure was well organized (39% alpha-helix, 33% beta-structure, and 28% remainder) according to the far-ultraviolet circular dichroism. The fluorescence was heterogeneous for the presence of two tryptophan classes. Structure perturbation by pH and denaturant revealed cooperative structural transitions which are characteristics of a globular organization. A single-step unfolding curve induced by Gdn-HCl (midpoint = 1.38 M Gdn-HCl) was monitored by emission maximum shift as well as by far-ultraviolet circular dichroism. This transition was analyzed as a two-state process. The standard free energy of unfolding in the absence of the denaturant, delta Go (H2O), was found to be 10.80 +/- 0.25 kJ/mol at 20 degrees C and pH 7.4. The fragment also shows an unusual thermal resistance. Its structure was unperturbed up to 90 degrees C according to the fluorescence and dichroism. This last property, its peculiar amino acid composition, and the sequence of a small segment are shared, among crystallins, only with the N-terminal region of the alpha-crystallin B chain. A search for proteolysis sites along the alpha-crystallin B chain sequence revealed that it possesses specific points for proteinase attack. These sites are particularly exposed and clustered in a very flexible region in the middle of the protein sequence. They are also well represented in the C-terminal extension of the molecule while a few are buried in the N-terminal region.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence for temperature-dependent conformational changes in the L-lactate dehydrogenase from Bacillus stearothermophilus

L-Lactate dehydrogenase from Bacillus stearothermophilus (BSLDH) has been shown to change its conformation in a temperature-dependent manner in the temperature range between 25 and 70 degrees C. To provide a more detailed understanding of this reversible structural reorganization of the tetrameric form of BSLDH, we have determined in the presence of 5 mM fructose, 1,6-bisphosphate (FBP) the effect of temperature on far-UV and near-UV circular dichroism (CD), Nile red-binding to the enzyme surface, NADH binding, fluorescence polarization of fluorescamine-labeled protein, and hydrogen-deuterium exchange. In addition, we have analyzed the temperature dependence of the dimer-tetramer equilibrium of this protein by steady-state enzyme kinetics in the absence of FBP. The results obtained from these measurements at various temperatures can be summarized as follows. No changes in the secondary-structure distribution are detectable from far-UV CD measurements. On the other hand, near-UV CD data reveal that changes in the arrangements of aromatic side chains do occur. With increasing temperature, the asymmetry of the environment around aromatic residues decreases with a small change at 45 degrees C and a more pronounced change at 65 degrees C. Nile red-binding data suggest that the BSLDH surface hydrophobicity changes with temperature. It appears that decreasing the surface hydrophobicity may be a strategy to increase the protein stability of the active enzyme. We have noted significant alterations in the thermodynamic binding parameters of NADH above 45 degrees C, indicating a conformational change in the active site at 45 degrees C. The hydrodynamic volume of BSLDH is also temperature dependent.(ABSTRACT TRUNCATED AT 250 WORDS)

The structure of neutral protease from Bacillus cereus at 0.2-nm resolution

The crystal structure of the neutral protease from Bacillus cereus has been refined to an R factor of 17.5% at 0.2-nm resolution. The enzyme, an extracellular metalloendopeptidase, consists of two domains and binds one zinc and four calcium ions. The structure is very similar to that of thermolysin, with which the enzyme shares 73% amino-acid sequence identity. The active-site cleft between the two domains is wider in neutral protease than in thermolysin. This suggests the presence of a flexible hinge region between the two domains, which may assist enzyme action. The high-resolution analysis allows detailed examination of possible causes for the difference in thermostability between neutral protease and thermolysin.

Effect of temperature on the propylamine transferase from Sulfolobus solfataricus, an extreme thermophilic archaebacterium. 2. Denaturation and structural stability

The thermal stability of propylamine transferase from Sulfolobus solfataricus, an extreme thermophilic archaebacterium, has been characterized thermodynamically by a Van't Hoff analysis. Conformational transitions induced by guanidine hydrochloride, as well as by temperature, have been linked together in a scheme involving six equilibria, which arise from both dissociation and unfolding. The mechanism by which the protein achieves thermal stabilization is quite unusual. It is driven by a conformational equilibrium between two forms of different stability. The stability of each form towards denaturation is characterized by a specific temperature dependence. The low-temperature form, indicated as 'form A', is stable over 12-89 degrees C. Its stability maximum is 36.8 kJ/mol at 50 degrees C. 'Form B', which is populated at higher temperature, spans the interval 28-146 degrees C. Its stability maximum is 71.6 kJ/mol at 87 degrees C. A possible explanation for the mechanism underlying this behaviour is discussed assuming that two major terms contribute to stability, i.e. hydrophobic interactions arising from burying of the accessible surface residues as well as conformational entropy. The thermal stabilization of the enzyme seems to depend on effects related to both an overall increase of flexibility and a concomitant decrease of the area buried upon folding. In this regard proteins from extreme thermophilic organisms appear to be a useful model to shed new light on the general problem of protein stability.

Effect of temperature on the propylamine transferase from Sulfolobus solfataricus, an extreme thermophilic archaebacterium. 1. Conformational behavior of the oligomeric enzyme in solution

The effect of temperature on the molecular structure of propylamine transferase from Sulfolobus solfataricus has been investigated. Sulfolobus solfataricus is an extreme thermophilic archaebacterium with an optimum living condition at 90 degrees C. The enzyme is an oligomeric (trimer) protein of molecular mass 112 kDa. The frictional ratio for the native protein suggests an irregularly shaped compact globular structure. The protein matrix is well organized as suggested by far ultraviolet circular dichroism at 25 degrees C (18% alpha helix, 43% beta structure, 19% beta bends and 20% unordered: root mean square = 7). Structural effects of temperature were investigated over 25-85 degrees C. The protein retains its quaternary structure in this temperature range. A highly reversible subtle conformational transition was detected by numerous structure-dependent techniques over 40-50 degrees C, with a midpoint centered at 45 degrees C. Functional data also support this view. In fact, two enzyme forms, characterized by different catalytic properties, are present in solution. The Arrhenius plot suggests the occurrence of two different activation-energy-dependent processes, one at a temperature higher and one at a temperature lower than 45 degrees C. The transition has been considered as a molecular switch between two protein populations at equilibrium with different functional and structural properties, temperature modulated. A physiological role for the molecular switch has also been postulated. The protein also shows some subtle and reversible spectroscopic changes around 75 degrees C. The molecular basis of the thermophilic nature of this enzyme seems to reside in its capability to dynamically couple catalytic and structural events to the thermal properties of the ambient medium.

Differential scanning calorimetric study of carboxypeptidase B, procarboxypeptidase B and its globular activation domain

High-sensitivity differential scanning calorimetry has been applied to the study of porcine pancreatic carboxypeptidase B, the proenzyme and its 81-residue activation domain. The thermal study has been carried out over a range of scan rates, ionic strengths and pH values. The thermal unfolding of the isolated activation domain has been found to be reversible and corresponds to that of a typical compact globular structure, with melting temperatures higher than those of the enzyme and proenzyme. Both proteins, on the other hand, undergo an irreversible, highly scan-rate-dependent thermal denaturation under all the experimental conditions investigated. The denaturation of the enzyme at pH 7.5 and the proenzyme at pH 7.5 and 9.0 follows the two-state irreversible model [Sánchez-Ruiz, J.M., López-Lacomba, J.L., Cortijo, M. & Mateo, P.L. (1988) Biochemistry 27, 1648-1652]. Thus the kinetic constants and activation parameters of the denaturation process could be obtained and compared to those for other proteins, particularly those of the closely related carboxypeptidase A system.

Analysis and modulation of protein stability

Numerous site-directed mutagenesis experiments have provided new insights into the stabilizing role of the individual forces and interactions within a globular protein molecule. Some useful guidelines and procedures are now available for producing genetically more stable proteins. Examples are the introduction of disulfide bonds, ion-binding sites, salt bridges, hydrophobic residues or hydrogen bonds, and the improvement of hydrophobic packing or alpha-helix propensity. Moreover, it is now clearly recognized that thermophilic (and, in general, extremophilic) bacteria produce highly stable proteins and enzymes of practical interest.

Functionally-stabilized proteins — A review

The maintenance or stabilization of protein or enzyme function is of vital importance in Biotechnology. Investigations of thermophilic organisms, studies of denaturation and the use of enzymes in organic solvents have each contributed to an understanding of protein stability. Enzymes can reliably and reproducibly be stabilized by variety of means including immobilization, use of additives, chemical modification in solution and protein engineering. Examples of each of these are discussed. With these recent advances it appears that a rational strategy for achieving a particular stabilized enzyme or protein may be within reach.

Substrate inhibition or activation kinetics of the beta-galactosidase from the extreme thermoacidophile archaebacterium Caldariella acidophila

The kinetics of the hydrolysis of p-nitrophenyl-beta-D-galactopyranoside (pNPG) by a thermophile, beta-galactosidase, was studied at different temperatures. This enzyme was isolated from the thermophilic microorganism archaebacterium Caldariella acidophila. The hydrolysis of pNPG by beta-galactosidase does not follow Michaelis-Menten law. This enzyme is inhibited by excess substrate at low temperatures and it is activated by excess substrate at high temperatures. A minimum mechanistic model is proposed to explain the behaviour. This model assumes the binding of an additional substrate molecule on the glycosidyl enzyme intermediate. This model is in good agreement with the postulated mechanism for beta-galactosidase from Escherichia coli. The kinetic parameters are calculated at six different temperatures.

Stability and activity of a thermostable malic enzyme in denaturants and water-miscible organic solvents

A study was made of the effects of common protein denaturants and water-miscible organic solvents on both the stability and activity of the malic enzyme [(S)-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating); EC 1.1.1.40] from the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus. At 25 degrees C, the enzyme was not inactivated in 4 M urea or 0.05% SDS over 24 h, while the half-life was 30 min in 6 M guanidine hydrochloride and 5 h in 0.075% SDS. The enzyme stability in water-miscible organic solvents at 25 degrees C is somewhat surprising: after a 24-h incubation, the enzyme was completely active in 50% dimethylformamide; it lost 15% of its initial activity in 50% methanol or 15% ethanol. However, the resistance to organic solvents was greatly reduced at higher temperatures. The enzyme was able to catalyze the malate conversion even in the presence of 1.5% Triton X-100 or sodium deoxycholate. A number of solvents were found to stimulate the malic activity independent of time. Studies with 50% methanol revealed that the activation was reversible and inversely related to the temperature; moreover, the solvent was demonstrated to exclusively affect the maximal velocity of catalysis, the Km values for both substrates being unchanged. Investigation was made to find out whether there was a correlation between enzyme stability, as well as activation, and hydrophobicity of the organic medium. The residual malic activity after incubation in the water/organic medium correlated inversely with the logarithm of the partition coefficient in octanol/H2O of the mixture used as a hydrophobicity index. On the other hand, the extent of activation depended directly on the logarithm of the molar concentration of the organic solvent required for maximal enzymatic activation. Because of its remarkable resistance to organic solvents required for maximal enzymatic activation. Because of its remarkable resistance to organic solvents and protein denaturants in general, the malic enzyme from Sulfolobus solfataricus can be considered suitable for biotechnological applications.

Engineering protein thermal stability. Sequence statistics point to residue substitutions in alpha-helices

Amino acid sequences have been compared for thermophilic and mesophilic molecules from six different protein families, which include lactate and glyceraldehyde-3-phosphate dehydrogenases, triose phosphate isomerases, superoxide dismutases, thermolysins and subtilisins. Since a three-dimensional structure was known for at least one of the sequences in each family, analysis of preferred residue substitutions, presumably to achieve thermal stability, could be examined from a structural context. The overall results, which are generally consistent across all the families, suggested decreased flexibility and increased hydrophobicity in alpha-helical regions as the main stabilizing principles. The most favoured residual exchanges, hopefully useful in engineering stability into proteins, are discussed.