Triad Of Serine Proteases Research Articles

Probing contacts of inhibitor locked in transition states in the catalytic triad of DENV2 type serine protease and its mutants by 1H, 19F and 15\u2009N NMR spectroscopy

BackgroundDetailed structural knowledge of enzyme-inhibitor complexes trapped in intermediate state is the key for a fundamental understanding of reaction mechanisms taking place in enzymes and is indispensable as a structure-guided drug design tool. Solution state NMR uniquely allows the study of active sites of enzymes in equilibrium between different tautomeric forms. In this study 1H, 19F and 15 N NMR spectroscopy has been used to probe the interaction contacts of inhibitors locked in transition states of the catalytic triad of a serine protease. It was demonstrated on the serotype II Dengue virus NS2B:NS3pro serine protease and its mutants, H51N and S135A, in complex with high-affinity ligands containing trifluoromethyl ketone (tfk) and boronic groups in the C-terminal of tetra-peptides.ResultsMonitoring 19F resonances, shows that only one of the two isomers of the tfk tetra-peptide binds with NS2B:NS3pro and that access to the bulk of the active site is limited. Moreover, there were no bound water found in proximity of the active site for any of the ligands manifesting in a favorable condition for formation of low barrier hydrogen bonds (LBHB) in the catalytic triad. Based on this data we were able to identify a locked conformation of the protein active site. The data also indicates that the different parts of the binding site most likely act independently of each other.ConclusionsOur reported findings increases the knowledge of the detailed function of the catalytic triad in serine proteases and could facilitate the development of rational structure based inhibitors that can selectively target the NS3 protease of Dengue type II (DENV2) virus. In addition the results shows the usefulness of probing active sites using 19F NMR spectroscopy.

Structural and Kinetic Analysis of Bacillus subtilis N-Acetylglucosaminidase Reveals a Unique Asp-His Dyad Mechanism

Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.

Theoretical studies of the proton transfer behaviors in molecular complexes analogous to catalytic triad of serine protease: Toward understanding the existence and significance of the low-barrier hydrogen-bond in enzymatic catalysis

A representative acetate-(5-methylimidazole)-methanol system has been employed as a model of catalytic triad in serine protease to validate the formation processes of low-barrier H-bonds (LBHB) at the B3LYP/6-311++G** level of theory, and variable H-bonding characters from conventional ones to LBHBs have been represented along with the proceedings of proton transfer. Solvent effect is an important factor in modulation of the existence of an LBHB, where an LBHB (or a conventional H-bond) in the gas phase can be changed into a non-LBHB (an LBHB) upon solvation. The origin of the additional stabilization energy arising from the LBHB may be attributed to the H-bonding energy difference before and after proton transfer because the shared proton can freely move between the proton donor and proton acceptor. Most importantly, the order of magnitude of the stabilization energy depends on the studied systems. Furthermore, the nonexistence of LBHBs in the catalytic triad of serine proteases has been verified in a more sophisticated model treated using the ONIOM method. As a result, only the single proton transfer mechanism in the catalytic triad has been confirmed and the origin of the powerful catalytic efficiency of serine proteases should be attributed to other factors rather than the LBHB.

Genetic characterization and expression of the novel fungal protease, EPg222 active in dry-cured meat products

EPg222 protease is a novel extracellular enzyme produced by Penicillium chrysogenum (Pg222) isolated from dry-cured hams that has the potential for use over a broad range of applications in industries that produce dry-cured meat products. The gene encoding EPg222 protease has been identified. Peptide sequences of EPg222 were obtained by de novo sequencing of tryptic peptides using mass spectrometry. The corresponding gene was amplified by PCR using degenerated primers based on a combination of conserved serine protease-encoding sequences and reverse translation of the peptide sequences. EPg222 is encoded as a gene of 1,361 bp interrupted by two introns. The deduced amino acid sequence indicated that the enzyme is synthesized as a preproenzyme with a putative signal sequence of 19 amino acids (aa), a prosequence of 96 aa and a mature protein of 283 aa. A cDNA encoding EPg222 has been cloned and expressed as a functionally active enzyme in Pichia pastoris. The recombinant enzyme exhibits similar activities to the native enzyme against a wide range of protein substrates including muscle myofibrillar protein. The mature sequence contains conserved aa residues characteristic of those forming the catalytic triad of serine proteases (Asp42, His76 and Ser228) but notably the food enzyme exhibits specific aa substitutions in the immunoglobulin-E recognition regions that have been identified in protein homologues that are allergenic.

A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase.

FprA is a mycobacterial oxidoreductase that catalyzes the transfer of reducing equivalents from NADPH to a protein acceptor. We determined the atomic resolution structure of FprA in the oxidized (1.05 A resolution) and NADPH-reduced (1.25 A resolution) forms. The comparison of these FprA structures with that of bovine adrenodoxin reductase showed no significant overall differences. Hence, these enzymes, which belong to the structural family of the disulfide oxidoreductases, are structurally conserved in very distant organisms such as mycobacteria and mammals. Despite the conservation of the overall fold, the details of the active site of FprA show some peculiar features. In the oxidized enzyme complex, the bound NADP+ exhibits a covalent modification, which has been identified as an oxygen atom linked through a carbonylic bond to the reactive C4 atom of the nicotinamide ring. Mass spectrometry has confirmed this assignment. This NADP+ derivative is likely to form by oxidation of the NADP+ adduct resulting from nucleophilic attack by an active-site water molecule. A Glu-His pair is well positioned to activate the attacking water through a mechanism analogous to that of the catalytic triad in serine proteases. The NADP+ nicotinamide ring exhibits the unusual cis conformation, which may favor derivative formation. The physiological significance of this reaction is presently unknown. However, it could assist with drug-design studies in that the modified NADP+ could serve as a lead compound for the development of specific inhibitors.

CDNA Cloning and Functional Analysis of Ascidian Sperm Proacrosin

cDNA cloning and functional analysis of proacrosin from the ascidian Halocynthia roretzi were undertaken. The isolated cDNA of the ascidian preproacrosin consists of 2367 nucleotides, and an open reading frame encodes 505 amino acids, which corresponds to the molecular mass of 55,003 Da. The mRNA of proacrosin was found to be specifically expressed in the gonad by Northern blotting and in the spermatocytes or spermatids by in situ hybridization. The amino acid sequences around His(76), Asp(132), and Ser(227), which make up a catalytic triad, showed high homology to those of the trypsin family. Ascidian acrosin has paired basic residues (Lys(56)-His(57)) in the N-terminal region, which is one of the most characteristic features of mammalian acrosin. This region seems to play a key role in the binding of (pro)acrosin to the vitelline coat, because the peptide containing the paired basic residues, but not the peptide substituted with Ala, was capable of binding to the vitelline coat. Unlike mammalian proacrosin, ascidian proacrosin contains two CUB domains in the C-terminal region, in which CUB domain 1 seems to be involved in its binding to the vitelline coat. Four components of the vitelline coat that are capable of binding to CUB domain 1 in proacrosin were identified. In response to sperm activation, acrosin was released from sperm into the surrounding seawater, suggesting that ascidian acrosin plays a key role in sperm penetration through the coat. These results indicate that ascidian sperm contains a mammalian acrosin homologue, a multi-functional protein working in fertilization.

Knowledge-based modeling of the serine protease triad into non-proteases.

The Asp-His-Ser triad of serine proteases has been regarded, in the present study, as an independent catalytic motif, because in nature it has been incorporated at the active sites of enzymes as diverse as the serine proteases and the lipases. Incorporating this motif into non-protease scaffolds, by rational design and mutagenesis, might lead to the generation of novel catalysts. As an aid to such experiments, a knowledge-based computer modeling procedure has been developed to model the protease Asp-His-Ser triad into non-proteases. Catalytic triads from a set of trypsin family proteases have been analyzed and criteria that characterize the geometry of the triads have been obtained. Using these criteria, the modeling procedure first identifies sites in non-proteases that are suitable for modeling the protease triad. H-bonded Asp-His-Ser triads, that mimic the protease catalytic triad in geometry, are then modeled in at these sites, provided it is stereochemically possible to do so. Thus non-protease sites at which H-bonded Asp-His-Ser triads are successfully modeled in may be considered for mutagenesis experiments that aim at introducing the protease triad into non-proteases. The triad modeling procedure has been used to identify sites for introducing the protease triad in three binding proteins and an immunoglobulin. A scoring function, depending on inter-residue distances, solvent accessibility and the substitution potential of amino acid residues at the modeling sites in the host proteins, has been used to assess the quality of the model triads.

Strong N-H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases.

Low-barrier hydrogen bond (LBHB) involvement in enzyme catalysis is examined by analysis of experimental nuclear and electron densities of a model compound for the catalytic triad in serine proteases (shown schematically), which is based on a cocrystal of betaine, imidazole, and picric acid. The three short, strong N-H⋅⋅⋅O hydrogen bonds in the structure have varying degrees of covalent bonding contributions suggesting a gradual transition to the LBHB situation.

Quantum chemical calculations on the intramolecular hydrogen bond of cis-urocanic acid

The intramolecular hydrogen bond (IMHB) of the neutral, cationic, and anionic cis-urocanic acid ( cis-UCA, (Z)-3-(I′ H-imidazol-4′(5′)-yl)propenoic acid) is studied using ab initio calculations up to the MP2/6-31+G** level of theory. The IMHB energies are estimated by first showing a near to perfect linear correlation between the hydrogen bond energies of modified cis-urocanic acid structures and the Mulliken bond orders of their hydrogen bonds — the electron densities at the critical points of the hydrogen bonds have a weaker correlation with the hydrogen bond energies than the bond orders — and then using this correlation in order to evaluate the IMHB energies of the cis-UCA structures themselves. This method gives high (>50 kJ mol −1) IMHB energies for the neutral and cationic cis-UCA structures and very high (>100 kJ mol −1) IMHB energies for the anionic cis-UCA structures in the gas phase. The effect of salvation on the IMHB in cis-UCA is studied using both MP2/6-31G* water–UCA supermolecule optimizations and HF/6-31G* SCI-PCM (self-consistent isodensity polarized continuum model) reaction field calculations. Solvation changes the IMHB energies by upto 30 kJ mol −1. The IMHB of the imidazole protonated structures is weakened, while that of the carboxylate group protonated structures is strengthened in aqueous solution. Solvation does not change the optimal conformation of cis-UCA from the IMHB-ed closed conformation to an open conformation. The supermolecule calculations and the SCI-PCM calculations give consistent changes of the IMHB strengths in aqueous solution. Inclusion of only 1–3 water molecules nearest to the IMHB seems to be enough to demonstrate most of the solvent effect on the IMHB. The semiempirical AM l method is shown to be a valuable tool in finding good initial positions for the water molecules in ab initio calculations. The adequacy of cis-UCA as a model compound for the hydrogen bonded His–Asp component of the catalytic triad in serine proteases is investigated. The IMHB in the anionic cis-UCA is a low-barrier hydrogen bond (LBHB) in the gas phase, while the IMHB in the neutral cis-UCA is not. In aqueous solution, modeled by HF/6-31G* SCI-PCM calculations, the IN4HB in both the neutral and the anionic cis-UCA seems to be an LBHB. The anionic cis-UCA is suggested as an experimental model for the initial state, and the neutral cis-UCA as that for the final state of the proton transfer process in the His–Asp system of the catalytic triad

A low-barrier hydrogen bond in subtilisin: 1H and 15N NMR studies with peptidyl trifluoromethyl ketones.

The N delta 1 proton of His 64 forms a hydrogen bond with Asp 32, as part of the catalytic triad in serine proteases of the subtilisin family. His 64 in subtilisin has been studied by 1H and 15N NMR spectroscopy in the presence and absence of peptidyl trifluoromethyl ketones (TFMKs) that are transition state analog inhibitors. For subtilisin Carlsberg, the downfield resonance of the imidazolium N delta 1 proton is approximately 18.3 ppm and the D/H fractionation factor is 0.55 +/- 0.04 at pH 5.5 (11 degrees C), and 0.63 +/- 0.04 (5 degrees C) and 0.68 +/- 0.04 at pH 6 (11 degrees C). In the complex between subtilisin Carlsberg and Z-L-leucyl-L-leucyl-L-phenylalanyltrifluoromethyl ketone (Z-LLF-CF3) at pH values between 6.5 and 10.6, His 64 remains positively charged, and the D/H fractionation factor of its N delta 1 proton is 0.85 +/- 0.05. In the complex between a subtilisin variant from Bacillus lentus and Z-LLF-CF3, the proton resonance at 18.8 ppm is correlated with a 15N resonance at 197.6 ppm downfield from liquid NH3 with a 1JNH of 81 Hz. The chemical shifts of subtilisin complexes with peptidyl TFMKs are among the most downfield shifts reported for any protein. At pH 9.5, His 64 is neutral and the D/H fractionation factor increases to 1.2 with a chemical shift of 15.0. His 64 is positively charged in the free enzyme at low pH, the inhibitor hemiketal complex at neutral pH, and the transition state for amide bond hydrolysis. These data thus provide indirect evidence for the presence of a low-barrier hydrogen bond in the catalytic mechanism of subtilisin proteases.

A new model for the agonistic binding site on the histamine H 2-receptor: The catalytic triad in serine proteases as a model for the binding site of

The historical model for the agonistic binding site on the histamine H 2-receptor is based on a postulated activation mechanism: it has been suggested that the histamine monocation binds to the histamine H 2-receptor via the formation of three hydrogen bonds. The cationic ammonium group in the side chain and the —NH— group in the π-position of the imidazole act as proton donors, whereas the N— atom in the π-position of the imidazole acts as a proton acceptor. Participation of the ammonium group in H-bonding with a presumed negative charge on the receptor leads to a decrease in positive charge, which is thought to induce a tautomeric change in the imidazole ring system from N τ-H to N π-H. A consequence of this tautomeric shift is the donation of a proton from the receptor to the agonist on one side, while on the other side a proton is donated from the agonist to the receptor. The proposed tautomeric shift has been suggested to trigger the H 2-stimulating effect. However, this model for the constitution of the agonistic binding site and the accessory activation mechanism cannot explain the weak histamine H 2-activity of β-histine and the activity of several other recently synthesized H 2-agonists. Based on a thorough literature study and with the aid of molecular electrostatic potentials (MEPs) we demonstrate that the sulphur atom present in histamine H 2-agonists as dimaprit and 2-amino-5-(2-aminoethyl)thiazole does not function as a proton acceptor, which implicitly means that a tautomeric shift is not a prerequisite for H 2-stimulation. As a consequence, the model for the agonistic binding site is adjusted, resulting in a strong resemblance to the nature and orientation of the amino acids constituting the catalytic triad in serine proteases. Within this concept, the N π-H tautomer of histamine is the biologically active form, in contrast with the existing model in which the N τ-H tautomer is the active form.