The data are inconsistent with previous proposals and suggest a model in which substrates for each of the four possible half-reactions bind in a mutually exclusive manner and with equal affinity to prothrombinase in a cleavage site-independent way. Despite equivalent exosite binding interactions between all four possible substrates and the enzyme, we propose that ordered bond cleavage results from the constraints associated with the binding of substrates in one of two conformations to a single form of prothrombinase.The formation of thrombin, a key reaction of the blood coagulation cascade, arises from specific and limited proteolysis of prothrombin (1). Although the serine proteinase, factor Xa, can catalyze this reaction, the rate of thrombin formation is greatly increased following its assembly into prothrombinase through interactions with membranes and factor Va (1-3). Prothrombinase is considered the physiologically relevant catalyst for rapid thrombin formation following the initiation of coagulation (2, 4).Thrombin formation results from cleavage of human prothrombin 1 following Arg 271 and Arg 320 (5,6). Initial cleavage at Arg 271 followed by cleavage at Arg 320 (Scheme I, Reactions 3 and 4) yields thrombin via the formation of prethrombin 2 and fragment 1.2 (P2 plus F1.2) 2 as intermediates. This cleavage pathway is evident in the action of factor Xa on prothrombin (7,8). Cleavage at Arg 320 followed by cleavage at Arg 271 (Scheme I, Reactions 1 and 2) results in thrombin formation via production of meizothrombin (mIIa) 3 as an intermediate. Within detection limits, bond cleavage in this order appears to quantitatively account for thrombin formation catalyzed by prothrombinase (9 -11). Prothrombinase cleaves the substrate in an apparently ordered fashion even though both Arg 320 and Arg 271 appear accessible to cleavage in prothrombin (9). The kinetic and molecular bases for these observations remain obscure.Kinetic explanations for bond selectivity in prothrombin have been sought from studies using P2 plus F1.2 and mIIa as substrates (9 -13). The individual bonds in both intermediates are cleaved by prothrombinase (Scheme I, Reactions 2 or 4) with approximately equal catalytic efficiency (9 -12). Consequently, an explanation for ordered bond cleavage by prothrombinase requires that Arg 271 and Arg 320 in intact prothrombin are cleaved with different catalytic efficiencies. Therefore, formal consideration of the reactions of prothrombin activation requires a distinction to be made between cleavage at Arg 271 before and after Arg 320 cleavage (Arg 271 and Arg 271 *, Scheme I) or at Arg 320 before and after Arg 271 cleavage (Arg 320 * This work was supported by National Institutes of Health Grants HL-62523 and HL-74124 (to S. K.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.¶ To whom correspondence should be addressed: Josep...

Prothrombinase catalyzes thrombin formation by the ordered cleavage of two peptide bonds in prothrombin. Although these bonds are likely Ϸ36 Å apart, sequential cleavage of prothrombin at Arg-320 to produce meizothrombin, followed by its cleavage at Arg-271, are both accomplished by equivalent exosite interactions that tether each substrate to the enzyme and facilitate presentation of the scissile bond to the active site of the catalyst. We show that impairing the conformational transition from zymogen to active proteinase that accompanies the formation of meizothrombin has no effect on initial cleavage at Arg-320 but inhibits subsequent cleavage at Arg-271. Full thermodynamic rescue of this defective mutant was achieved by stabilizing the proteinase-like conformation of the intermediate with a reversible, active sitespecific inhibitor. Irreversible stabilization of intact prothrombin in a proteinase-like state, even without prior cleavage at Arg-320, also enhanced cleavage at Arg-271. Our results indicate that the sequential presentation and cleavage of the two scissile bonds in prothrombin activation is accomplished by substrate bound either in the zymogen or proteinase conformations. The ordered cleavage of prothrombin by prothrombinase is driven by ratcheting of the substrate from the zymogen to the proteinase-like states.blood coagulation ͉ enzymology ͉ proteolytic cleavage ͉ serine protease ͉ zymogen activation T hrombin (IIa) is produced in a pivotal reaction of the blood coagulation cascade by specific proteolysis of prothrombin at two sites (1). The membrane-assembled prothrombinase complex is considered the physiologically relevant catalyst for this reaction (1, 2). Prothrombinase acts on the two scissile bonds through sequential cleavage reactions in an apparently ordered fashion. Provided that membrane binding by prothrombin is not compromised, prothrombin is cleaved after Arg-320 to yield meizothrombin ¶ (mIIa) as an intermediate, followed by subsequent cleavage at Arg-271 to produce IIa (3, 4). The molecular bases for these findings remain obscure.Because both cleavage sites in the zymogen appear accessible to proteolysis, prothrombin can be converted to thrombin by two possible cleavage pathways (3-6). Substrates for each of the four possible half-reactions in prothrombin activation bind prothrombinase in a mutually exclusive fashion and with equivalent affinity (4, 7). Three of the four possible reactions exhibit identical catalytic efficiencies, whereas cleavage at Arg-271 in intact prothrombin proceeds with a V max that is Ϸ30-fold lower (4). These findings establish the quantitative basis for preferential cleavage at Arg-320 over Arg-271 in intact prothrombin and the largely ordered cleavage pathway that ensues (4). They fail, however, to provide an explanation for why a difference in V max , and not affinity, drives selective recognition of the Arg-320 bond in intact prothrombin or why initial cleavage at Arg-320 greatly enhances the V max for subsequent cleavage at Arg-271 without also affec...

The specific action of serine proteinases on protein substrates is a hallmark of blood coagulation and numerous other physiological processes. Enzymic recognition of substrate sequences preceding the scissile bond is considered to contribute dominantly to specificity and function. We have investigated the contribution of active site docking by unique substrate residues preceding the scissile bond to the function of prothrombinase. Mutagenesis of the authentic P 1 -P 3 sequence in prethrombin 2/fragment 1.2 yielded substrate variants that could be converted to thrombin by prothrombinase. Proteolytic activation was also observed with a substrate variant containing the P 1 -P 3 sequence found in a coagulation zymogen not known to be activated by prothrombinase. Lower rates of activation of the variants derived from a decrease in maximum catalytic rate but not in substrate affinity. Replacement of the P 1 residue with Gln yielded an uncleavable derivative that retained the affinity of the wild type substrate for prothrombinase but did not engage the active site of the enzyme. Thus, active site docking of the substrate contributes to catalytic efficiency, but it is does not determine substrate affinity nor does it fully explain the specificity of prothrombinase. Therefore, extended interactions between prothrombinase and substrate regions removed from the cleavage site drive substrate affinity and enforce the substrate specificity of this enzyme complex.Blood coagulation is dependent on a series of highly specific proteolytic activation steps that are catalyzed by membraneassembled enzyme complexes (1, 2). The catalytic component in each of these reactions is a serine proteinase of the chymotrypsin family that can act on arginine-containing substrates (3). Yet, the coagulation enzymes act on their protein substrates with marked and distinctive specificity (1). Narrow specificity is also observed for proteinases of this family that function in diverse physiological processes (3). Based on the structural paradigms established for substrate recognition by the less selective digestive serine proteinases (4), the precise recognition of side chains flanking the cleavage site by the active site of the proteinase is considered a fundamental contributor to substrate affinity and specificity in these systems (5).The proteolytic conversion of prothrombin to thrombin by the cleavage of two peptide bonds is a key step of coagulation. It is catalyzed by prothrombinase, an archetypal enzyme complex of coagulation, consisting of the serine protease factor Xa and its cofactor Va assembled through reversible interactions on membrane surfaces in a Ca 2ϩ -dependent manner (1). The formation of thrombin results from two proteolytic cleavages in prothrombin each following an Asp/Glu-Gly-Arg sequence that is not found at the activation sites of other coagulation zymogens (6). Thus, the specific action of prothrombinase on prothrombin could be explained by the precise engagement of unique sequences preceding the scissile bond in the substra...

The preparation of sufficient amounts of high-quality protein samples is the major bottleneck for structural proteomics. The use of recombinant proteins has increased significantly during the past decades. The most commonly used host, Escherichia coli, presents many challenges including protein misfolding, protein degradation, and low solubility. A novel SUMO fusion technology appears to enhance protein expression and solubility ( http://www.lifesensors.com ). Efficient removal of the SUMO tag by SUMO protease in vitro facilitates the generation of target protein with a native N-terminus. In addition to its physiological relevance in eukaryotes, SUMO can be used as a powerful biotechnology tool for enhanced functional protein expression in prokaryotes and eukaryotes.

As the importance of ubiquitylation in certain disease states becomes increasingly apparent, the enzymes responsible for removal of ubiquitin (Ub) from target proteins, deubiquitylases (DUBs), are becoming attractive targets for drug discovery. For rapid identification of compounds that alter DUB function, in vitro assays must be able to provide statistically robust data over a wide dynamic range of both substrate and enzyme concentrations during high throughput screening (HTS). The most established reagents for HTS are Ubs with a quenched fluorophore conjugated to the C-terminus; however, a luciferase-based strategy for detecting DUB activity (DUB-Glo™, Promega) provides a wider dynamic range than traditional fluorogenic reagents. Unfortunately, this assay requires high enzyme concentrations and lacks specificity for DUBs over other isopeptidases (e.g. desumoylases), as it is based on an aminoluciferin (AML) derivative of a peptide derived from the C-terminus of Ub (Z-RLRGG-). Conjugation of aminoluciferin to a full-length Ub (Ub-AML) yields a substrate that has a wide dynamic range, yet displays detection limits for DUBs 100- to 1000-fold lower than observed with DUB-Glo™. Ub-AML was even a sensitive substrate for DUBs (e.g. JosD1 and USP14) that do not show appreciable activity with DUB-Glo™. Aminoluciferin derivatives of hSUMO2 and NEDD8 were also shown to be sensitive substrates for desumoylases and deneddylases, respectively. Ub/Ubl-AML substrates are amenable to HTS (Z′ =0.67) yielding robust signal, and providing an alternative drug discovery platform for Ub/Ubl isopeptidases.

Background: Prothrombin variants lacking membrane binding have probed the contribution of the substrate-membrane interaction in thrombin formation by prothrombinase. Results: Loss of membrane binding yields modest changes in rate but affects the pathway for substrate cleavage. Conclusion: Membrane binding by the substrate constrains the presentation of prothrombin for cleavage by prothrombinase. Significance: New insights into how the action of prothrombinase on prothrombin is regulated.

PAI-749 is a potent and selective synthetic antagonist of plasminogen activator inhibitor 1 (PAI-1) that preserved tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA) activities in the presence of PAI-1 (IC 50 values, 157 and 87 nM, respectively). The fluorescence (Fl) of fluorophore-tagged PAI-1 (PAI-NBD119) was quenched by PAI-749; the apparent K d (254 nM) was similar to the IC 50 (140 nM) for PAI-NBD119 inactivation. PAI-749 analogs displayed the same potency rank order for neutralizing PAI-1 activity and perturbing PAI-NBD119 Fl; hence, binding of PAI-749 to PAI-1 and inactivation of PAI-1 activity are tightly linked. Exposure of PAI-1 to PAI-749 for 5 min (sufficient for full inactivation) followed by PAI-749 sequestration with Tween 80 micelles yielded active PAI-1; thus, PAI-749 did not irreversibly inactivate PAI-1, a known metastable protein. Treatment of PAI-1 with a PAI-749 homolog (producing less assay interference) blocked the ability of PAI-1 to displace p-aminobenzamidine from the uPA active site. Consistent with this observation, PAI-749 abolished formation of the SDS-stable tPA/PAI-1 complex. PAI-749-mediated neutralization of PAI-1 was associated with induction of PAI-1 polymerization as assessed by native gel electrophoresis. PAI-749 did not turn PAI-1 into a substrate for tPA; however, PAI-749 promoted plasmin-mediated degradation of PAI-1. In conclusion, PAI-1 inactivation by PAI-749 using purified components can result from a dual mechanism of action. First, PAI-749 binds directly to PAI-1, blocks PAI-1 from accessing the active site of tPA, and abrogates formation of the SDS-stable tPA/PAI-1 complex. Second, binding of PAI-749 to PAI-1 renders PAI-1 vulnerable to plasmin-mediated proteolytic degradation.Plasminogen activator inhibitor 1 (PAI-1) is a rapidly acting inhibitor of tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA) (Dellas and Loskutoff, 2005). PAI-1 is a member of the serpin class of serine protease inhibitors that characteristically produce SDS-stable complexes with their cognate protease targets (Silverman et al., 2001). Formation of the acyl-enzyme adduct between PAI-1 and the protease involves initial formation of a Michaelis-type noncovalent complex without significant conformational change, followed by reversible acylation and irreversible reactive loop conformational changes that trap the protease in a covalent complex (Olson et al., 2001). Two other conformation states of PAI-1 are known. First, the acyl-enzyme adduct between PAI-1 and tPA (or uPA) can be hydrolyzed to form cleaved (inactive) PAI-1 and regenerate active plasminogen activator (PA) (Declerck et al., 1992). Second, active PAI-1 can undergo a spontaneous large conformation change that gives rise to an inactive (latent) state of the inhibitor (Levin and Santell, 1987;Mottonen et al., 1992).PAI-1 plays a pivotal role in a myriad of physiological processes that involve activation of plasminogen (Dellas and Loskutoff, 2005). High ...

Bispecific antibodies (bsAbs) combine the antigen specificities of two distinct Abs and demonstrate therapeutic promise based on novel mechanisms of action. Among the many platforms for creating bsAbs, controlled Fab-arm exchange (cFAE) has proven useful based on minimal changes to native Ab structure and the simplicity with which bsAbs can be formed from two parental Abs. Despite a published protocol for cFAE and its widespread use in the pharmaceutical industry, the reaction mechanism has not been determined. Knowledge of the mechanism could lead to improved yields of bsAb at faster rates as well as foster adoption of process control. In this work, a combination of Förster resonance energy transfer (FRET), nonreducing SDS-PAGE, and strategic mutation of the Ab hinge region was employed to identify and characterize the individual steps of cFAE. Fluorescence correlation spectroscopy (FCS) was used to determine the affinity of parental (homodimer) and bispecific (heterodimer) interactions within the CH3 domain, further clarifying the thermodynamic basis for bsAb formation. The result is a clear sequence of events with rate constants that vary with experimental conditions, where dissociation of the K409R parental Ab into half-Ab controls the rate of the reaction.