scholarly journals The interaction between captured human thrombin and antithrombin studied by surface plasmon resonance, and the effect of melagatran

2002 ◽  
Vol 16 (3-4) ◽  
pp. 257-270 ◽  
Author(s):  
Susanne Elg ◽  
Johanna Deinum
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Rate Constant ◽  
Plasmon Resonance ◽  
Active Site ◽  
Order Rate Constant ◽  
Second Order ◽  
Thrombin Inhibitor ◽  
Order Rate ◽  
Human Thrombin

The kinetics of the interactions between thrombin and antithrombin were studied by surface plasmon resonance. Although amine coupled thrombin binds low molecular weight active site inhibitors with a one-to-one stoichiometry hirudin only bound to 75% of the coupled active thrombin. However, antithrombin or thrombomodulin could not bind at all to amine-coupled thrombin. To make it possible to follow the reaction with antithrombin in time thrombin was therefore captured on an antibody against thrombin. Alternatively, antithrombin was captured on an antibody against antithrombin to follow complex formation with thrombin. With these techniques the second-order rate constant for the interaction of antithrombin with thrombin in the presence of heparin, was estimated to beka≥0.4×106 M−1 s−1withKD═ 50 nM for the formation of the initial complex. These values are similar to those found in solution. In the absence of heparin, the second-order rate constant for the interaction of thrombin with captured antithrombin was onlyka═ 9×103 M−1 s−1. Thus, with this technique rate constants for the interaction of proteases with serpins can be determined in a convenient way, without the need for stopped-flow. The rapid‒binding, active-site-directed thrombin inhibitor, melagatran, competed with the antithrombin-thrombin interaction. Although melagatran, a reversible thrombin inhibitor, initially prevented formation of the complex, ultimately the irreversible thrombin-antithrombin complex was always formed.

Structural and Functional Investigations of Active Site Binding Regions in Factor VIIa.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2029-2029
Author(s):  
S. Paul Bajaj ◽  
Amanda Sutton ◽  
Sreejesh Shanker ◽  
Amy E Schmidt ◽  
Sayeh Agah ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Rate Constant ◽  
Active Site ◽  
Rate Constants ◽  
Site Occupancy ◽  
Order Rate Constant ◽  
Second Order ◽  
Factor Vii ◽  
Protease Domain ◽  
Order Rate

Abstract Factor VII (FVII) consists of an N-terminal γ-carboxyglutamic acid (Gla) domain followed by two epidermal growth factor-like (EGF1 and EGF2) domains and the C-terminal protease domain. Activation of FVII results in a two-chain FVIIa molecule consisting of a light chain (Gla-EGF1-EGF2 domains) and a heavy chain (protease domain) held together by a single disulfide bond. The complex of tissue factor (TF) and FVIIa activates FIX and FX during coagulation. FVIIa on its own is structurally more “zymogen-like” and when bound to TF it is more “active enzyme-like.” We obtained crystal structures of EGR-VIIa/soluble (s) TF (2.9 Å resolution), dansyl-EGR-VIIa/sTF (1.9 Å resolution) and benzamidine-VIIa/sTF (1.6 Å resolution). We also investigated the effect of TF binding on the S1, S2, and S3/S4 subsites (Schechter and Berger, BBRC, 27:157-162, 1967) in FVIIa. The affinity of variously inhibited FVIIa to sTF was also measured using Biacore technology. For obtaining second order inhibition rate constants, FVIIa ± soluble (s) TF was incubated with each inhibitor for various times, diluted several fold and assayed for the residual FVIIa activity. The second order rate constants were obtained by plotting the first order rate constants versus the inhibitor concentrations. These data are summarized in the table below. From these data it appears that all subsites are affected upon FVIIa binding to sTF. Since in the crystal structure of EGR-VIIa/sTF the P1 Arg residue is the only residue that makes contact with FVIIa, it follows that the S1 site is affected ~10-fold upon binding to sTF. Adding a dansyl group that partially occupies the S3/S4 position (1.9 Å structure) increases the second order rate constant 7-fold (2.41 versus 0.35) over that of EGR-ck. Moreover the addition of Pro (DFPR-ck) or Phe (DFFR-ck) residue occupying the S2 position increases the second order rate constant 357-fold and 1500- fold, respectively (125 and 525 versus 0.35). Thus, comparison of dEGR, DFPR, DFFR inhibition suggests that FVIIa prefers Phe at S2 and at S3/S4 positions, and that TF opens up the S1/S2/S3/S4 sites for substrate or inhibitor occupancy. These data are consistent with LTR (P3/P2/P1) residues in FX at its activation cleavage site as well as with LTR (P3/P2/P1) residues and FTR (P3/P2/P1) residues at the 145-146 and 180-181 FIX activation cleavage sites, respectively. Thus, these studies with chloromethylketone inhibitors have biologic relevance. For Biacore studies, sTF was amine coupled to a CM5 chip. The binding of unoccupied active site FVIIa in 5 mM calcium to sTF was characterized by a KD of 7 nM. Benzamidine (10 mM)-VIIa, p-aminobenzamidine (pAB, 1 mM)-VIIa, EGR-VIIa, dEGR-VIIa, DFPR-VIIa and DFFR-VIIa each bound to sTF with KD values ranging from 1- 2 nM. These affinity measurements indicate that the S1 site occupied FVIIa molecule (benzamidine-FVIIa, pAB-VIIa) has essentially the same conformation as the S1/S2/S3/S4 occupied FVIIa. This conclusion is consistent with similar crystal structures of variously inhibited FVIIa molecules complexed with sTF. The differential rates of incorporation of various chloromethylketone inhibitors could be due to the interaction of various residues (P1, P2, P3, P4) with the corresponding active subsites (S1/S2/S3/S4) of FVIIa. Additionally, the rate of incorporation of chloromethylketone inhibitors into FVIIa also involves the irreversible alkylation step, which could be faster for DFFR-ck and DFPR-ck. Once these inhibitors are incorporated, it appears that they induce the same conformation in FVIIa as achieved by S1 site occupancy alone. Thus S1 site occupancy in FVIIa induces the required conformation to modestly increase the affinity for TF. Second Order Rate Constants for Inhibition of FVIIa ± sTF with Various Chloromethylketone (ck) Inhibitors Inhibitor Minus sTF k (min−1 mM−1) Plus sTF k (min−1 mM−1) Fold Difference EGR-ck 0.04 0.35 8.8 dansyl EGR-ck 0.07 2.41 34.4 (D)FPR-ck 2.3 125 54.3 D)FFR-ck 5.6 525 93.8

scholarly journals Active-site-serine d-alanyl-d-alanine-cleaving-peptidase-catalysed acyl-transfer reactions. Procedures for studying the penicillin-binding proteins of bacterial plasma membranes

1986 ◽  
Vol 235 (1) ◽  
pp. 159-165 ◽  
Author(s):  
J M Ghuysen ◽  
J M Frère ◽  
M Leyh-Bouille ◽  
M Nguyen-Distèche ◽  
J Coyette
Keyword(s):  
Rate Constant ◽  
Active Site ◽  
Plasma Membranes ◽  
Binding Proteins ◽  
Order Rate Constant ◽  
Second Order ◽  
Beta Lactam ◽  
Penicillin Binding Proteins ◽  
First Order ◽  
Order Rate

Under certain conditions, the values of the parameters that govern the interactions between the active-site-serine D-alanyl-D-alanine-cleaving peptidases and both carbonyl-donor substrates and beta-lactam suicide substrates can be determined on the basis of the amounts of (serine ester-linked) acyl-protein formed during the reactions. Expressing the ‘affinity’ of a beta-lactam compound for a DD-peptidase in terms of second-order rate constant of enzyme acylation and first-order rate constant of acyl-enzyme breakdown rests upon specific features of the interaction (at a given temperature) and permits study of structure-activity relationships, analysis of the mechanism of intrinsic resistance and use of a ‘specificity index’ to define the capacity of a beta-lactam compound of discriminating between various sensitive enzymes. From knowledge of the first-order rate constant of acyl-enzyme breakdown and the given time of incubation, the beta-lactam compound concentrations that are necessary to achieve given extents of DD-peptidase inactivation can be converted into the second-order rate constant of enzyme acylation. The principles thus developed can be applied to the study of the multiple penicillin-binding proteins that occur in the plasma membranes of bacteria.

scholarly journals The reactivities and ionization properties of the active-site dithiol groups of mammalian protein disulphide-isomerase

1991 ◽  
Vol 275 (2) ◽  
pp. 335-339 ◽  
Author(s):  
H C Hawkins ◽  
R B Freedman
Keyword(s):  
Rate Constant ◽  
Ph Dependence ◽  
Order Rate Constant ◽  
Second Order ◽  
Native Enzyme ◽  
Liver Protein ◽  
Thiol Groups ◽  
Protein Disulphide Isomerase ◽  
Order Rate ◽  
Reactive Groups

1. The number of reactive thiol groups in mammalian liver protein disulphide-isomerase (PDI) in various conditions was investigated by alkylation with iodo[14C]acetate. 2. Both the native enzyme, as isolated, and the urea-denatured enzyme contained negligible reactive thiol groups; the enzyme reduced with dithiothreitol contained two groups reactive towards iodoacetic acid at pH 7.5, and up to five reactive groups were detectable in the reduced denatured enzyme. 3. Modification of the two reactive groups in the reduced native enzyme led to complete inactivation, and the relationship between the loss of activity and the extent of modification was approximately linear. 4. Inactivation of PDI by alkylation of the reduced enzyme followed pseudo-first-order kinetics; a plot of the pH-dependence of the second-order rate constant for inactivation indicated that the essential reactive groups had a pK of 6.7 and a limiting second-order rate constant at high pH of 11 M-1.s-1. 5. Since sequence data on PDI show the presence within the polypeptide of two regions closely similar to thioredoxin, the data strongly indicate that these regions are chemically and functionally equivalent to thioredoxin. 6. The activity of PDI in thiol/disulphide interchange derives from the presence of vicinal dithiol groups in which one thiol group of each pair has an unusually low pK and high nucleophilic reactivity at physiological pH.

Interactions of Heparin and a Covalently Linked Antithrombin Heparin Complex with the Components of the Fibrinolytic Pathway.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2211-2211
Author(s):  
Ankush Chander ◽  
Helen M Atkinson ◽  
Leslie R. Berry ◽  
Anthony K.C. Chan
Keyword(s):  
Enzyme Activity ◽  
Rate Constant ◽  
Serine Proteases ◽  
Conflicts Of Interest ◽  
Order Rate Constant ◽  
Second Order ◽  
Coagulation Cascade ◽  
Simultaneous Addition ◽  
Order Rate ◽  
Significant Difference

Abstract Abstract 2211 Introduction: Unfractionated heparin (UFH) is used for the prophylaxis and treatment of thromboembolic diseases. UFH catalyzes inhibition by antithrombin (AT) of the serine proteases in the coagulation cascade. Additionally, UFH has been shown to interact with components of the fibrinolytic pathway in vitro. However UFH has several limitations which impact its utility as a therapeutic agent. Our lab has developed a novel covalent antithrombin-heparin complex (ATH) which inhibits most serine proteases of the coagulation pathway significantly faster when compared to non covalent mixtures of AT and UFH. However, the interactions of ATH with the components of the fibrinolytic pathway have not been studied before. Thus, the present study investigates possible serpin-heparin interactions of AT + UFH vs ATH within the fibrinolytic pathway. Methods: Discontinuous second order rate constant assays under pseudo-first order conditions were carried out to obtain second order rate constant (k2) values for the inhibition of plasmin by AT+UFH versus ATH. Briefly, at specific time intervals 20 nM plasmin was inhibited by 200 nM AT + 0–5000 nM UFH or by 200 nM ATH in the presence of 2.5 mM Ca2+. Reactions were neutralized by the simultaneous addition of a solution containing polybrene and plasmin substrate S-2366™ in buffer. Residual plasmin activity was measured and the final k2 values calculated. For experiments involving tPA, wells containing 40nM tPA and increasing concentrations of AT, UFH or ATH, at mole ratios ranging from 0 to 20:1, were incubated for 15 min. Reactions with tPA were neutralized by simultaneous addition of a solution containing either polybrene and tPA substrate, S-2288™ in buffer, (ATH and UFH) or only the substrate S-2288™ in buffer (AT). Enzyme activity was then determined by measuring rate of substrate cleavage (Vmax). Results: When plasmin was inhibited by AT in the absence of UFH, k2 values of 2.82×105 +/− 4.46×104 M−1 min−1 were observed. The k2 values increased with addition of successively higher concentrations of UFH up to a plateau with maximal k2 of 5.74×106 +/− 2.78×105 M−1 min−1 at a UFH concentration of 3000nM. For inhibition of plasmin by ATH, k2 values of 6.39 × 106 +/− 5.88 × 105 M−1 min−1 were observed. Inhibition of plasmin by ATH was not significantly different when compared to the highest k2 values obtained with UFH. (p=0.36) No statistically significant difference in tPA enzyme activity was observed when Vmax values for tPA alone were compared with those in the presence of AT, UFH or ATH. (p=0.932, p=0.085, p=0.31 respectively) Significance: The characteristic shape of the curve obtained from the k2vs. UFH plot suggests that the mechanism responsible for inhibition of plasmin by AT+UFH involves conformational activation of the serpin. The k2 values in this study for inhibition of plasmin by both AT+UFH and ATH were three orders of magnitude lower than k2 values for inhibition of thrombin or factor Xa. Furthermore these results suggest that tPA is not inhibited by AT + UFH or ATH, and is not influenced by the presence of UFH alone. Cumulatively, this indicates that the fibrinolytic pathway is minimally impacted by AT + UFH or ATH, allowing maximal antithrombotic potential to be achieved during anticoagulation. Overall, the favourable anticoagulant properties of ATH combined with the findings of this study strengthens the utility of the covalent conjugate over conventional UFH for the treatment of thromboembolic disorders. Disclosures: No relevant conflicts of interest to declare.

Ambident nucleophiles. II. Nitrogen-bonded and carbon-bonded σ-complex formation in the reaction of pyrrolide anions with 1,3,5-trinitrobenzene

1982 ◽  
Vol 60 (15) ◽  
pp. 1988-1995 ◽  
Author(s):  
J. C. Halle ◽  
M. J. Pouet ◽  
M. P. Simonnin ◽  
F. Debleds ◽  
F. Terrier
Keyword(s):  
Aqueous Solution ◽  
Complex Formation ◽  
Rate Constant ◽  
Order Rate Constant ◽  
Reactive Species ◽  
Second Order ◽  
Potassium Salts ◽  
Strong Base ◽  
Order Rate

Reaction of 1,3,5-trinitrobenzene (TNB) with pyrrole, 2,5-dimethyl pyrrole, and 2,4-dimethyl-3-ethyl pyrrole in the presence of a strong base (CH3O−) yields nitrogen- and/or carbon-bonded 1:1 σ-complexes in dimethylsulphoxide (DMSO). Depending on the stoichiometry of the reagents, 1:2 and 2:1 pyrrole–TNB diadducts are also formed. Identification of all complexes was effected by nmr. The reactive species are shown to be the pyrrolide ions and the results emphasize the ambident character of these anions towards an aromatic electrophile. Some of the complexes have been isolated as crystalline potassium salts when experiments are performed in acetonitrile. Among the isolable complexes, the kineticallybutnotthermodynamicallyfavored nitrogen adduct of pyrrole (5a) is remarkably unreactive. The second-order rate constant kH+ for is H+-catalyzed decomposition in aqueous solution is only 1 L mol−1 s−1 (t = 25 °C).

scholarly journals Kinetic studies on the nitrite reductase of Wolinella succinogenes

1986 ◽  
Vol 233 (2) ◽  
pp. 553-557 ◽  
Author(s):  
R Blackmore ◽  
T Brittain
Keyword(s):  
Rate Constant ◽  
Nitrite Reductase ◽  
Flash Photolysis ◽  
Spectral Characteristics ◽  
Order Rate Constant ◽  
Second Order ◽  
Stopped Flow ◽  
Dependent Manner ◽  
Wolinella Succinogenes ◽  
Order Rate

The six haem groups of the nitrite reductase enzyme isolated from Wolinella succinogenes are rapidly reduced by the addition of dithionite (S2O4(2-)). The reduction, however, is not homogeneous. Two of the haem groups, namely those that show spectral characteristics typical of five-co-ordinated haem groups, are reduced in a dithionite-concentration-dependent fashion with a rate limit of 1.5 S-1. The other four haem groups, which show spectral characteristics very similar to those of normal six-co-ordinate c-haem groups, reduce in a linear dithionite-concentration-dependent manner with a second-order rate constant of 150 M-1/2 X S-1. The ratio of the amplitudes of the two reduction phases observed in stopped-flow studies is found to be dependent on the concentration of dithionite used. A model is proposed to account for these observations, and computer simulations show that the model represents a good fit to the experimental data. The two haem groups with five-co-ordinate spectral characteristics bind CO. Flash photolysis of the CO complex exhibits one major recombination process with a linear dependence in rate on CO concentration with a second-order rate constant of 2 × 106 M-1 × S-1. By contrast, stopped-flow mixing of the reduced protein with CO shows a very complex pattern of combination, with most of the observed absorbance change associated with a concentration-independent step. These findings are rationalized in terms of structural changes in the protein consequent to ligand binding.

Formation and spectra of flavin radicals in the presence of β-mercaptoethanol at pH 9 and 10

1984 ◽  
Vol 62 (3) ◽  
pp. 580-585 ◽  
Author(s):  
Parminder S. Surdhar ◽  
Rizwan Ahmad ◽  
David A. Armstrong
Keyword(s):  
Rate Constant ◽  
Rate Constants ◽  
Order Rate Constant ◽  
Second Order ◽  
Radical Species ◽  
Spectral Changes ◽  
Order Rate ◽  
Visible Spectra ◽  
Uv Visible ◽  
Presence And Absence

Spectral changes and rates of reaction of flavins and several radical species have been investigated at pH 7, 9, and 10 in the presence and absence of β-mercaptoethanol. The radicals •CO2−, eaq−, and [Formula: see text] reacted with FAD at pH 10 to give a spectrum of FAD •Fl− with rate constants of 7 ± 1 × 108 and 4 ± 1 × 108 M−1 s−1 for •CO2− and [Formula: see text] respectively. At pH 7 only •FlH was observed and at pH 9 a mixture of •FIH and •Fl−.Interactions between flavin radicals and sulphydryl at 10−4 M concentration did not cause perturbations in the uv–visible spectra until either the radical and/or the sulphydryl were ionized. With FAD at pH 9 or 10 and LFl at pH 10 the 370 nm peak of •Fl− was enhanced by about 15% and a second larger growth occurred near 450 nm in the presence of 10−4 to 10−2 M sulphydryl. We attribute this to the formation of labile intermediate RSHFl•−, which must also be involved in the reduction of Fl by [Formula: see text] at pH 9 or 10.The second order rate constant k13 for reaction of [Formula: see text] with FAD at pH 9 and 10 was found to be 4.2 ± 0.5 × 108 M−1 s−1 and 2.0 ± 0.4 × 108 M−1 s−1 respectively. The rate constant for the reaction between [Formula: see text] and LFl at pH 10 was slightly faster, 7 ± 1 × 108 M−1 s−1, probably reflecting the fact that LFl lacks the bulky negatively charged adenine dinucleotide group of FAD.

Studies on Sulphamic Acid and Related Compounds. II. Kinetics and Mechanism of Hydrolysis of Trimethylamine- and of Triethylamine Sulphur Trioxide Addition Compounds

1962 ◽  
Vol 15 (2) ◽  
pp. 251 ◽  
Author(s):  
BE Fleischfresser ◽  
I Lauder
Keyword(s):  
Rate Constant ◽  
Order Rate Constant ◽  
Aqueous Acetone ◽  
Second Order ◽  
Fluoride Ions ◽  
Order Rate ◽  
Mechanism Of Hydrolysis ◽  
Reaction With Water ◽  
Sulphamic Acid ◽  
Hydrolysis Of

The kinetics of hydrolysis of trimethylamine- and of triethylaminesulphur trioxide addition compounds have been studied in water and in aqueous acetone. Reaction occurs according to the equation,������������� f - + R,N.SO,+H,O-tR,XH+HSO~.The solvolysis reactions are first-order and are not catalyzed by acids. The halide ions, Cl', Br', and 1', show only a normal salt effect on the rate of hydrolysis of + - (CH,),N.SO, but in the presence of fluoride ions, the rate constant for the production + - of acid from (C,H,),N.SO, in water at 95 OC is about one-seventh of that in the absence of fluoride under the same conditions. It is suggested that the fluorosulphonate ion is formed rapidly, and that this ion then undergoes slow hydrolysis :�In the presence of alkali, using water as the solvent, second-order kinetics are observed, the equation for the reaction being,�������������� + - R,N.SO,+~OH-+R,X+SO~= +H,O. Assuming the reaction with water is bimolecular, the ratio of the (bimolecular) rate constants at 35 OC, ko~-/k~,o is approximately lo8 for each complex. In aqueous acetone, at low water concentrations, the hydrolysis reactions of the trialkylaminesulphur trioxide complexes show second-order kinetics. At 35 OC for the hydrolysis of + - (CH,),N.SO, the ratio of the second-order rate constant in aqueous acetone to the + - (calculated) second-order rate constant in water is approximately 550 ; for (C,H,),N.SO, the same ratio is 6900. It is considered that hydrolysis occurs in water and in aqueous acetone via a bi- molecular attack at sulphur.

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