Conformational selection or induced fit? A critical appraisal of the kinetic mechanism.

For almost five decades, two competing mechanisms of ligand recognition, conformational selection and induced fit, have dominated our interpretation of ligand binding in biological macromolecules. When binding-dissociation events are fast compared to conformational transitions, the rate of approach to equilibrium, k(obs), becomes diagnostic of conformational selection or induced fit based on whether it decreases or increases, respectively, with the ligand concentration, [L]. However, this simple conclusion based on the rapid equilibrium approximation is not valid in general. Here we show that conformational selection is associated with a rich repertoire of kinetic properties, with k(obs) decreasing or increasing with [L] depending on the relative magnitude of the rate of ligand dissociation, k(off), and the rate of conformational isomerization, k(r). We prove that, even for the simplest two-step mechanism of ligand binding, a decrease in k(obs) with [L] is unequivocal evidence of conformational selection, but an increase in k(obs) with [L] is not unequivocal evidence of induced fit. Ligand binding to glucokinase, thrombin, and its precursor prethrombin-2 are used as relevant examples. We conclude that conformational selection as a mechanism for a ligand binding to its target may be far more common than currently believed.

Pharmacokinetics of Beriplex P/N prothrombin complex concentrate in healthy volunteers.

Prothrombin complex concentrates (PCCs) are widely administered for emergency oral anticoagulation reversal and for coagulation defects in liver disease. Pharmacokinetic data may help to optimize treatment. The objective of this study was to characterize the pharmacokinetics of a PCC (Beriplex P/N) containing coagulation factors II (FII), VII (FVII), IX (FIX) and X (FX) and anticoagulant proteins C and S. Fifteen healthy volunteers received a single rapid 50 IU/kg infusion of PCC and underwent frequent blood sampling until 144 hours (h) after infusion. Coagulation factors and anticoagulant protein pharmacokinetic parameters were estimated by non-linear regression. The mean infusion rate of PCC was 7.9 ml/min, equivalent to 196.4 IU/min. By the earliest post-infusion sampling point at 5 minutes (min), plasma FIX concentration increased by a median of 73%. Median increases in FII, FVII and FX at 5 min were 122%, 62% and 158%, respectively. Proteins C and S also increased rapidly. The median terminal half-life of FIX was 16.7 h, FII 59.7 h, FVII 4.2 h and FX 30.7 h. The median in-vivo recovery of FIX was 1.57 %/IU/kg and that of the other three coagulation factors > 2 %/IU/kg. Plasma concentration of thrombogenicity marker D-dimer did not increase, and there was no clinical evidence of thrombosis. Through up to 12 weeks follow-up there were no laboratory findings indicating PCC-related viral exposure. Rapid PCC infusion produced prompt sustained increases in coagulation factors and anticoagulant proteins with no clinical evidence of thrombosis or viral transmission.

Pharmacologic modulation of thrombin generation associated with human clots by human purified antithrombin alone or in the presence of low molecular weight heparin or unfractionated heparin.

Procoagulant activities associated with human clots may contribute to thrombus extension. We investigate the inhibition of clot-associated factor Xa and thrombin activities by purified human antithrombin either alone or as combination with a low molecular weight heparin (enoxaparin) as compared with unfractionated heparin (UFH). The standard clots were prepared by recalcification of frozen platelet-poor human plasma. Clot-associated thrombin was measured on the clot after clot incubation in recalcified buffer or recalcified prothrombin solution. The enzymatic reaction was measured using a specific substrate for thrombin (CBS 3447). The thrombin concentration was determined both on the clots and in the reaction mixtures. In parallel, prothrombin fragment 1.2 and thrombin-antithrombin complexes (TAT) were measured using enzyme-linked immunosorbent assay methods. We demonstrated that in the presence of purified human prothrombin and antithrombin (AT), a partial inhibition of clot associated thrombin activity correlated with an increase of TAT complexes. However, antithrombin was unable to inhibit thrombin generation induced by the clot-associated factor Xa. Enoxaparin (low molecular weight heparin) and UFH did not enhance clot-bound thrombin inhibition induced by AT. We conclude that clot-bound thrombin is accessible to human antithrombin alone. AT is also able to inhibit thrombin generated by factor Xa-associated clot. However, neither a low molecular weight heparin or UFH enhanced the effect of AT alone.

Pharmacokinetics, thrombogenicity and safety of a double-treated prothrombin complex concentrate.

The pharmacokinetic profile, the thrombogenicity and the virus safety of Preconativ, a PCC subjected both to virus removal procedure and dry-heat treatment were studied. Preconativ is produced from plasma pool, negative both for HBsAg and for antibodies to HIV. To further reduce the risk of virus transmission, the manufacturing process includes hydrophobic gel chromatography and dry-heat treatment at +68 degrees C for 48 hours. Nine patients with hemophilia B participated in a single dose, pharmacokinetic study. The decay curves of factor IX clotting activity were evaluated by model-independent methods. The Clearance and the Mean Residence Time were very similar to those previously reported for untreated PCC. The Volume of Distribution Area and In Vivo Recovery resulted inversely correlated and respectively larger and smaller than those of untreated PCC. A slight fall in platelet count and Antithrombin III level and an increase of Beta-Thromboglobulin and Fibrinopeptide A concentration were found, indicating a clear-cut activation of the coagulation process during the first hours following Preconativ administration. Seven patients (2 of the ones enrolled in the pharmacokinetic study) were completely fulfilling the SSC-ISTH criteria for virus safety prospective study. The follow up of these patients did not show any transaminases elevation or seroconversion against HBV, HCV or HIV. These findings did not change over a 3-5 year follow up in 3 out of 7 patients, repeatedly infused with Preconativ.

Purified factor IX using monoclonal immunoaffinity technique: clinical trials in hemophilia B and comparison to prothrombin complex concentrates.

Replacement therapy for hemophilia B (factor IX deficiency) using prothrombin complex concentrate (PCC) has been associated with serious complications of thromboembolic events and transmission of viral infections. Monoclonal antibody-purified factor IX (Mononine) provides a highly purified factor IX concentrate, while eliminating other vitamin K-dependent factors (II, VII, and X). Mononine was evaluated for in vivo recovery, half-life, and for its safety and efficacy in 10 patients with hemophilia B. The in vivo recovery of factor IX with Mononine was a 0.67 +/- 0.14 U/dL (mean +/- SD) increase per 1U/kg of infused factor IX, and the biologic half-life (t1/2), determined using the terminal phase of elimination, was 22.6 +/- 8.1 hours. Comparison of in vivo recovery of other vitamin K-dependent factors following a single infusion of either Mononine or PCC showed that, whereas Mononine infusion caused no changes in other vitamin K-dependent factors or in prothrombin activation fragment (F1+2), PCC infusion was associated with significant increases of factors II (2.7 U/dL per 1 U/dL of IX increase) and X (2.2 U/dL for 1 U/dL for 1 U/dL of IX). Patients who used Mononine as their sole therapeutic material during the 12-month period showed an excellent response in hemostasis for their bleeding episodes. Their experience with long-term use of Mononine was at least equivalent to their previous experience with PCC in the frequency and amount of factor usage. No patients developed antibody against mouse IgG or an increase in IX inhibitor during the 12-month period. These results indicate that monoclonal antibody-purified factor IX concentrate provides hemostatically effective factor IX replacement while avoiding extraneous thrombogenic substances.

Prothrombin plasma clearance is not mediated by hepatic asialoglycoprotein receptors.

The hepatic asialoglycoprotein receptor (AGPR) system can efficiently internalize and degrade circulating glycoproteins which lack terminal sialic acids on their carbohydrate chains. Since pro-thrombin is a glycosylated plasma protein, possible involvement of AGPR system in its clearance from circulation was evaluated. The half lives of bovine 125I-prothrombin and 125I-asialoprothrombin, injected intravenously into rats, were 192 and 1.8 minutes, respectively. Asialoprothrombin appeared to be cleared by the hepatic AGPRs since 33% of it accumulated in the liver at 30 minutes and its clearance was competitively blocked by simultaneous administration of increasing amounts of asialofetuin. Only 5% of prothrombin accumulated in the liver at 3 hours and injections asialofetuin in amounts capable of saturating the AGPR for the duration of four asialoprothrombin half lives had no effect on the disappearance of prothrombin. Our observations indicate that, although asialoprothrombin is readily cleared from plasma by the AGPR system, prothrombin is not. Thus these receptors do not appear to be involved in physiological processes that control prothrombin half life.

Surface exclusion and molecular mobility may explain Vroman effects in protein adsorption.

Data on protein adsorption usually show that for increasing surface coverage the adsorption velocity decreases much faster than linearly. This contrasts to the classical Langmuir model with an adsorption velocity proportional to the number of unoccupied binding sites. It has been shown that this non-linearity may explain phenomena like transient adsorption of different proteins from a protein mixture or dilution-dependent changes in binding properties, collectively called Vroman effects. However, the molecular mechanisms explaining this non-linear behavior remain to be established. A Monte Carlo simulation model is presented that incorporates steric hindrance, lateral mobility and mutual interactions of adsorbed molecules. Experimental data on the adsorption kinetics of prothrombin and annexin V, a recently discovered anticoagulant protein, at phospholipid bilayers are analyzed with this model. A major conclusion is that the steep decline in adsorption rates for increasing surface coverage can be explained, without assuming repulsive forces between adsorbed molecules, as a surface exclusion effect combined with lateral mobility of adsorbed molecules. The fact that annexin V shows this effect to a much lesser degree than prothrombin is tentatively explained by clustering of adsorbed annexin V molecules. A qualitative effect of lateral mobility on the adsorption characteristics, predicted by the model, is confirmed in experiments in which the fluidity of the bilayers was manipulated.

The prothrombin activation peptide regulates synthesis of the vitamin K-dependent proteins in the rabbit.

The turnover of 125I-bovine prothrombin fragment 1 was studied in the rabbit. The t1/2 of the peptide in the intravascular compartment was 11.5 hours and this compartment accounted for between 7.9 and 14.4% of the injected radioactivity. The rest of the radioactivity was distributed between two compartments in the extravascular space. The injection of the peptide (10 mg/rabbit) was associated with a transient increase in the plasma concentration of prothrombin and of factor X, with maximum concentration of prothrombin between 40 and 66 hours from the injection and between 26 and 40 hours for factor X. It is concluded that the injection of fragment 1 in the rabbit induced a transient increase in the synthesis of the vitamin K-dependent proteins that is compensated for by an increased absolute catabolic rate. It is suggested that the prothrombin activation peptide serves as regulatory message which induces the subsequent restoration of the appropriate concentration of the vitamin K-dependent proteins.

Biosynthesis and clearance of prothrombin in warfarin-treated rats.

The steady-state concentration of abnormal plasma prothrombin in warfarin-treated rats (10 mg/kg) was found to be approx. 6% of the plasma prothrombin level in normal rats. The clearance of abnormal plasma prothrombin in warfarin-treated rats was studied using either cycloheximide, to inhibit the synthesis, or vitamin K, to block the appearance of abnormal prothrombin in plasma. The clearance of abnormal plasma prothrombin corresponded to a half-life of approx. 6 h, which is similar to the half-life of normal plasma prothrombin. The de novo synthesis of prothrombin in warfarin-treated and normal rats was compared by measuring the incorporation of [3H]leucine into plasma prothrombin 90 min after an intravenous injection of the isotope. In warfarin-treated rats, accumulated prothrombin precursor was carboxylated and transported into circulation by injecting vitamin K 30 min after isotope administration. On comparing the incorporation of [3H]leucine into plasma prothrombin in warfarin-treated and normal rats, no significant difference in the de novo synthesis was detected. Our results suggest that the secretion of prothrombin in warfarin-treated rats is decreased to 6% of the normal rate. As the de novo synthesis is not affected by warfarin treatment, more than 90% of the newly synthesized prothrombin appears to be degraded intracellularly.