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Biomedical subjects

M L Bender

Publications and source records attributed to M L Bender.

At least 19 recordsLinked to original sources
PubMed2000

Global carbon sinks and their variability inferred from atmospheric O2 and delta13C.

Recent time-series measurements of atmospheric O2 show that the land biosphere and world oceans annually sequestered 1.4 +/- 0.8 and 2.0 +/- 0.6 gigatons of carbon, respectively, between mid-1991 and mid-1997. The rapid storage of carbon by the land biosphere from 1991 to 1997 contrasts with the 1980s, when the land biosphere was approximately neutral. Comparison with measurements of delta13CO2 implies an isotopic flux of 89 +/- 21 gigatons of carbon per mil per year, in agreement with model- and inventory-based estimates of this flux. Both the delta13C and the O2 data show significant interannual variability in carbon storage over the period of record. The general agreement of the independent estimates from O2 and delta13C is a robust signal of variable carbon uptake by both the land biosphere and the oceans.

Atmosphere↗
PubMed1987

Preparation and purification of microplasmin.

A catalytically active, human microplasmin was produced by incubation of [Lys]plasmin in buffer at pH 11.0 for up to 12 hr. The microplasmin was purified by affinity chromatography that used lysine-Sepharose and soybean trypsin inhibitor-Sepharose columns. It is homogeneous and pure by electrophoretic analysis in NaDodSO4/polyacrylamide gels and by gel filtration on a Superose 12 column. The molecular weight of the microplasmin determined by NaDodSO4 gel electrophoresis is 29,000 and 26,500 under reducing condition, whereas the molecular weight of native plasmin is 76,500. Microplasmin consists mainly of the ligh (B) chain of native human plasmin and possesses one active site per protein molecule when titrated with p-nitrophenyl p'-guanidinobenzoate. Microplasmin hydrolyzes the peptide substrate NH2-D-Val-Leu-Lys-p-nitroanilide (S-2251) with a Km of 0.361 +/- 0.017 mM and a kcat of 40.3 +/- 3.3 s-1 at pH 7.4 and 37 degrees C, whereas native plasmin has a Km of 0.355 +/- 0.002 mM and a kcat of 27.9 +/- 0.3 s-1 under the same conditions.

Chromatography, Affinity↗
PubMed1987

Structure and formation of microplasmin.

The structure of human microplasmin, prepared from plasmin in alkaline solution, has been studied. Microplasmin consists of two polypeptide chains connected by disulfide bonds. One polypeptide is the B chain of plasmin consisting of 230 amino acids, and the other peptide is the COOH-terminal portion of the A chain of plasmin consisting of 31 amino acid residues. Microplasmin has a molecular weight of 28,635, calculated from its primary sequence. It is slightly more positively charged than plasminogen and is a more hydrophobic molecule. The proposed scheme for the formation of microplasmin involves autolysis at specific peptide bonds and scrambling of especially sensitive disulfide bonds in alkaline solution.

Amino Acid Sequence↗
PubMed1987

Thermal and pH stability of "beta-benzyme".

The thermal and pH stability of "beta-benzyme", an artificial chymotrypsin based on beta-cyclodextrin, has been studied and compared with the stability of real chymotrypsin. Artificial chymotrypsin is vastly superior to real chymotrypsin with regard to both temperature and pH stability. The reasons for this increased stability are discussed.

Chymotrypsin↗
PubMed1985

Synthesis and evaluation of a miniature organic model of chymotrypsin.

An artificial chymotrypsin, with all the features of the real chymotrypsin, namely a binding site (from cyclodextrin) attached to a catalytic site containing an imidazolyl group, a carboxylate group and a hydroxyl group, has been synthesized. This artificial chymotrypsin has a molecular weight of only 1,365 while the real enzyme has a molecular weight of 24,800. However, from preliminary measurements, both the real and artificial enzymes have approximately the same catalytic activity (both rate and binding constants).

Chymotrypsin↗
PubMed1984

Inhibition of porcine elastase and anhydroelastase by boronic acids.

Porcine pancreatic elastase binds and is inhibited by the arylboronic acids with Ki values on the order of 10(-4)M, binding tighter than butaneboronic acid or methaneboronic acid. The pH dependence of the Ki values shows two pK values, pK1 = 6.8, assigned to enzyme ionization, and pK2, assigned to inhibitor ionization. The substituent effect of the arylboronic acids on Ki, investigated by a Hammett plot, suggests that the boron atom of the inhibitor interacts strongly with a nucleophilic site of elastase and probably forms an enzyme-bound tetrahedral structure. Anhydroelastase was formed by the removal of active site Ser-OH of elastase. Anhydroelastase has a much reduced affinity for the arylboronic acids or specific aldehyde inhibitors than the native enzyme, agreeing with the tetrahedral postulate.

Animals↗
PubMed1983

Fluorine magnetic resonance studies of fluorine-substituted benzoyl chymotrypsins.

The fluorine magnetic resonance spectra of 4-fluorobenzoyl and 3,5-di(trifluoromethyl)benzoyl-alpha-chymotrypsins and the corresponding methyl esters were determined. An unusually large downfield displacement of the chemical shift (-10 ppm) was observed for the 4-fluorobenzoyl-alpha-chymotrypsin compared to the free acid in water. The shift of the ethyl ester was displaced upfield on going from a partly aqueous solvent to dioxane or methanol. The line broadening of the fluorine resonance of the 3,5-di(trifluoromethyl)benzoyl-alpha-chymotrypsin was minimal and there was no evidence of two peaks in the spectrum. The resonance was displaced only slightly downfield from the corresponding acid in water. Unusual chemical shifts for fluorinated acylchymotrypsins have been reported for other acyl groups and they appear to be unrelated to the anomalous deacylation rates observed for some fluorine substituted acylenzymes.

Binding Sites↗
PubMed1983

Kinetics of subtilisin and thiolsubtilisin.

Subtilisin is a bacterial serine protease with a broad specificity in the S1 subsite. It has been very extensively studied using a variety of kinetic and physical techniques. A chemical derivative, thiolsubtilisin, has been subjected to similar studies in order to analyze the effects of the OH to SH conversion on enzyme activity. The native structure of thiolsubtilisin is indicated by a variety of physical techniques. Oligopeptides bind nearly equally well to both enzymes, and a peptide chloromethylketone is much more reactive to thiolsubtilisin than to subtilisin. Both enzymes have a similar level of activity towards activated nonspecific amides and esters. However, thiolsubtilisin is inactive towards highly specific peptide amides and esters. Thiolsubtilisin also does not show good binding to boronic and arsonic acids. The observation that these transition state analog inhibitors bind poorly to thiolsubtilisin while other compounds bind nearly equally well to both enzymes suggests that thiolsubtilisin may not be able to stabilize the transition state during acylation by specific substrates.

Acylation↗
PubMed1979

Conformation of the active site of thiolsubtilisin: reaction with specific chloromethyl ketones and arylacryloylimidazoles.

The conformation of the active site of thiolsubtilisin, prepared from subtilisin by transformation of the active site Ser to Cys, was compared with that of subtilisin by kinetic and spectroscopic methods. Carbobenzyloxy-L-alanylglycyl-L-phenylalanine chloromethyl ketone inhibited thiolsubtilisin approximately 10(2) times faster than subtilisin; alkylation occurred at the sulfhydryl rather than the imidazolyl group of the active site. pH dependence of the inhibition is different from that of the reaction between a simple thiol with haloacetamide. Furthermore, several native chromophoric arylacryloyl-thiolsubtilisins and arylacryloyl-subtilisins showed similar red shifts when compared with their denatured forms. The rate of deacylation of arylacryloyl-thiolsubtilisins was faster than (or of the same order of magnitude as) the deacylation rate of the analogous arylacryloyl-subtilisins in 30% dioxane (v/v), pH 5--10. The deacylation rate--pH profiles of these arylacryloyl-thiolsubtilisins in 30% dioxane all give pK values of 7.7 which is identical with the pK in the deacylation of acyl-subtilisins. These facts strongly suggest that the active-site conformation remains intact on conversion from subtilisin to thiolsubtilisin. The low esterase and peptidase activities of thiolsubtilisin are most likely due to the relatively low basicity of -SH (compared with -OH).

Amino Acid Chloromethyl Ketones↗
PubMed1979

Comparison of the kinetic specificity of subtilisin and thiolsubtilisin toward n-alkyl p-nitrophenyl esters.

The p-nitrophenyl esters of straight-chain fatty acids were used as substrates of the enzyme subtilisin Novo (EC 3.4.4.16) and its chemically produced artificial enzyme thiolsubtilisin. Subtilisin and thiolsubtilisin pH--activity profiles were determined, and kinetic effects of the active site O-S substitution were observed. Among the substrates tested, both enzymes show highest specificity with p-nitrophenyl butyrate. It was also found that subtilisin is more sensitive to changes in substrate chain length than is thiolsubtilisin. Second-order acylation rate constants (k2/Ks) are remarkably similar for both enzymes. However, thiolsubtilisin deacylation rate constants and Km values are lower than analogous subtilisin constants. While thiolsubtilisin deacylation rate constants give a pH profile identical with that of subtilisin, the pH profile of thiolsubtilisin acylation rate constants shows an active site pK value lowered from the subtilisin pK of 7.15 and exhibits an inflection point at pH 8.45, which is absent in subtilisin.

Binding Sites↗
PubMed1979

Do cleavages of amides by serine proteases occur through a stepwise pathway involving tetrahedral intermediates?

The mechanism of the serine protease-catalyzed cleavage of amides (acylation) was examined in terms of the basicity of the functional groups participating in the catalysis. It is proposed that the reaction does not proceed through a stepwise pathway, as opposed to the cleavage of esters and anilides, which start with general base-catalyzed formation of the tetrahedral intermediate followed by its general acid-catalyzed breakdown. Instead, the proton abstracted from the hydroxyl group of the serine by the imidazolyl group of the histidine is donated to the nitrogen atom of the leaving group of the amide before the bond between the carbonyl carbon atom of the amide and the attacking serine oxygen atom is completed. Reactions proceed by a SN2-like reaction through the cooperation of acid catalysis by the imidazolyl cation and nucleophilic attack by the serine. The mechanisms of the enzymatic hydrolyses of anilides and esters proceed through a discrete tetrahedral intermediate, but the enzymatic hydrolyses of amides probably do not.

Amides↗
PubMed1977

Binding rates, O--S substitution effects, and the pH dependence of chymotrypsin reactions.

The pH dependence for acylation of alpha-chymotrypsin by N-acetyltryptophan p-nitrophenyl-, p-nitrothiophenyl-, ethyl-, and thiolethyl esters has been studied by the stopped-flow technique. Values for the acylation rate constant, k2, and the binding constant, KS, were obtained by using measurements of phenolate release, for the p-nitrophenyl esters, and proflavin displacement, for the ethyl esters. The oxygen esters tested have slightly higher k2 values, and substantially higher KS values relative to the analogous thiol esters. Whereas k2/KS for the thiolethyl ester is higher than that for the analogous oxygen ester, the k2/KS values for oxy- and thio-p-nitrophenyl esters are nearly identical. These data are interpreted to indicate rate-determining formation of a tetrahedral intermediate in acylation of alpha-chymotrypsin by p-nitrophenyl esters, and rate-determining breakdown of such an intermediate in the case of the ethyl esters. It is also concluded that the oxygen to sulfur substitution causes a substantial increase in the proportion of nonproductive binding in these substrates. pH dependent k2 and KS values were used to calculate values for k1 and k-1, the binding and debinding rate constants for the two p-nitrophenyl compounds. This is the first such calculation based on experimentally determined acylation rate constants.

Chymotrypsin↗
PubMed1977

Kinetic studies of immobilized alpha-chymotrypsin in apolar solvents.

The mechanism of alpha-chymotrypsin action has been probed by extending studies of native chymotrypsin to immobilized chymotrypsin, where the organic content of the solution can be raised to much higher levels and thus one can explicitly look at the role of water. When one does this, one finds that water only appears in the deacylation reaction. The premise that one can go from native chymotrypsin (souble) to immobilized chymotrypsin (insoluble) has been tested by several criteria. It has been found in many instances that the two are identical: in absolute rate, in pKa. They are, however, not identical to one another in binding, due to differences in diffusion, which is to be expected. Thus, mechanistically immobilized and native chymotrypsin are identical to one another and the use of immobilized chymotrypsin can be used to specify the mechanism even more: it must proceed through two tetrahedral intermediates and two acyl-enzyme intermediates.

Chymotrypsin↗
PubMed1977

Intramolecular general base-catalyzed ester hydrolyses by the imidazolyl group.

Intramolecular general base catalysis by the imidazolyl group was found in the hydrolyses of endo-5-[4;(5')-imidazolyl]-bicyclo[2.2.1]hept-endo-2-yl trans-cinnamate and endo-5-[4'(5')-imidazolyl]bicyclo[2.2.2]oct-endo-2-yl trans-cinnamate in which the imidazolyl and trans-cinnamoyl groups are bound in close proximity to each other by rigid bicyclic rings. The rate constants for the intramolecular general base-catalyzed hydrolyses at 60 degrees are 6.4 X 10(-7) sec-1 for the former and 1.8 X 10(-7) sec-1 for the latter and the deuterium oxide solvent isotope effects are 3.0 for both. On the other hand, no intramolecular catalytic participation of the imidazolyl group was observed in the hydrolyses of the endo-exo isomers, exo- 5-[4'(5')-imidazolyl]bicyclo[2.2.1]hept-endo-2-yl trans-cinnamate and endo-5[4'(5')-imidazolyl]bicyclo[2.2.2]oct-exo-2-yl trans-cinnamate, in which the imidazolyl groups are located far from the trans-cinnamoyl groups. Intramolecular general base-catalyzed hydrolyses by the imidazolyl groups in endo-5[4'(5')-imidazolyl]bicyclo[2.2.1]hept-endo-2-yl trans-cinnamate and endo-5-[4'(5')-imidazolyl]bicyclo[2.2.2]oct-endo-2-yl trans-cinnamate can serve as models of serine esterase-catalyzed hydrolyses.

Catalysis↗