Electrostatic potential maps at the quantum chemistry level of the active sites of the serine peptidases, alpha-chymotrypsin and subtilisin

The electronic properties of the active-sites of the structurally unrelated serine peptidases, alpha-chymotrypsin and subtilisin, have been expressed in the form of three-dimensional electrostatic potential maps derived from integrals calculated at the quantum chemistry level. As a consequence of the asymmetrical distribution of the secondary structures that occur within a 7 A sphere around the serine of the catalytic triad, the active sites are highly polarized entities and exhibit large dipole moments. One part of the active sites generates a nucleophilic suction-pump. Its isocontour at -10 kcal mol-1 defines an impressive, negatively-charged volume which bears a narrow channel in the immediate vicinity of the active-site serine 195 in alpha-chymotrypsin or 221 in subtilisin. In native alpha-chymotrypsin, there is a perfect complementation between this nucleophilic suction-pump and the positively-charged electrophilic hole that is generated by the backbone NH of Ser 195 and Gly 193. In subtilisin, generation of the complementing electrophilic hole requires binding of a carbonyl donor ligand and may be achieved by rotation of the side-chain amide of Asn 155 towards the backbone NH of Ser 221. Small variations in the atomic co-ordinates of alpha-chymotrypsin used for the calculations, the presence of water molecules in its active site and the occurrence of point mutations in the amino acid sequence of subtilisin have little effects on the shape and characteristics of the electrostatic potential.     

Preparation of highly active alpha-chymotrypsin for catalysis in organic media

A simple one step process for the preparation of free alpha-chymotrypsin, using an organic solvent to precipitate the enzyme from a buffered solution, followed by washing with organic solvents, is described. This preparation gave 132 times greater esterification activity than lyophilized powder.     

Fluorescence energy transfer between active sites in aspartate transaminase.

The method of fluorescence energy transfer has been used to measure the distance between the active sites in a dimeric enzyme, aspartate aminotransferase. The procedure involves the prior preparation of a hybrid enzyme with the natural chromophore, pyridoxal phosphate, in one subunit as the aldimine and of the reduced aldimine in the other subunit. The two active site chromophores are used as donor and acceptor of the energy transfer and a distance of 21 Å is obtained for the separation of the active sites.     

Relationship between length and degree of polymerization of TEMPO-oxidized cellulose nanofibrils

The influence of 2,2,6,6-tetrametylpiperidine-1-oxyl (TEMPO)-mediated oxidation of wood cellulose and the mechanical disintegration of oxidized cellulose in water on degree of polymerization determined by viscosity measurement (DP(v)) and the apparent length of the TEMPO-oxidized cellulose nanofibrils (TOCNs) was investigated. DP(v) values decreased from 1270 to 500-600 with increasing addition of NaClO in the TEMPO-mediated oxidation stage. The DP(v) values were further decreased by mechanical fibrillation in water. There is a linear relationship between the average fibril length and DP(v); the lengths of TOCNs can be approximated from DP(v) using 0.5 M copper ethylenediamine as a solvent of both the cellulose and oxidized celluloses in TOCNs. Based on the cellulose fibril models and TEMPO oxidation mechanism, the depolymerization behavior of TOCNs is tentatively explained in terms of distribution of disordered regions in wood cellulose fibrils and formation of C6-aldehydes in cellulose fibrils during TEMPO-mediated oxidation.     

Channeling between the active sites of formiminotransferase-cyclodeaminase. Binding and kinetic studies

Formiminotransferase-cyclodeaminase, a circular tetramer of dimers, binds four tetrahydropteroylpolyglutamates/octamer, which indicates that these polyglutamate sites are formed by one type of subunit interface. The transferase and deaminase are separate catalytic sites as determined by inhibition studies with (6R)-tetrahydropteroylglutamate and by the observation that the activities can operate simultaneously. Under conditions where the transferase is saturated with tetrahydropteroyl(glutamate)n substrate, exogenously added formimino intermediate is utilized by the deaminase only if at least one of the substrate/intermediate pair is a monoglutamate. These properties indicate the existence of only one polyglutamate site/pair of catalytic sites. Kinetic specificity for each activity as measured by Vm/Km increases for longer polyglutamates, but does not differentiate among 4, 5, 6, and 7 glutamates. The enzyme shows distinct preference for hexaglutamate based on Kd as well as on Km values. With all substrates, Vm of the deaminase is greater than that of the transferase, allowing for potential channeling of the intermediate between active sites. Efficiency of channeling, optimal with pentaglutamate, does not correspond with affinity for binding. This demonstrates that a steric requirement predominates over simple sequestering of intermediates on the enzyme surface as the fundamental mechanism for channeling.     

Photoaffinity labelling of cholinesterases. Discrimination between active and peripheral sites.

Two para-dialkylaminobenzenediazonium salts, the dimethylamino (A) and dibutylamino (B) derivatives, are presented as structural probes for acetylcholinesterase and butyrylcholinesterase. While being reversible competitive inhibitors in the dark, A and B behave, upon irradiation and through the formation of arylcation species, as irreversible labels of ammonium-binding sites of both enzymes. The observed variations of the different inactivation rate constants point to a different structural environment for acetylcholinesterase-binding and butyrylcholinesterase-binding sites. Moreover, in the case of acetylcholinesterase, protection experiments with specific ligands (edrophonium and propidium) showed that the dimethylamino salt A exclusively labels the hydrolytic anionic site, whereas the dibutylamino salt B also labels the peripheral site. Specificities and stoechiometries of the incorporations were determined and, in the case of acetylcholinesterase, the irradiated protein was submitted to chemical degradation. Peptide maps were obtained by gel-permeation chromatography and HPLC, giving access to labelled peptides which belong either to the active or to the peripheral site.     

Communication between the active sites in dimeric mercuric ion reductase: an alternating sites hypothesis for catalysis

Mercuric reductase, a flavoprotein disulfide oxidoreductase, catalyzes the two-electron reduction of Hg(II) to Hg(0) by NADPH. As with all the members of this class of proteins, the enzyme is a dimer of identical subunits with two active sites per dimer, each composed of one FAD and catalytically essential residues from both subunits. In the enzyme from Tn501, these residues include, at a minimum, FAD and cysteines 135 and 140 from one subunit and cysteines 558' and 559' from the other. With this sort of active site arrangement, the enzyme seems perfectly set up for some type of subunit communication. In this report, we present results from several titrations, as well as kinetics studies, that, taken together, are consistent with the occurrence of subunit communication. In particular, the results indicate that pyridine nucleotide complexed dimers of the enzyme are asymmetric. Since the EH2-NADPH complex of the enzyme is the relevant reductant of Hg(II), these observations suggest that the enzyme may function asymmetrically during catalysis. An alternating sites model is proposed for the catalytic reduction of Hg(II), where both subunits of the dimer function in catalysis, but the steps are staggered and the subunits reverse roles after part of the reaction. An attractive feature of this proposal is that it provides a reasonable solution to the thermodynamic dilemma the enzyme faces in needing to both bind Hg(II) very tightly and reduce it.     

Relationship between native and exotic plant species at multiple savannah sites

We tested whether the recently proposed two‐part measure of degree of invasion (DI) of a community relating exotic proportion of cover to exotic proportion of richness can characterize patterns of plant invasions at multiple savannah sites in Southern Africa. Regression analysis was performed on transformed data to assess how this two‐part measure of DI compares to other metrics of community invasibility. The results indicate that at the plot level, the absolute cover of exotics was not significantly related to native cover for three sites out of four assessed (R² ≤ 0.17; P > 0.05). Also, at all four sites, no significant relationships were detected between native and exotic plant richness at both the 1‐m² and 400‐m² plot scales. By contrast, significant (P < 0.05) positive linear relationships were observed between exotic proportion of richness and exotic proportion of cover at all sites (R² was as high as 0.67 and 0.97 for two sites). Our results indicate that the new two‐part measure of DI is able to characterize patterns of plant invasions across plant communities in African savannahs.     

Interaction between complementary polymerization sites in the structural D and E domains of human fibrin.

Plasmic degradation products of human fibrin, fragments DD, D, and E, bind to fibrin. It has been inferred from this observation that the binding occurs by attraction of complementary sites located in the NH2- and COOH-terminal domains of the fibrin molecule. The interaction between fragments D1 and E1 has been investigated in this work since it represents the first step in the process of fibrin clot formation. Fragment D1, that was initially as active as fragment DD, lost most of its anticoagulant activity after purification by cation-exchange chromatography. The lability of fragment D1 function explained the previous unsuccessful attempts to form a complex between fragments D1 and E1. The loss of fragment D1 anticoagulant activity was not associated with the cleavage of the gamma 63-85 chain segment, since fragments D1A and D1 identically inhibited the fibrin monomer polymerization rate. In order to demonstrate the formation of a complex between fragments D1 and E1, three lines of experiments were advanced. First, the anticoagulant activity of fragment D1 was neutralized by fragment E1 in a dose-dependent manner, demonstrating that the association between these fragments involved polymerization sites. Second, two products, D1.E1 and D1.E1.D1, were stabilized in a reaction with bifunctional cross-linking reagents, proving the formation of D.E complexes in aqueous solution. Third, immobilized fragment D1 bound fragments E1 and E2, but not fragment E3, showing that fragments E1 and E2 attached via a polymerization site to the complementary one in fragment D1, since this association was disrupted by fibrin polymerization inhibitory peptide GPRP. These results provided direct evidence for specific binding between the structural D and E domains of fibrin mediated through complementary polymerization sites. Thus, the initial formation of fibrin clot fibers appears to be driven by specific association of these sites.     

Biosynthesis of heparin. Relationship between the polymerization and sulphation processes.

Incubation of a mouse mastocytoma microsomal fraction with UDP-[3H]GlcA and UDP-GlcNAc yielded proteoglycans containing non-sulphated polysaccharide chains. Similar incubations performed in the presence of sulphate donor 3'-phosphoadenosine 5'-phosphosulphate (PAPS) produced both sulphated and non-sulphated proteoglycans, which were separated by chromatography on DEAE-cellulose Analysis by gel chromatography of single polysaccharide chains, released from the proteoglycans by alkali treatment, showed that the non-sulphated chains produced during incubation for 5 min or 25 min, either in the absence or in the presence of PAPS, were of fairly small molecular size, with an average peak Mr of approx. 10 x 10(3)-15 x 10(3). In contrast, the sulphated chains exceeded Mr 100 x 10(3) Pulse-chase experiments suggested that sulphated chains were capable of further elongation. These results indicate that sulphation promotes, by so far unknown mechanisms, further chain elongation. Sulphated proteoglycan (retarded on DEAE-cellulose chromatography) isolated after similar incubation of the microsomal fraction for 1 min only was found to contain a mixture of sulphated and virtually non-sulphated polysaccharide chains. However, when [35S]PAPS was included in the incubations, some 35S was found to be associated, essentially as N-sulphate groups, also with the latter type of chains, preferentially the high-Mr fraction. These results are interpreted in terms of a biosynthetic model by which the heparin proteoglycan is generated through transient interactions of macromolecular intermediates with distinctly separate complexes of membranebound enzymes.