Although exosites 1 and 2 regulate thrombin activity by binding substrates and cofactors and by allosterically modulating the active site, it is unclear whether there is direct allosteric linkage between the two exosites. To begin to address this, we first titrated a thrombin variant fluorescently labeled at exosite 1 with exosite 2 ligands, HD22 (a DNA aptamer), ␥-peptide (an analog of the COOH terminus of the ␥-chain of fibrinogen) or heparin. Concentration-dependent and saturable changes in fluorescence were elicited, supporting inter-exosite linkage. To explore the functional consequences of this phenomenon, we evaluated the capacity of exosite 2 ligands to inhibit thrombin binding to ␥ A /␥ A -fibrin, an interaction mediated solely by exosite 1. When ␥ A /␥ A -fibrinogen was clotted with thrombin in the presence of HD22, ␥-peptide, or prothrombin fragment 2 there was a dose-dependent and saturable decrease in thrombin binding to the resultant fibrin clots. Furthermore, HD22 reduced the affinity of thrombin for ␥ A /␥ A -fibrin 6-fold and accelerated the dissociation of thrombin from preformed ␥ A /␥ A -fibrin clots. Similar responses were obtained when surface plasmon resonance was used to monitor the interaction of thrombin with ␥ A /␥ Afibrinogen or fibrin. There is bidirectional communication between the exosites, because exosite 1 ligands, HD1 (a DNA aptamer) or hirudin-(54 -65) (an analog of the COOH terminus of hirudin), inhibited the exosite 2-mediated interaction of thrombin with immobilized ␥-peptide. These findings provide evidence for long range allosteric linkage between exosites 1 and 2 on thrombin, revealing further complexity to the mechanisms of thrombin regulation.As the central effector of hemostasis, thrombin is engaged in procoagulant, anticoagulant, and fibrinolytic processes. These seemingly contrasting roles are regulated, at least in part, by thrombin's interactions with other factors in the blood and vasculature. The binding of ligands to thrombin is promoted by exosites 1 and 2, which are positively charged domains that flank the active site. These exosites facilitate the binding of substrates or cofactors and align them for optimal interaction with the active site (1).Exosite 1 is predominantly used to gain access to the active site by substrates such as fibrinogen (2), factors V (3) and VIII (4), and the protease-activated receptors (PARs) 2 on platelets (5). Effectors that modulate thrombin activity, including thrombomodulin (6), hirudin (7), and heparin cofactor II (8), also utilize exosite 1. Thrombomodulin alters the specificity of thrombin by hindering access of other substrates to exosite 1 (9) and by providing new binding sites for protein C and thrombin-activable fibrinolysis inhibitor, thereby promoting anticoagulant and antifibrinolytic pathways, respectively (10, 11). Fewer processes are mediated by exosite 2, which serves largely as a tether that anchors thrombin for participation in other reactions. Thus, heparin binds exosite 2 (12) and catalyzes thrombin inhibition...

Key Points Juvenile zebrafish tolerate widespread coagulopathy due to complete ablation of antithrombin III, but develop lethal thrombosis as adults. In vivo structure/function analysis of antithrombin III in zebrafish reveals limited roles for heparin-binding and anti-IXa/Xa activity.

Incorporation of prothrombin into the prothrombinase complex is essential for rapid thrombin generation at sites of vascular injury. Prothrombin binds directly to anionic phospholipid membrane surfaces where it interacts with the enzyme, factor Xa, and its cofactor, factor Va. We demonstrate that HD1, a thrombin-directed aptamer, binds prothrombin and thrombin with similar affinities (K d values of 86 and 34 nM, respectively) and attenuates prothrombin activation by prothrombinase by over 90% without altering the activation pathway. HD1-mediated inhibition of prothrombin activation by prothrombinase is factor Va-dependent because (a) the inhibitory activity of HD1 is lost if factor Va is omitted from the prothrombinase complex and (b) prothrombin binding to immobilized HD1 is reduced by factor Va. These data suggest that HD1 competes with factor Va for prothrombin binding. Kinetic analyses reveal that HD1 produces a 2-fold reduction in the k cat for prothrombin activation by prothrombinase and a 6-fold increase in the K m , highlighting the contribution of the factor Va-prothrombin interaction to prothrombin activation. As a high affinity, prothrombin exosite 1-directed ligand, HD1 inhibits prothrombin activation more efficiently than Hir 54 -65 (SO 3 ؊ ). These findings suggest that exosite 1 on prothrombin exists as a proexosite only for ligands whose primary target is thrombin rather than prothrombin.Thrombin is the most versatile component of the hemostatic system, mediating procoagulant, anticoagulant, and anti-fibrinolytic pathways (1). The diverse activities of thrombin are regulated, at least in part, by electropositive exosites flanking its active site (2). Exosite 1 binds ligands that interact with the active site of thrombin, including fibrinogen, heparin cofactor II, and protease-activated receptor, the major thrombin receptor on cells (2). In contrast, exosite 2, which binds ligands such as heparin (3, 4) and platelet glycoprotein Ib␣ (5-7), serves to tether thrombin for subsequent interactions with substrates or inhibitors.Prothrombin, the precursor of thrombin, lacks an active site and has immature or inaccessible exosites (8 -10). Because exosite 1 on prothrombin exhibits reduced affinity for certain ligands, it has been designated proexosite 1 (8). This proexosite gains functional activity during prothrombin conversion to thrombin, as evidenced by fluorescent ligand binding studies (11). Thus, Anderson and Bock (11) (SO 3 Ϫ ) that increase with the extent of activation (11, 12). Diminished affinity of other thrombin ligands for proexosite 1 on prothrombin also has been observed (13,14).In contrast to the progressive maturation of proexosite 1, exosite 2 displays more abrupt development. Exosite 2 is not accessible until fragment 2 (F2) is released from prothrombin. Thus, prethrombin 2 (pre2) and thrombin have similar affinities for heparin, whereas meizothrombin (mIIa) and meizothrombin des F1 [mIIa(-F1)], which retain the F2 domain, do not bind heparin (15).Understanding the functional maturat...

• The D9D3 domains of VWF are sufficient to stabilize FVIII in vivo.• The prolongation of VWF D9D3 survival in vivo by Fc fusion elevates FVIII levels in the setting of VWF but not FVIII deficiency.Plasma factor VIII (FVIII) and von Willebrand factor (VWF) circulate together as a complex. We identify VWF fragments sufficient for FVIII stabilization in vivo and show that hepatic expression of the VWF D9D3 domains (S764-P1247), either as a monomer or a dimer, is sufficient to raise FVIII levels in Vwf 2/2 mice from a baseline of ∼5% to 10%, to ∼50% to 100%. These results demonstrate that a fragment containing only ∼20% of the VWF sequence is sufficient to support FVIII stability in vivo. Expression of the VWF D9D3 fragment fused at its C terminus to the Fc segment of immunoglobulin G1 results in markedly enhanced survival in the circulation (t 1/2 > 7 days), concomitant with elevated plasma FVIII levels (>25% at 7 days) in Vwf 2/2 mice. Although the VWF D9D3-Fc chimera also exhibits markedly prolonged survival when transfused into FVIII-deficient mice, the cotransfused FVIII is rapidly cleared. Kinetic binding studies show that VWF propeptide processing of VWF D9D3 fragments is required for optimal FVIII affinity. The reduced affinity of VWF D9D3 and VWF D9D3-Fc for FVIII suggests that the shortened FVIII survival in FVIII-deficient mice transfused with FVIII and VWF D9D3/D9D3-Fc is due to ineffective competition of these fragments with endogenous VWF for FVIII binding. (Blood. 2014; 124(3):445-452)

• The VWF D9 domains are flexibly tethered entities projecting outside antiparallel dimers of the VWF D3 domain. • Extensive interactionsbetween the VWF D9 domain and primarily the FVIII C1 domain mediate VWF-FVIII association.Binding to the von Willebrand factor (VWF) D9D3 domains protects factor VIII (FVIII) from rapid clearance. We performed single-particle electron microscopy (EM) analysis of negatively stained specimens to examine the architecture of D9D3 alone and in complex with FVIII. The D9D3 dimer ([D9D3] 2 ) comprises 2 antiparallel D3 monomers with flexibly attached protrusions of D9. FVIII-VWF association is primarily established between the FVIII C1 domain and the VWF D9 domain, whereas weaker interactions appear to be mediated between both FVIII C domains and the VWF D3 core. IntroductionThe strong association of plasma factor VIII (FVIII) with circulating von Willebrand factor (VWF) secures FVIII from rapid clearance in the blood. The VWF-FVIII complex forms through a high-affinity interaction between the FVIII light chain and the VWF D9D3 domains. 1Mutations within VWF that abrogate or abolish this high-affinity binding lead to type 2N von Willebrand disease, a condition characterized by reduced plasma levels of FVIII. 2The tertiary structure of mature VWF, particularly at the N-terminal D9D3 domains, regulates the affinity for FVIII. VWF circulates as a multi-subunit protein comprising repeated domains that distinctly facilitate VWF packaging and hemostasis.3 The VWF propeptide (domains D1and D2) catalyzes the multimerization of VWF via intermolecular disulfide bonds at the D3 domain ( Figure 1A). 4 In the absence of propeptide-dependent posttranslational modifications to the D9D3 domains, VWF binds FVIII with reduced affinity.5 Cleavage of the propeptide by furin facilitates FVIII stabilization in the circulation. 6 We and others have previously reported that VWF fragments are sufficient to bind FVIII and that propeptide processing of these VWF fragments enhances the affinity for FVIII.7-9 Several of these VWF fragments were also sufficient to elevate FVIII levels in VWF-deficient mice. 7To further explore the association between VWF and FVIII, we used single-particle negative-stain electron microscopy (EM) to characterize the architecture of dimeric VWF D9D3 domains ([D9D3] 2 ) alone and in complex with FVIII. Study designProtein expression, purification, and analyses are detailed in supplemental Data available on the Blood Web site. The online version of this article contains a data supplement. Results and discussionThere is an Inside Blood Commentary on this article in this issue.The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked "advertisement" in accordance with 18 USC section 1734. , each monomer appears as an ovoid density along the dimer symmetry axis accompanied by a weaker elongated density, which we term the "handle," in the periphery. The dimensions of the handle are ;20Å ...

Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (k cat /K M ) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1′ substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.phage display | protease | high-throughput sequencing | ADAMTS13 | von Willebrand factor P rotease specificity is critical for maintaining diversity and compartmentalization of function, and is tightly controlled. For many proteases, a substrate initially docks to an exosite, which captures and orients the substrate scissile bond toward the active site of the enzyme. At the active site, the Px-Px′ (1) substrate amino acid side chains align with the complementary Sx-Sx′ pockets of the enzyme to optimize recognition by the active site residues that execute the proteolytic reaction (2).Conventional techniques for probing the substrate recognition requirements of a protease are cumbersome and time-consuming and require intimate knowledge of the enzyme/substrate pair. Such methods include engineering deletion mutants (3), use of competitive ligands (4, 5), and site-directed mutagenesis (6, 7). In contrast to these techniques, substrate phage display is a highthroughput, unbiased approach to studying protease substrate specificity (8-10). In this method, a library consisting of 10 6 -10 9 independent phage clones, each expressing a unique potential substrate on its surface, is panned for multiple rounds with a protease, and the cleaved or uncleaved phages after each reaction are removed and amplified for subsequent rounds of selection. In this manner, the library complexity is iteratively reduced and becomes populated by peptide sequences that are most informative. This methodology, although useful, is limited by the number of clones selected for individual Sanger sequencing after the last round of selection, and the selection of phages based on competitive growth advantages unrelated to enzyme specificity. The availability of high-throughput DNA sequencing technology (11) has facilitated detailed analysis of the changing complexity within a phage display library (12-16) without requiring multip...

The serine protease inhibitor (SERPIN) plasminogen activator inhibitor-1 (PAI-1) is a key regulator of the fibrinolytic system, inhibiting the serine proteases tissue- and urokinase-type plasminogen activator (tPA and uPA, respectively). Missense variants render PAI-1 non-functional through misfolding, leading to its turnover as a protease substrate, or to a more rapid transition to the latent/inactive state. Deep mutational scanning was performed to evaluate the impact of amino acid sequence variation on PAI-1 inhibition of uPA using an M13 filamentous phage display system. Error prone PCR was used to construct a mutagenized PAI-1 library encompassing ~ 70% of potential single amino acid substitutions. The relative effects of 27% of all possible missense variants on PAI-1 inhibition of uPA were determined using high-throughput DNA sequencing. 826 missense variants demonstrated conserved inhibitory activity while 1137 resulted in loss of PAI-1 inhibitory function. The least evolutionarily conserved regions of PAI-1 were also identified as being the most tolerant of missense mutations. The results of this screen confirm previous low-throughput mutational studies, including those of the reactive center loop. These data provide a powerful resource for explaining structure–function relationships for PAI-1 and for the interpretation of human genomic sequence variants.

Key Points• Three independent association signals at ADAMTS13 and smoking were identified as major predictors of plasma ADAMTS13 levels.• Evidence was presented that 2 nonsynonymous ADAMTS13 variants were driving the variation of plasma ADAMTS13 concentrations. P 5 1.2E-30) and rs3124762 (b, 3.5%; P 5 8.9E-9) close to ADAMTS13 and rs4075970 (b, 2.4%; P 5 6.8E-9) on 21q22.3. Linkage analysis also identified the region around ADAMTS13 (9q34.2) as the top signal (LOD 3.5), consistent with our SNP association analyses. Two nonsynonymous ADAMTS13 variants in the top 2 independent linkage disequilibrium blocks (Q448E and A732V) were identified and characterized in vitro. This study uncovered specific common genetic polymorphisms that are key genetic determinants of the variation in plasma ADAMTS13 levels in healthy individuals.