X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate

Studies on the catalytic mechanism and inhibition of serine proteases are widely used as paradigms for teaching enzyme catalysis. Ground-breaking work on the structures of chymotrypsin and subtilisin led to the idea of a conserved catalytic triad formed by the active site Ser, His and Asp residues. An oxyanion hole, consisting of the peptide amide of the active site serine and a neighbouring glycine, was identified, and hydrogen bonding in the oxyanion hole was suggested to stabilize the two proposed tetrahedral intermediates on the catalytic pathway. Here we show electron density changes consistent with the formation of a tetrahedral intermediate during the hydrolysis of an acyl-enzyme complex formed between a natural heptapeptide and elastase. No electron density for an enzyme-product complex was observed. The structures also suggest a mechanism for the synchronization of hydrolysis and peptide release triggered by the conversion of the sp2 hybridized carbonyl carbon to an sp3 carbon in the tetrahedral intermediate. This affects the location of the peptide in the active site cleft, triggering the collapse of a hydrogen bonding network between the peptide and the beta-sheet of the active site.     

Electronic aspects of serine protease catalysis

A new electrostatic approach is applied to serine protease catalysis. It is is based upon the demonstration that the polarities, or partial charges, of the atomic components of the molecules involved in the reaction alternate in sign. When the atomic components of opposite polarities of the enzyme and substrate approach close to each other during the catalysis, the electrostatic interactions between them increase in intensity. These increasing interactions are related to the decrease in the energy barrier. When the serine protease--catalyzed reaction is followed from this perspective, it is shown to result in a marked simplification of the catalytic mechanism. A number of concerted proton transfers and electron density displacements around the active site are indicated. This approach is not inconsistent with other electrostatic methods, and is supported by independent partial charge calculations.     

Structural analyses on intermediates in serine protease catalysis

Although the subject of many studies, detailed structural information on aspects of the catalytic cycle of serine proteases is lacking. Crystallographic analyses were performed in which an acyl-enzyme complex, formed from elastase and a peptide, was reacted with a series of nucleophilic dipeptides. Multiple analyses led to electron density maps consistent with the formation of a tetrahedral species. In certain cases, apparent peptide bond formation at the active site was observed, and the electron density maps suggested production of a cis-amide rather than a trans-amide. Evidence for a cis-amide configuration was also observed in the noncovalent complex between elastase and an alpha1-antitrypsin-derived tetrapeptide. Although there are caveats on the relevance of the crystallographic data to solution catalysis, the results enable detailed proposals for the pathway of the acylation step to be made. At least in some cases, it is proposed that the alcohol of Ser-195 may preferentially attack the carbonyl of the cis-amide form of the substrate, in a stereoelectronically favored manner, to give a tetrahedral oxyanion intermediate, which undergoes N-inversion and/or C-N bond rotation to enable protonation of the leaving group nitrogen. The mechanistic proposals may have consequences for protease inhibition, in particular for the design of high energy intermediate analogues.     

Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis

Purified protein-disulphide isomerase has been examined for effects on the pathway and kinetics of the unfolding and refolding which accompanies disulphide bond breakage and reformation in bovine pancreatic trypsin inhibitor and bovine ribonuclease A. The intermediates of the pathways were not altered, although some interconversions which normally are not significant became so in the presence of the isomerase. The rate of every step involving both substantial protein conformational changes and protein disulphide bond formation, breakage or rearrangement was found to be increased significantly, but only when the conformational changes were rate-determining. The protein-disulphide isomerase appears to be a true catalyst of protein unfolding and refolding involving disulphide bond breakage, formation or rearrangement.     

Thionesters as a probe for electrophilic catalysis in the serine protease mechanism

Specific and nonspecific thionester substrates for alpha-chymotrypsin and subtilisin Carlsberg have been synthesized and the kinetic parameters for their enzyme-catalyzed hydrolyses measured. Despite equal nonenzymic reactivities of ester-thionester pairs, each thionester is considerably less reactive toward enzymic hydrolysis, the difference being greatest for the specific substrates. The data support the operation of electrophilic catalysis by a hydrogen bond network at the carbonyl oxygen adjacent to the scissile bond of the substrate. The free energy of stabilization is 19 kJ mol-1 for a specific thionester substrate and will be higher for oxygen esters and amides. Chymotrypsin binds esters and thionesters about equally well, whereas subtilisin binds thionesters more tightly. This is consistent with continuous hydrogen bonding in the chymotrypsin mechanism and with a differential hydrogen bonding mechanism for subtilisin. A comparison of the relative rates of enzyme-catalyzed hydrolysis of ester and thionester substrates with their relative reactivities toward amines does not support an acyl histidine intermediate in the serine protease mechanism.     

Intramolecular orbital alignments in serine protease/protein inhibitor complexes

By an analysis of PDB crystal structures, the mean conformations of protein strands bound in serine protease active sites are shown to contain extensively aligned atomic orbitals. The active-serine-bearing segment of each enzyme (subtilisin BPN' and beta-trypsin) also contains such alignments. The participating orbitals are almost identical in each system. All of the alignments converge on the targeted linkage. They suggest that a kind of through-strand polarizability is being optimized by evolution, presumably due to corresponding benefits in proteolysis rate. Such polarizability would help to explain the high values of kcat seen for long oligopeptide substrates. The idea predicts long substrates to be relatively reactive even under non-enzymatic conditions, which in fact they are.     

Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis

Atomic resolution (相似文献   

The 1.8 A structure of the complex between chymostatin and Streptomyces griseus protease A. A model for serine protease catalytic tetrahedral intermediates

The naturally occurring serine protease inhibitor, chymostatin, forms a hemiacetal adduct with the catalytic Ser195 residue of Streptomyces griseus protease A. Restrained parameter least-squares refinement of this complex to 1.8 A resolution has produced an R index of 0 X 123 for the 11,755 observed reflections. The refined distance of the carbonyl carbon atom of the aldehyde to O gamma of Ser195 is 1 X 62 A. Both the R and S configurations of the hemiacetal occur in equal populations, with the end result resembling the expected configuration for a covalent tetrahedral product intermediate of a true substrate. This study strengthens the concept that serine proteases stabilize a covalent, tetrahedrally co-ordinated species and elaborates those features of the enzyme responsible for this effect. We propose that a major driving force for the hydrolysis of peptide bonds by serine proteases is the non-planar distortion of the scissile bond by the enzyme, which thereby lowers the activation energy barrier to hydrolysis by eliminating the resonance stabilization energy of the peptide bond.     

Structure and stability of anionic liposomes complexes with PEG-chitosan branched copolymer

Application of branched copolymers of polyethylene glycol and chitosan (PEG-chitosan) as stabilizing agents for anionic liposomes was shown to improve considerably liposomes storage stability. In the course of the work, an efficient and convenient approach to synthesis of PEG-chitosan copolymers through chemical modification of chitosan amino groups with monomethoxy-PEG-N-hydroxysuccinimidyl succinate (mPEG-suc-NHS) was developed. Chitosan with varying degree of PEGylation were obtained and used as stabilizing agents for anionic liposomes prepared of dipalmitoylphosphatidylcholine-cardiolipin, 80/20 by weight. The molecular mechanism of complex formation between the anionic liposomes and PEG-chitosan was studied by methods of FTIR spectroscopy and dynamic light scattering. Phosphate and carbonyl groups were found to be the main sites of the aminopolysaccharide binding. Stabilization of the complexes is mainly achieved through electrostatic interactions between anionic groups of cardiolipin and free amino groups of PEG-chitosan. The method of liposome stabilization is promising for the development of new drug delivery systems.     

Endogenous protease activation of ENaC: effect of serine protease inhibition on ENaC single channel properties

Endogenous serine proteases have been reported to control the reabsorption of Na(+) by kidney- and lung-derived epithelial cells via stimulation of electrogenic Na(+) transport mediated by the epithelial Na(+) channel (ENaC). In this study we investigated the effects of aprotinin on ENaC single channel properties using transepithelial fluctuation analysis in the amphibian kidney epithelium, A6. Aprotinin caused a time- and concentration-dependent inhibition (84 +/- 10.5%) in the amiloride-sensitive sodium transport (I(Na)) with a time constant of 18 min and half maximal inhibition constant of 1 microM. Analysis of amiloride analogue blocker-induced fluctuations in I(Na) showed linear rate-concentration plots with identical blocker on and off rates in control and aprotinin-inhibited conditions. Verification of open-block kinetics allowed for the use of a pulse protocol method (Helman, S.I., X. Liu, K. Baldwin, B.L. Blazer-Yost, and W.J. Els. 1998. Am. J. Physiol. 274:C947-C957) to study the same cells under different conditions as well as the reversibility of the aprotinin effect on single channel properties. Aprotinin caused reversible changes in all three single channel properties but only the change in the number of open channels was consistent with the inhibition of I(Na). A 50% decrease in I(Na) was accompanied by 50% increases in the single channel current and open probability but an 80% decrease in the number of open channels. Washout of aprotinin led to a time-dependent restoration of I(Na) as well as the single channel properties to the control, pre-aprotinin, values. We conclude that protease regulation of I(Na) is mediated by changes in the number of open channels in the apical membrane. The increase in the single channel current caused by protease inhibition can be explained by a hyperpolarization of the apical membrane potential as active Na(+) channels are retrieved. The paradoxical increase in channel open probability caused by protease inhibition will require further investigation but does suggest a potential compensatory regulatory mechanism to maintain I(Na) at some minimal threshold value.     

Potent and selective inhibition of membrane-type serine protease 1 by human single-chain antibodies

Specific human antibodies targeting proteases expressed on cancer cells can be valuable reagents for diagnosis, prognosis, and therapy of cancer. To this end, a phage-displayed antibody library was screened against a cancer-associated serine protease, MT-SP1. A protein inhibitor of serine proteases that binds to a defined surface of MT-SP1 was used in an affinity-based washing procedure. Six antibodies were selected on the basis of their ELISA profiles and ability to serve as useful immunological reagents. The apparent K(i), indicative of the potency of the antibodies at inhibiting human MT-SP1 activity, ranged from 50 pM to 129 nM. Two of the antibodies had approximately 800-fold and 1500-fold selectivity when tested against the most homologous serine protease family member, mouse MT-SP1, that exhibits 86.6% sequence identity. Surface plasmon resonance was used as an independent means of determining the binding constants of the six antibodies. Association rates were as high as 1.15 x 10(7) s(-)(1) M(-)(1), and dissociation rates were as low as 3.8 x 10(-)(4) s(-)(1). One antibody was shown to detect denatured MT-SP1 with no cross reactivity to other family members in HeLa or PC3 cells. Another antibody recognized the enzyme in human prostate tissue samples for immunohistochemistry analysis. The mode of binding among the six antibodies and the protease was analyzed by competition ELISA using three distinctly different inhibitors that mapped the enzyme surface. These antibodies constitute a new class of highly selective protease inhibitors that can be used to dissect the biological roles of proteolytic enzymes as well as to develop diagnostic and therapeutic reagents.     

Time-dependent inhibition of tuberculin-induced lymphocyte DNA synthesis by a serine protease inhibitor

Diisopropylfluorophosphate (DFP), a group-specific irreversible inhibitor of serine proteases, has been shown to exert time-dependent inhibition of DNA synthesis of lymphocytes stimulated by three different B lymphocyte mitogens: purified protein derivative of tuberculin (PPD), endotoxin protein (EP), and lipopolysaccharide (LPS). The time-dependent inhibition profile found in B lymphocytes is absent in concanavalin A (Con A)-stimulated T lymphocytes. Structural analogs of DFP, which have lost the phosphorylating ability, are not inhibitory. Inhibition of DNA synthesis by DFP is reversible in the first 8 hr of mitogenic stimulation. Maximal and irreversible inhibition by DFP occurs around the 16th hour of stimulation. These data support the postulate that a mitogenesis-linked protease, or proteases, in B lymphocytes is absent in the resting cells but is made available several hours before the initiation of DNA synthesis in the late G1 phase of the cell cycle.     

The novel bovine serpin endopin 2C demonstrates selective inhibition of the cysteine protease cathepsin L compared to the serine protease elastase, in cross-class inhibition

Molecular cloning revealed the unique serpin endopin 2C that demonstrates selective inhibition of cathepsin L compared to papain or elastase. Endopin 2C, thus, functions as a serpin with the property of cross-class inhibition. Endopin 2C possesses homology in primary sequence to endopin 2A and other isoforms of endopins related to alpha1-antichymotrypsin, yet endopin 2C differs in its target protease specificity. Recombinant endopin 2C showed effective inhibition of cathepsin L with a stoichiometry of inhibition (SI) of 1/1 (molar ratio of inhibitor/protease), with the second-order rate constant, k(ass), of 7.2 x 10(5) M(-1) s(-1). Less effective endopin 2C inhibition of papain and elastase occurred with k(ass) association rate constants of approximately 1 x 10(4) M(-1) s(-1) with high SI values. Endopin 2C formed SDS-stable complexes with cathepsin L, papain, and elastase that are typical of serpins. These results are among the first to demonstrate stable serpin complexes with target cysteine proteases. Interactions of endopin 2C with cathepsin L and elastase were indicated by protease cleavage of the RSL region between P1-P1' residues of Thr-Ser. The hydrophobic Phe residue in the P2 position of the RSL region is consistent with the specificity of cathepsin L for hydrophobic residues in the P2 position of its substrate cleavage site. The NH2-terminal signal sequence of endopin 2C, like that of cathepsin L, predicts their colocalization to subcellular organelles. These findings demonstrate endopin 2C as a novel serpin that possesses cross-class inhibition with selectivity for inhibition of cathepsin L.     

Method of determining the relative stability of different conformational states of biological macromolecules

A general approach to the determination of relative stability of any pair of con-formational states of biological macromolecules or their complexes (in particular, to the determination of relative stability of native and disordered states of the macromolecule) has been suggested. For determining the free energy difference of the two states under the conditions when one of them is considerably more advantageous than the other, it is necessary for the macromolecule to be influenced by the transforming agent which levels free energies of both the conformational states, and to determine the external parameter derivative of the free energy difference in the region of the conformational transition induced by the change in this parameter. If the character of the dependence of this derivative on the external parameter (temperature, solvent composition, etc.) is known, then this allows the determination of the free energy difference of the two states under the conditions considered, even including conditions far from the transition region. The value of the derivative of the free energy difference in the transition region in many cases can be measured directly (in particular, when using calorimetry), while in cases when a direct measurement of the derivative is impossible, it can often he estimated experimentally from the steepness of the conformational transition. The methods of this estimation and also a possible character of the change of the considered derivative during variation of the external parameter are considered for the case when the transforming agent is one of the components of the solvent and, consequently, the derivative of the free energy difference is equal to the difference of number of molecules of this component hound with the macromolecule in two conformational states.     

Factors determining the structure and diversity of parasitoid complexes in tephritid fruit flies

Summary The relative importance of phylogenetic affinity of hosts versus their ecological characteristics in determining the composition of their parasitoid complexes was examined using the parasitoid complexes of six species of frugivorous fruit flies from Central Europe. The hosts were four Rhagoletis and two other trypetine species, ranging in their relatedness from host races to members of different genera. They also differed in ecological characteristics, utilizing host plants of three different families, and developing either as pulp- or seedfeeders inside the host fruit. These features made it feasible to test the following pair of hypotheses. The ecological hypothesis predicts that ecological traits such as host-plant and fruit fly phenologies and host-fruit texture should be more important for the composition of parasitoid complexes than the taxonomic relatedness of the fly species. Assuming that ecological relationships do not parallel phylogenetic ones, the alternative phylogenetic hypothesis predicts the opposite. In fruit and soil samples, taken between 1983 and 1989, three guilds of parasitoids comprising 20 species were found: guild 1 — koinobiotic larval parasitoids (e.g. Opius spp., which attack the host larvae but develop inside the host puparia); guild 2 — idiobiotic larval parasitoids (e.g. Pteromalus spp., which consume the host larvae at once); and guild 3 — idiobiotic puparium parasitoids (e.g. Phygadeuon spp.). Although some results support the phylogenetic hypothesis, the majority of results support the ecological hypothesis.     

Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability

Abstract

Can one infer the amino acids of the enzymes that are responsible for the stability or the level of the catalytic activity by computationally experimenting on the inhibited enzyme in the enzyme–inhibitor complex? In this article, we answer this question positively both by designing molecular dynamics simulations and by devising coarse-grained methodologies on the subtilisin serine protease. Both methodologies are based on the cross-correlations of the fluctuations of the residues, obtained either by monitoring the trajectories from the simulation or by constructing the inverse Laplacian of the elastic network model, of the complex. A perturbation scanning is applied to the complex using these correlations. The results indicate that the two methods almost point out the same regions on the flexible of the enzyme. These regions are: (i) 50–61, (ii) 155–164 and (iii) 192–194, all of which are designated to be important by experimental studies in the literature.     

Kinetic characterization and inhibition of the rat MAB elastase-2, an angiotensin I-converting serine protease

An elastase-2 has been recently described as the major angiotensin (Ang) II-forming enzyme of the rat mesenteric arterial bed (MAB) perfusate. Here, we have investigated the interaction of affinity-purified rat MAB elastase-2 with some substrates and inhibitors of both pancreatic elastases-2 and Ang II-forming chymases. The Ang II precursor [Pro 11 -D-Ala 12]-Ang I was converted into Ang II by the rat MAB elastase-2 with catalytic efficiency of 8.6 min-1 microM-1, and the chromogenic substrates N-succinyl-Ala-Ala-Pro-Leu-p-nitroanilide and N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide were hydrolyzed by the enzyme with catalytic efficiencies of 10.6 min-1 microM-1 and 7.6 min-1 microM-1, respectively. The non-cleavable peptide inhibitor CH-5450 inhibited the rat MAB elastase-2 activities toward the substrates Ang I (IC50 = 49 microM) and N-succinly-Ala-Ala-Pro-Phe-p-nitroanilide (IC 50 = 4.8 microM), whereas N-acetyl-Ala-Ala-Pro-Leu-chloromethylketone, an effective active site-directed inhibitor of pancreatic elastase-2, efficiently blocked the Ang II-generating activity of the rat MAB enzyme (IC 50 = 4.5 microM). Altogether, the data presented here confirm and extend the enzymological similarities between pancreatic elastase-2 and its rat MAB counterpart. Moreover, the thus far unrealized interaction of elastase-2 with [Pro 11-D-Ala 12]-Ang I and CH-5450, both regarded as selective for chymases, suggests that evidence for the in vivo formation of Ang II by chymases may have been overestimated in previous investigations of Ang II-forming pathways.     

Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.

Thrombin is a serine protease that plays a central role in blood coagulation. It is inhibited by hirudin, a polypeptide of 65 amino acids, through the formation of a tight, noncovalent complex. Tetragonal crystals of the complex formed between human alpha-thrombin and recombinant hirudin (variant 1) have been grown and the crystal structure of this complex has been determined to a resolution of 2.95 A. This structure shows that hirudin inhibits thrombin by a previously unobserved mechanism. In contrast to other inhibitors of serine proteases, the specificity of hirudin is not due to interaction with the primary specificity pocket of thrombin, but rather through binding at sites both close to and distant from the active site. The carboxyl tail of hirudin (residues 48-65) wraps around thrombin along the putative fibrinogen secondary binding site. This long groove extends from the active site cleft and is flanked by the thrombin loops 35-39 and 70-80. Hirudin makes a number of ionic and hydrophobic interactions with thrombin in this area. Furthermore hirudin binds with its N-terminal three residues Val, Val, Tyr to the thrombin active site cleft. Val1 occupies the position P2 and Tyr3 approximately the position P3 of the synthetic inhibitor D-Phe-Pro-ArgCH2Cl. Thus the hirudin polypeptide chain runs in a direction opposite to that expected for fibrinogen and that observed for the substrate-like inhibitor D-Phe-Pro-ArgCH2Cl.