Direct proton magnetic resonance determination of the pKa of the active center histidine in thiolsubtilisin

The serine proteases constitute a group of endopeptidases whose members owe their catalytic activity to the presence of a catalytic triad of amino acids consisting of a serine, a histidine and an aspartate. The pK(a) values for this histidine have been determined for several cases in which there is a negative charge installed at the serine to mimic the oxyanionic intermediate and related transition state for the catalytic pathway. Instances from this laboratory include (1) replacement of the serine by a cysteine in subtilisin to create a thiolate; (2) formation of monoisopropylphosphoryl-Ser 195 monoanionic phosphodiesters (in trypsin and chymotrypsin, Ser 221 in subtilisins); and (3) tetrahedral boronates formed with peptide boronic acids. The nuclear magnetic resonance (NMR) signals pertinent to this histidine, or signals indirectly reflecting the state of ionization of this histidine, have been used effectively to monitor changes in the active center ionization state. In every case studied, there is elevation of the pK(a) at the histidine when the negative charge is installed at the serine position. Herein is reported the first NMR measurement of the active center His 63 pK(a) in thiolsubtilisin Carlsberg; it is elevated by 3 units compared with the parent enzyme. Using a numerical solution (finite difference) of the Poisson-Boltzmann equation, a protein dielectric constant of 4 provides a good estimate of the experimentally observed pK(a) elevations. Very significantly, a very low protein dielectric constant (epsilon(p) = 3-5) is required in all of the comparisons, and for all three enzymes used (chymotrypsin, trypsin, and subtilisin). Finally, we discuss why the electrostatic perturbation sensed at His of the active center is more amplified by a negative charge on the Ser side than the same charge on the Asp side. A plausible explanation is that the positive charge on the imidazolium ring of the His is localized, with the N(delta 1) carrying a smaller fraction, the N(epsilon 2) carrying the bulk of the positive charge.     

Subunit protein-affinity isolation of Drosophila DNA polymerase catalytic subunit

gfLittle is known at present about the biochemical properties of very large-sized Drosophila DNA polymerases. In a previous study, we tried to purify Drosophila pol. catalytic subunit from embryos through seven column chromatographies and study its biochemical properties. However, we failed to characterize it precisely because an insufficient amount of the enzyme was generated. In this report, we describe direct purification from Drosophila embryos to near homogeneity using Drosophila DNA polymerase second subunit (Drosophila pol. 2) protein-conjugated affinity column chromatography and characterization of the enzyme in detail. To our knowledge this is the first demonstration of native DNA polymerase purification with activity using a subunit protein-affinity column. We observed new characteristics of Drosophila pol. catalytic subunit as follows: Drosophila pol. catalytic subunit synthesized DNA processively in the presence of both Mn(2+) and Mg(2+) ions, but Mn(2+) inhibited the 3'-5' proofreading activity, thereby decreasing the fidelity of DNA replication by 50%.     

A novel approach to predict active sites of enzyme molecules

Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. Proteins 2004. © 2004 Wiley-Liss, Inc.     

Stereoselectivity in formation of oxacephams from 1,3-alkylidene-threitols

The [2+2]cycloaddition of CSI to the (Z)-propenyl ethers derived from respective 1,3-methylidene- and 1,3-ethylidene-threitols, contrary to the corresponding erythritol derivatives, is characterized by a low stereoselectivity and a lack of stereospecificity. On the other hand, the alternative method of the oxacepham formation, based on the 4-vinyloxy-azetidinone, proceeds with an excellent stereoselectivity. The CD-spectroscopy offers an attractive tool for determination of the absolute configuration of the bridgehead carbon atom at the 5-oxacepham skeleton.     

Hybrid Mn-Peroxidase from the Ligninolytic Fungus Panus tigrinus 8/18. Isolation, Substrate Specificity, and Catalytic Cycle

Increased manganese concentration during submerged cultivation of the ligninolytic white rot fungus Panus tigrinus 8/18 on N-limited mineral medium resulted in the induction of Mn-peroxidase and laccase. The Mn-peroxidase was purified with the purity factor RZ (A ₄₀₆/A ₂₈₀) = 4.3. The purified enzyme catalyzed H₂O₂-dependent oxidation of phenol oxidase substrates (aromatic amines, 2,2"-azinobis-(3-ethylbenzthiazolinesulfonic acid), hydroquinone, 2,6-dimethoxyphenol) without Mn²⁺, which is not typical for the usual Mn-peroxidases. Guaiacol and 2,4,6-trichlorophenol were not oxidized in the absence of Mn²⁺. Study of absorption spectra of the intermediates of the catalytic cycle revealed that this peroxidase is able to complete the redox cycle, reducing one-electron oxidized intermediate (Compound II) by Mn²⁺, as well as by an organic substrate (hydroquinone). This means that the enzyme is a hybrid Mn-peroxidase, different from the common Mn-peroxidases from ligninolytic fungi.     

Crystal structures of BnSP-7 and BnSP-6, two Lys49-phospholipases A(2): quaternary structure and inhibition mechanism insights

Phospholipases A(2) are components of Bothrops venoms responsible for disruption of cell membrane integrity via hydrolysis of its phospholipids. A class of PLA(2)-like proteins has been described which despite PLA(2) activity on artificial substrate, due to a D49K mutation, is still highly myonecrotic. This work reports the X-ray structure determination of two Lys49-PLA(2)s from Bothrops neuwiedi pauloensis (BnSP-7 and BnSP-6) and, for the first time, the comparison of eight dimeric Lys49-PLA(2)s. This comparison reveals that there are not just two ("open" and "closed") but at least six different conformations. The binding of fatty acid observed in three recent Lys49-PLA(2) structures seems to be independent of their quaternary conformation. Cys29 polarization by Lys122 is not significant for BnSP-7 and BnSP-6 or other structures not bound by fatty acids. These structures may be in an "active" state when nothing is bound to them and the Lys122/Cys29 interactions are weak or absent.     

Enantiomerically pure nucleophiles in diastereoselective palladium catalysed allylic substitution reactions

Enantiomerically pure alpha-amino esters were applied in palladium catalysed allylic substitution reactions with moderate diastereoselectivity (up to 70% d.e.) using achiral ligands on symmetrical allylic acetates. Nucleophilic substitution of amino esters with enantiomerically pure ligands enabled diastereoselective ratios of 95:5 to be obtained.     

Unique reactivity of alpha,beta-unsaturated carboxylic acid imidazolides: catalytic asymmetric synthesis of alpha,beta-epoxy esters and alpha,beta-epoxy carboxylic acid derivatives

Catalytic asymmetric synthesis of alpha,beta-epoxy esters and alpha,beta-epoxy carboxylic acid derivatives is described. Catalytic asymmetric epoxidation of alpha,beta-unsaturated carboxylic acid imidazolides using La-BINOL-Ph(3)As=O complex gave the corresponding alpha,beta-epoxy peroxy tert-butyl esters, which were directly converted to the alpha,beta-epoxy methyl esters by adding methanol to the reaction. This catalytic system had broad generality for epoxidation of various substrates. With the use of 5-10 mol% of the catalyst, both beta-aryl and beta-alkyl-substituted-alpha,beta-epoxy methyl esters were obtained in up to 91% yield and in up to 93% enantiomeric excess. In addition, efficient transformations of alpha,beta-epoxy peroxy tert-butyl esters into the alpha,beta-epoxy amides, alpha,beta-epoxy aldehydes, and gamma,delta-epoxy beta-keto esters are also reported.     

Ligand-accelerated cadmium-catalyzed asymmetric allylation reactions in aqueous media

Catalytic asymmetric allylation of aldehydes with allyltributyltin in aqueous media has been realized using combinations of cadmium bromide and chiral diamine ligands. These ligands were found to accelerate the reactions significantly.