Fragment 1 Research Articles

Ovalbumin’s potential as a wound-healing medicament in tooth extraction socket by induction of cell proliferation through the ERK2 pathway in silico

Background: The trend of studies on dental medicaments is increasing rapidly. Antibacterial or anti-inflammatory activity is most frequently studied. Ovalbumin is one of the proteins whose benefits have been studied, but these benefits are still limited because of ovalbumin’s potential for proliferative bioactivity. Purpose: The aim of this study is to examine ovalbumin’s potential as a woundhealing medicament through molecular docking analysis on a protein related to the extracellular signal-regulated kinases/mitogenactivated protein kinase (ERK/MAPK) signaling pathway. Methods: Ovalbumin was hydrolyzed through BIOPEP-UWM (The BIOPEPUWM™ database of bioactive peptides). Protein target and interaction were predicted using Similarity Ensemble Approach target prediction webserver, SuperPred webserver, STRING webserver, and Cytoscape version 3.9.1. Selected fragments were docked using Autodock Vina in PyRx 0.8 with Tukey’s multiple comparison test and Biovia Discovery Studio version 19.1.0.18287 for visualization. Results: This study found that ovalbumin has the potential to positively regulate cell proliferation, angiogenesis, and fibroblast growth factor production. Six of the 131 fragments of ovalbumin could interact with 73 proteins, and the 20 proteins with the highest probability and score of betweenness centrality showed potential for bioactivity. Five fragments and povidone-iodine interacted inside the Adenosine triphosphate (ATP) phosphorylation site of ERK2, whereas fragment 1 (F1) and glycerin interacted outside the site. F1 could decrease the binding energy required for adenosine 5′-[,-methylene]triphosphate or an ATP-analogue chemical compound to interact with ERK2 compared to the control, with a score that was not significant. Conclusion: Ovalbumin has the potential to induce cell proliferation by affecting ERK2-ligand interactions.

Assembly of alternative prothrombinase by extracellular histones initiates and disseminates intravascular coagulation

AbstractThrombin generation is pivotal to both physiological blood clot formation and pathological development of disseminated intravascular coagulation (DIC). In critical illness, extensive cell damage can release histones into the circulation, which can increase thrombin generation and cause DIC, but the molecular mechanism is not clear. Typically, thrombin is generated by the prothrombinase complex, comprising activated factor X (FXa), activated cofactor V (FVa), and phospholipids to cleave prothrombin in the presence of calcium. In this study, we found that in the presence of extracellular histones, an alternative prothrombinase could form without FVa and phospholipids. Histones directly bind to prothrombin fragment 1 (F1) and fragment 2 (F2) specifically to facilitate FXa cleavage of prothrombin to release active thrombin, unlike FVa, which requires phospholipid surfaces to anchor the classical prothrombinase complex. In vivo, histone infusion into mice induced DIC, which was significantly abrogated when prothrombin F1 + F2 were infused prior to histones, to act as decoy. In a cohort of intensive care unit patients with sepsis (n = 144), circulating histone levels were significantly elevated in patients with DIC. These data suggest that histone-induced alternative prothrombinase without phospholipid anchorage may disseminate intravascular coagulation and reveal a new molecular mechanism of thrombin generation and DIC development. In addition, histones significantly reduced the requirement for FXa in the coagulation cascade to enable clot formation in factor VIII (FVIII)– and FIX-deficient plasma, as well as in FVIII-deficient mice. In summary, this study highlights a novel mechanism in coagulation with therapeutic potential in both targeting systemic coagulation activation and correcting coagulation factor deficiency.

Meizothrombin: Zymogen or Proteinase? Slow, Ligand-Dependent Equilibration Between Equally Populated Zymogen-Like and Proteinase-Like Forms Explains Its Selectively Anticoagulant Function

Abstract 533Prothrombinase activates prothrombin by catalyzing its ordered proteolysis at Arg320 followed by cleavage at Arg271. Initial cleavage at Arg320 yields the proteinase meizothrombin (mIIa), which accumulates abundantly as an intermediate before its conversion to thrombin (IIa). Although mIIa is a proteinase, it only acts on a limited subset of substrates cleaved by IIa. mIIa is considered an anticoagulant proteinase because it functions efficiently in protein C activation while exhibiting poor clotting activity or reactivity towards antithrombin III. This limited substrate repertoire of mIIa has remained enigmatic and is generally considered to lie in the retention of covalent linkage to the fragment 1.2 (F12) domain allowing for membrane binding. Instead, our recent findings with IIa, illustrating its ligand dependent interconversions between zymogen-like and proteinase-like states, predict that covalent linkage of F12 to the proteinase domain in mIIa would impart it with zymogen-like properties. We produced stable and active mIIa (mIIaQQQ) using a recombinant prothrombin variant in which the bonds susceptible to autolysis were rendered uncleavable by substitution of Arg at 155, 271 and 284 with Gln. Fluorescence stopped flow studies were pursued with the probes dansyl arginine 3-ethyl piperidine amide (DAPA) or Nα-dansyl-(p-guanidino)-L-phenylalanine-piperidide (I-2581) to characterize the binding of ligands to the active site of mIIaQQQ and IIa. Binding to IIa was rapid and consistent with a rate limiting, bimolecular interaction between probe and the active site of the proteinase. In contrast, traces with mIIaQQQ were distinctly biphasic with ∼50% of the fluorescence change occurring on the millisecond timescale followed by a slow second phase (∼50%) that occurred over several seconds. Global fitting indicated that the findings were consistent with a pre-equilibrium between two forms of mIIa, one which binds the active site probe with μM affinity and a second that binds with nM affinity. The two forms interconvert with forward and reverse rate constants of ∼2 s−1. We surmise that these reflect zymogen-like and proteinase-like forms that are equally populated and interconvert slowly with each other in a ligand-dependent fashion. Accordingly, the distributions of the two forms could be altered by ligands established to affect the transition of IIa between zymogen-like and proteinase-like states. The equilibrium distribution was altered to favor the zymogen-like form by decreasing Na+ to 0 at constant ionic strength. In contrast, soluble thrombomodulin (sTM) drove the equilibrium towards the proteinase-like state in a manner consistent with a 1:1 interaction between mIIaQQQ and sTM. Surprisingly, the pre-equilibrium was heavily dependent on covalent linkage with fragment 1 (F1) or its structural integrity. Proteolytic removal of F1, chelation of Ca2+ with EDTA or elimination of 4-carboxyglutamic acid modifications had a profound effect on forcing the enzyme into the proteinase-like state. Thus, the equilibrium distribution of mIIa between zymogen-like and proteinase-like forms is affected by F1 and its Ca2+-stabilized conformation despite the fact that this domain is expected to be distant from the catalytic site. Our findings shed unexpected light into the mechanisms underlying the peculiar activity profile of mIIa relative to IIa. Its ability to interconvert slowly and reversibly between equally populated zymogen-like and proteinase-like states lies at the heart of its properties. By driving it to proteinase, thrombomodulin imparts full activity to mIIa allowing for efficient function in the anticoagulant pathway. In contrast, more weakly binding substrates, inhibitors or ligands will be less effective at perturbing the equilibrium thereby allowing mIIa to persist in blood with reduced activity towards procoagulant substrates. The F1 domain participates in an unexpected way in enforcing these unique features of mIIa. By virtue of its essential role in modulating the equilibrium distribution between zymogen-like and proteinase-like states, we document a new function for F1 in its role as a zymogenizer of mIIa. Disclosures:No relevant conflicts of interest to declare.

Active Site-labeled Prothrombin Inhibits Prothrombinase in Vitro and Thrombosis in Vivo

Mouse and human prothrombin (ProT) active site specifically labeled with D-Phe-Pro-Arg-CH(2)Cl (FPR-ProT) inhibited tissue factor-initiated thrombin generation in platelet-rich and platelet-poor mouse and human plasmas. FPR-prethrombin 1 (Pre 1), fragment 1 (F1), fragment 1.2 (F1.2), and FPR-thrombin produced no significant inhibition, demonstrating the requirement for all three ProT domains. Kinetics of inhibition of ProT activation by the inactive ProT(S195A) mutant were compatible with competitive inhibition as an alternate nonproductive substrate, although FPR-ProT deviated from this mechanism, implicating a more complex process. FPR-ProT exhibited ∼10-fold more potent anticoagulant activity compared with ProT(S195A) as a result of conformational changes in the ProT catalytic domain that induce a more proteinase-like conformation upon FPR labeling. Unlike ProT and ProT(S195A), the pathway of FPR-ProT cleavage by prothrombinase was redirected from meizothrombin toward formation of the FPR-prethrombin 2 (Pre 2)·F1.2 inhibitory intermediate. Localization of ProT labeled with Alexa Fluor® 660 tethered through FPR-CH(2)Cl ([AF660]FPR-ProT) during laser-induced thrombus formation in vivo in murine arterioles was examined in real time wide-field and confocal fluorescence microscopy. [AF660]FPR-ProT bound rapidly to the vessel wall at the site of injury, preceding platelet accumulation, and subsequently to the thrombus proximal, but not distal, to the vessel wall. [AF660]FPR-ProT inhibited thrombus growth, whereas [AF660]FPR-Pre 1, lacking the F1 membrane-binding domain did not bind or inhibit. Labeled F1.2 localized similarly to [AF660]FPR-ProT, indicating binding to phosphatidylserine-rich membranes, but did not inhibit thrombosis. The studies provide new insight into the mechanism of ProT activation in vivo and in vitro, and the properties of a unique exosite-directed prothrombinase inhibitor.

Fate of Membrane-bound Reactants and Products during the Activation of Human Prothrombin by Prothrombinase

Membrane binding by prothrombin, mediated by its N-terminal fragment 1 (F1) domain, plays an essential role in its proteolytic activation by prothrombinase. Thrombin is produced in two cleavage reactions. One at Arg(320) yields the proteinase meizothrombin that retains membrane binding properties. The second, at Arg(271), yields thrombin and severs covalent linkage with the N-terminal fragment 1.2 (F12) region. Covalent linkage with the membrane binding domain is also lost when prethrombin 2 (P2) and F12 are produced following initial cleavage at Arg(271). We show that at the physiological concentration of prothrombin, thrombin formation results in rapid release of the proteinase into solution. Product release from the surface can be explained by the weak interaction between the proteinase and F12 domains. In contrast, the zymogen intermediate P2, formed following cleavage at Arg(271), accumulates on the surface because of a approximately 20-fold higher affinity for F12. By kinetic studies, we show that this enhanced binding adequately explains the ability of unexpectedly low concentrations of F12 to greatly enhance the conversion of P2 to thrombin. Thus, the utilization of all three possible substrate species by prothrombinase is regulated by their ability to bind membranes regardless of whether covalent linkage to the F12 region is maintained. The product, thrombin, interacts with sufficiently poor affinity with F12 so that it is rapidly released from its site of production to participate in its numerous hemostatic functions.

Fate of Membrane-Bound Reactants and Products during Prothrombin Activation by Prothrombinase.

The activation of prothrombin by the prothrombinase complex yields the protease thrombin (IIa) and the activation peptide fragment 1.2 (F1.2). IIa and F1.2 are established to interact noncovalently through the fragment 2 (F2) domain. Since membrane binding is mediated by the fragment 1 domain, the interaction between IIa and F1.2 could allow the newly produced protease to remain bound to the membrane surface and modulate its biological functions. In this case, the feedback action of thrombin to cleave the Arg155-Ser156 site between the F1 and F2 domains would be expected to play a key regulatory role in releasing newly formed thrombin into solution. We have investigated the ability of F1.2 to localize nascent IIa to the membrane surface and the role of IIa-mediated feedback cleavages in regulating this phenomenon. We used a recombinant prothrombin mutant in which the two thrombin cleavage sites were rendered uncleavable by mutation to Gln (IImut), a prothrombin derivative (IIS195A) that yields catalytically inactive product, and a prothrombin derivative IImut/Q271, which yields stable meizothrombin. The binding of IIa and prethrombin 2 (P2) produced from IIS195A to F1.2, examined by isothermal titration calorimetry, yielded: F1.2 plus IIaS195A (Kd 4.5±0.3 μM, n 0.93±0.02, ΔH −13.6±0.4 kcal.mol-1), and F1.2 plus P2S195A (Kd 156±11 nM, n 1.17±0.01, ΔH −28.6±0.2 kcal.mol-1). The relatively weak interaction between IIaS195A and F1.2 indicates that only a modest fraction of IIa will be bound to F1.2 even at the highest possible concentrations achievable in vivo. In contrast, binding of F1.2 to the zymogen P2 is of considerably higher affinity, implying that conversion of zymogen to protease results in a ∼25-fold change in affinity for F1.2 binding. Membrane retention of products during prothrombin activation catalyzed by prothrombinase was studied at the physiologic prothrombin concentration by assessing the fate of membrane-bound species using light scattering correlated with progress curves for cleavage established by SDS-PAGE and quantitative densitometry. In the absence of steps taken to inhibit thrombin produced in situ, prothrombin cleavage by prothrombinase and the associated cleavage of substrate and products by thrombin was accompanied by a rapid decrease in light scattering to a level expected for membrane-bound F1. Surprisingly, similar light scattering profiles were observed in the activation of IImut and IIS195A even in the absence of feedback proteolysis of F1.2. In these cases, the light scattering signal decreased to a level expected for F1.2 bound to membranes and correlated with the appearance of F1.2. In contrast, activation studies with IImut/Q271 revealed that formation of stable meizothrombin as a limiting product produced essentially no decrease in light scattering indicating that this species remains membrane-bound. Thus, covalent linkage with the F1 domain allows meizothrombin to remain membrane bound with potentially modulated function. In addition, the higher affinity interaction between P2 and F1.2 likely plays a very significant role in influencing prothrombinase function under conditions when P2 is produced as an intermediate. In contrast, as a result of the much weaker interaction between IIa and F1.2, membrane binding mediated by F1.2 likely plays a minor role in localizing IIa to the membrane surface during activation of physiological concentrations of prothrombin irrespective of feedback reactions catalyzed by newly formed thrombin.

Phosphatidylserine (PS) Binding Sites in Kringle Modules Regulate the Domain Organization and Conformation of Bovine Prothrombin.

Phosphatidylserine (PS) specifically regulates prothrombin activation during blood coagulation by binding to specific on factor Xa (Koppaka et al. Biochemistry , 7483, 1996) and its cofactor, factor Va (Zhai et al. Biochemistry , 5675, 2002). Binding to PS-containing membranes also alters prothrombin conformation (Lentz et al., Biochemistry , 5460, 1994; Chen et al. ibid . 4701, 1997). We ask here whether specific PS binding sites on prothrombin also control these structural changes, and, if so, where these sites are located. Four methods (Trp fluorescence, circular dichroism [CD], differential scanning calorimetry [DSC], and quasi-elastic light scattering [QELS]) were used to define the structural consequences of soluble 1,2-dicaproyl-sn-glycero-3-phospho-L-serine; (C6PS) binding both to whole prothrombin and to its proteolytically generated fragments. Intrinsic fluorescence titrations suggested the existence of two linked C6PS binding sites in fragment 1.2 (F1.2) and prethrombin 1, both of which contain prothrombin's kringle pair. The existence of two sites was supported by direct equilibrium binding measurements with F1.2. CD measurements at increasing C6PS concentrations with both F1.2 and the kringle pair (F1.2 minus the γ-carboxy-glutamic acid [GLA] domain) were consistent with formation of a structure akin to an anti-parallel β sheet. Thermal denaturation profiles of F1.2 suggested calcium-independent, C6PS-induced domain reorganization within this fragment. Denaturation profiles and Trp fluorescence of the N-terminal, membrane binding domain (F1) and fragment 2 (F2) did not reveal any C6PS-induced changes. F2 consists mainly of the second cys-rich kringle module. The hydrodynamic radius of prothrombin was also found to decrease substantially (from 3.3 nm to 2.6 nm) in the presence of saturating (1mM) C6PS. Other lipids (phosphatidylglycerol and phosphatidyl-D-serine) did bind to prothrombin but did not produce comparable structural changes. The results show that C6PS 1) binds specifically to linked, calcium-independent sites within prothrombin's two kringle domains and 2) induces thereby a conformational reorganization in the whole molecule. Supported by USPHS grant HL072827 to BRL.

Role of Prothrombin Fragment 1 in the Pathway of Regulatory Exosite I Formation during Conversion of Human Prothrombin to Thrombin

Prothrombin (Pro) activation by factor Xa generates the thrombin catalytic site and exosites I and II. The role of fragment 1 (F1) in the pathway of exosite I expression during Pro activation was characterized in equilibrium binding studies using hirudin(54-65) labeled with 6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoate ([NBD]Hir(54-65)(SO3-)) or 5-(carboxy)fluorescein ([5F]Hir(54-65)(SO3-)). [NBD]Hir(54-65)(SO3-) distinguished exosite I environments on Pro, prethrombin 1 (Pre 1), and prethrombin 2 (Pre 2) but bound with the same affinities as [5F]Hir(54-65)(SO3-). Conversion of Pro to Pre 1 caused a 7-fold increase in affinity for the peptides. Conversely, fragment 1.2 (F1.2) decreased the affinity of Pre 2 for [5F]Hir(54-65)(SO3-) by 3-fold. This was correlated with a 16-fold increased affinity of F1.2 for Pre 2 in comparison to thrombin, demonstrating an enhancing effect of F1 on F1.2 binding. The active intermediate, meizothrombin, demonstrated a 50- to 220-fold increase in exosite affinity. Free thrombin and thrombin.F1.2 complex bound [5F]Hir(54-65)(SO3-) with indistinguishable affinity, indicating that the effect of F1 on peptide binding was eliminated upon expression of catalytic activity and exosite I. The results demonstrate a new zymogen-specific role for F1 in modulating the affinity of ligands for exosite I. This may reflect a direct interaction between the F1 and Pre 2 domains in Pro that is lost upon folding of the zymogen activation domain. The effect of F1 on (pro)exosite I and the role of (pro)exosite I in factor Va-dependent substrate recognition suggest that the Pro activation pathway may be regulated by (pro)exosite I interactions with factor Va.

Effects of Activation Peptide Bond Cleavage and Fragment 2 Interactions on the Pathway of Exosite I Expression during Activation of Human Prethrombin 1 to Thrombin

Activation of prothrombin (Pro) by factor Xa to form thrombin occurs by proteolysis of Arg271-Thr272 and Arg320-Ile321, resulting in expression of regulatory exosites I and II. Cleavage of Pro by thrombin liberates fragment 1 and generates the zymogen analog, prethrombin 1 (Pre 1). The properties of exosite I on Pre 1 and its factor Xa activation intermediates were characterized in spectroscopic and equilibrium binding studies using the fluorescein-labeled probe, hirudin(54-65) ([5F]Hir(54-65)-(SO3-)). Prethrombin 2 (Pre 2), formed by factor Xa cleavage of Pre 1 at Arg271-Thr272, had the same affinity for hirudin(54-65) peptides as Pre 1 in the absence or presence of near-saturating fragment 2 (F2). Pre 2 and thrombin also had indistinguishable affinities for F2. By contrast, cleavage of Pre 1 at Arg320-Ile321, to form active meizothrombin des-fragment 1 MzT(-F1), showed a 11- to 20-fold increase in affinity for hirudin(54-65), indistinguishable from the 13- to 20-fold increase seen for conversion of Pre 2 to thrombin. Thus, factor Xa cleavage of Pre 1 at Arg271-Thr272 does not effect exosite I expression, whereas cleavage at Arg320-Ile321 results in concomitant activation of the catalytic site and exosite I. Furthermore, expression of exosite I on the Pre 1 activation intermediates is not modulated by F2, and exosite II is not activated conformationally. The differential expression of exosite I affinity on the Pre 1 activation intermediates and the previously demonstrated role of (pro)exosite I in factor Va-dependent substrate recognition suggest that changes in exosite I expression may regulate the rate and direction of the Pre 1 activation pathway.

A peptide derived from human prothrombin fragment 2 inhibits prothrombinase and angiogenesis

We constructed the synthetic peptide library representing human prothrombin fragment 2 (F2) sequence and explored the inhibitory sequence for prothrombinase, which was reconstituted in vitro by adding factor Xa, factor Va, and calcium into phospholipids. The nonapeptide NSAVLQVEN (NSA9) suppressed prothrombinase reconstituted not only on phospholipid vesicles but also on the bovine capillary endothelial (BCE) cell surface. Kinetic analyses demonstrated that NSA9 is a mixed-type inhibitor of Xa. Furthermore, the nonapeptide inhibited the proliferation of BCE cells and also suppressed angiogenesis in chicken embryos. The inhibitory activities of NSA9 were abrogated by pre-incubation with anti-F2 monoclonal antibody, 4E7. These data demonstrate that anti-angiogenic activity of F2 may be related to its ability to inhibit prothrombinase.

Effect of prothrombin and its activation fragments on calcium oxalate crystal growth and aggregation in undiluted human urine in vitro: relationship between protein structure and inhibitory activity

In recent years there has been great interest in the putative role of prothrombin and its activation peptides, especially the urinary form of prothrombin fragment 1, in the pathogenesis of calcium oxalate (CaOx) urolithiasis. Previously, we showed that prothrombin and its activation peptides inhibit CaOx crystallization in inorganic conditions in vitro. The aim of the present study was to determine if this inhibitory activity is retained in undiluted human urine and, therefore, whether it is likely to have any influence under physiological conditions. A secondary objective was to assess the relationship between the structures of the proteins and their inhibitory activities. Prothrombin was purified from Prothrombinex-HT, cleaved with thrombin and the resulting fragment 1 (F1) and fragment 2 (F2) were purified. The purity of each protein was confirmed by SDS/PAGE, and their effects on CaOx crystallization in undiluted ultrafiltered human urine were determined at a final concentration 80.65 nmol/l using Coulter Counter and [(14)C]oxalate analysis. The precipitated crystals were visualized using scanning electron microscopy. The Coulter Counter data revealed that, whereas prothrombin and its activation peptides did not affect the urinary metastable limit and the size of the precipitated particles, F1 did significantly reduce the latter. These findings were corroborated with scanning electron microscopy which also revealed that the reduction in particle size caused by F1 resulted from a decrease in the degree of crystal aggregation, rather than in the size of the individual crystals. The [(14)C]oxalate data showed that none of the proteins added significantly inhibited the mineral deposition. It was concluded that with the exception of F1, which does inhibit CaOx crystal aggregation, prothrombin and its activation peptides do not alter the deposition and aggregation of CaOx crystals in ultrafiltered human urine in vitro. Also, the gamma-carboxyglutamic acid domain of prothrombin and F1, which is absent from thrombin and F2, is the region of the molecules that determines their potent inhibitory effects. The superior potency of F1, compared with prothrombin, probably results from the molecule's greater charge-to-mass ratio.

A simple strategy for breakpoint fragment determination in chronic myeloid leukemia

Molecular characterization is considered a part of the routine work-up of chronic myeloid leukemia (CML) cases. Southern blot analysis using the universal BCR (UBCR) probe on BglII-digested DNA samples is the most commonly used technique, while employing the human 3′ bcr probe (PR-1) is usually considered a complementary tool. In this study, we tried to develop a simple and economic strategy for molecular characterization of CML using the 3′ probe as it has been shown to be the one capable of locating the breakpoint site. Seventy-eight cases of CML were studied. Molecular analysis was performed using the Southern blot technique. DNA was digested with Bam HI, BglII, EcoRI, and XbaI. Hybridization was performed using the human 3′ bcr (PR-1) probe. BamHI and BglII could differentiate fragment 1 (F1) showing rearrangement (R) with Bam HI and germline configuration (G) with BglII; F2/3 showing R with both, and F4 showing R with BamHI and G with BglII. F2/3 cases were further divided by HindIII enzyme into F2 showing (G) and F3 showing (R). Fragment 0 showed G with both, but R with EcoRI and/or XbaI, while 3′ deletion gave G with all four enzymes. Our results showed a relative incidence of 6.4% for F0, 20.5% for F1, 32.1% for F2, 19.2% for F3, 15.4% for F4, and 6.4% for 3′ deletion. Sixty cases were evaluated clinically and hematologically and were followed up for disease evolution and survival. They included 32 cases in early chronic phase, 24 in late chronic phase, two in acceleration, and two in blastic crisis. No significant correlation was encountered between the breakpoint site and any of the clinical and hematological data except those patients with 3′ deletion who showed a very short survival. The study emphasizes Southern blotting as the method of choice for molecular characterization of CML and offers a simple and economic strategy for diagnosis and determination of breakpoint fragment.

Inhibition of calcium oxalate crystal growth and aggregation by prothrombin and its fragments in vitro: relationship between protein structure and inhibitory activity.

During blood coagulation, prothrombin (PT) is ultimately degraded to three fragments, thrombin, fragment 1 (F1) and fragment 2 (F2), which, collectively, contain all of the structural features of PT. One of these fragments, F1, is excreted in human urine and is the principal protein occluded into calcium oxalate (CaOx) crystals precipitated from it. This urinary form of F1, which we have named urinary prothrombin fragment 1 is present in calcium stones and is a potent inhibitor of CaOx crystallization in urine in vitro. The aim of this study was to determine whether PT itself and its other activation products, namely, thrombin, F1 and F2 also inhibit CaOx crystallization, by comparing their effects in a seeded, inorganic crystallization system. A secondary objective was to assess the relationship between the structures of the proteins and their inhibitory activities. PT was isolated from a human blood concentrate rich in vitamin K-dependent proteins. Following initial cleavage by thrombin, the resulting fragments, F1 and F2, were purified by a combination of reversed phase HPLC and low pressure column chromatography. The purity of the proteins was confirmed by SDS/PAGE and their individual effects on CaOx crystallization were determined at the same concentration (16.13 nM) in a seeded, metastable solution of CaOx using a Coulter Counter. [14C]Oxalate was used to assess deposition of CaOx and crystals were visualized using scanning electron microscopy. The Coulter Counter data revealed that the proteins reduced the size of precipitated crystals in the order F1 > PT > F2 > thrombin. These findings were confirmed by scanning electron microscopy which showed that the reduction in particle size resulted from a decrease in the degree of crystal aggregation. [14C]Oxalate analysis demonstrated that all proteins inhibited mineral deposition, in the order F1 (44%) > PT (27.4%) > thrombin (10.2%) > F2 (6.5%). It was concluded that the gamma-carboxyglutamic acid domain of PT and F1, which is absent from thrombin and F2, is the region of the molecules which determines their potent inhibitory effects. The superior potency of F1, in comparison with PT, probably results from the molecule's greater charge to mass ratio.

Identification of structural domains in inter-α-trypsin inhibitor involved in calcium oxalate crystallization

The urinary glycoprotein that inhibits calcium oxalate (CaOx) crystallization in vitro shows a structural similarity to urinary trypsin inhibitor (UTI; recently termed bikunin), the light chain of inter-alpha-trypsin inhibitor (I alpha I). The functional domains of I alpha I involved in its inhibitory activity of CaOx crystallization have been investigated using isolated intact domains of I alpha I produced from controlled proteolytic digests of the protein. The fragments investigated include the heavy chains of I alpha I, UTI, chondroitinase AC-treated UTI, and the carboxyl-terminal domain of UTI (termed HI-8). The effects of I alpha I and its fragments on the inhibitory activity of CaOx crystallization were evaluated in vitro using CaOx crystal aggregation and growth assays, and seeded crystal generation assay as well as using crystal matrix protein generation assay. UTI, but not the heavy chains of I alpha I, had a discernible effect on CaOx crystallization inhibitory activity. Less requirement of the carbohydrate moiety of UTI is implicated by the observation that chondroitinase AC-treated UTI fragment was also found to inhibit CaOx crystallization with almost the same activity as UTI. HI-8 also efficiently inhibited CaOx crystallization, while I alpha I showed a weak inhibitory activity. The results are almost consistent with a seed crystal generation assay and a crystal adsorption inhibition assay, in which I alpha I or its derivatives inhibits prothrombin fragment 1 (F1) adsorption to CaOx crystals. In conclusion, these results suggest that the part of the I alpha I protein responsible for inhibition of CaOx crystallization is the carboxyl-terminal domain of UTI.

Localization of the Thrombin-binding Domain on Prothrombin Fragment 2

Co-crystallographic studies have shown that the interaction of human prothrombin fragment 2 (F2) with thrombin involves the formation of salt bridges between the kringle inner loop of F2 and anion-binding exosite II of thrombin. When F2 binds to thrombin, it has been shown to evoke conformational changes at the active site and at exosite I of the enzyme. Using plasma, recombinant, and synthetic F2 peptides (F2, rF2, and sF2, respectively) we have further localized the thrombin-binding domain on F2. F2, rF2-(1-116), rF2-(55-116), and sF2-(63-116), all of which contain the kringle inner loop (residues 64-93) and the acidic COOH-terminal connecting peptide (residues 94-116), bind to thrombin-agarose. In contrast, analogues of the kringle inner loop, sF2-(63-90), or the COOH-terminal connecting peptide, sF2-(92-116), do not bind. Thus, contrary to predictions from the crystal structure, the COOH-terminal connecting peptide as well as the kringle inner loop are involved in the interaction of F2 with thrombin. F2 and sF2-(63-116) bind saturably to fluorescently labeled active site-blocked thrombin with Kd values of 4.1 and 51.3 microM, respectively. The affinity of sF2-(63-116) for thrombin increases about 5-fold (Kd = 10 microM) when Val at position 78 is substituted with Glu. F2 and sF2-(63-116) bind to exosite II on thrombin because both reduce the heparin-catalyzed rate of thrombin inhibition by antithrombin approximately 4-fold. In contrast, only F2 slows the uncatalyzed rate of thrombin inactivation by antithrombin. Like F2, sF2-(63-116) induces allosteric changes in the active site and exosite I of thrombin because it alters the rates of thrombin-mediated hydrolysis of chromogenic substrates and displaces fluorescently labeled hirudin54-65 from active site-blocked thrombin, respectively. Both peptides also prolong the thrombin clotting time of fibrinogen in a concentration-dependent fashion, reflecting their effects on the active site and/or exosite I. These studies provide further insight into the regions of F2 that evoke functional changes in thrombin.

Autocatalytic peptide bond cleavages in prothrombin and meizothrombin.

During factor Xa-catalyzed prothrombin activation, several other reaction products accumulate as a result of proteolysis of prothrombin and its activation products by thrombin and meizothrombin. Gel electrophoretic analysis and N-terminal sequencing of reaction products showed that in the absence of Ca2+ ions thrombin cleaved the following peptide bonds: Arg51-Thr52/Arg54-Asp55 in the fragment 1 (F1) domain (k = 0.4 x 10(4) M-1 s-1), Arg155-Ser156 in prothrombin (k = 2 x 10(4) M-1 s-1), and Arg284-Thr285 in prethrombin 1 (k = 0.02 x 10(4) M-1 s-1). In the presence of 2.5 mM CaCl2, cleavage in fragment 1 (Arg51-Thr52/Arg54-Asp55) was not detectable, whereas cleavage at Arg155-Ser156 (i.e., removal of F1) was inhibited 25-fold. Cleavage at Arg284-Thr285 (formation of prethrombin 2 des-1-13) was not affected by the presence of Ca2+ ions. Meizothrombin rapidly converted itself into meizothrombin des-F1. The half-life (t1/2 = approximately 30 s) of this reaction was independent of the meizothrombin concentration (0.1-1 microM meizothrombin), which is indicative for intramolecular autocatalysis (k = 0.02 s-1 in the presence of 2.5 mM Ca2+ ions). Since the rapid removal of fragment 1 precludes investigations of the cleavage at Arg284-Thr285 in intact meizothrombin, we analyzed the cleavage of this peptide bond in R155A-meizothrombin, a recombinant product that is resistant to autocatalytic removal of the fragment 1 domain. In the absence of phospholipids, R155A-meizothrombin converted itself into thrombin des-1-13 by a combination of intramolecular (k = 0.8 x 10(-4) s-1) and intermolecular autocatalysis (k = 0.2 x 10(3) M-1 s-1). Intramolecular autocatalytic conversion of R155A-meizothrombin into thrombin was not affected by the presence of phospholipids (k = 0.8 x 10(-4) s-1), whereas intermolecular autocatalysis was accelerated 25-fold (k = 5.6 x 10(3) M-1 s-1) by phospholipid vesicles. Since factor Xa/Va-catalyzed conversion of meizothrombin into thrombin occurs with k = 5.5 x 10(8) M-1 s-1, we conclude that in reaction systems containing purified proteins autocatalysis of meizothrombin hardly contributes to thrombin formation during factor Xa-catalyzed prothrombin activation.

New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK.

The conversion of prothrombin to thrombin by factor Xa is the penultimate step in the blood clotting cascade. In vivo, where the conversion occurs primarily on activated platelets in association with factor Va and Ca2+ ions, meizothrombin is the major intermediate of the two step reaction. Meizothrombin rapidly loses the fragment 1 domain (F1) by autolysis to become meizothrombin des F1 (mzTBN-F1). The physiological properties of mzTBN-F1 differ dramatically from those of thrombin due to the presence of prothrombin fragment 2 (F2), which remains covalently attached to the activated thrombin domain in mzTBN-F1. The crystal structure of mzTBN-F1 has been determined at 3.1 A resolution by molecular replacement, using only the thrombin domain, and refined to R and Rfree values of 0.205 and 0.242, respectively. The protease active site was inhibited with D-Phe-Pro-Arg-chloromethylketone (PPACK) to reduce autolysis. The mobile linker chain connecting the so-called kringle and thrombin domains and the first two N-acetylglucosamine residues attached to the latter were seen in electron-density maps improved with the program SQUASH. Previously these regions had only been modeled. The F2 kringle domain in mzTBN-F1 is bound to the electropositive heparin-binding site on thrombin in an orientation that is systematically shifted and has significantly more interdomain contacts compared to a noncovalent complex of free F2 and free thrombin. F2 in mzTBN-F1 forms novel hydrogen bonds to the carbohydrate chain of thrombin and perhaps stabilizes a unique, rigid conformation of the gamma-autolysis loop through non-local effects. The F2 linker chain, which does not interfere with the active site or fibrinogen-recognition site, is arranged so that the two sites cleaved by factor Xa are separated by 36 A. The two mzTBN-F1 molecules in the asymmetric unit share a tight 'dimer' contact in which the active site of one molecule is partially blocked by the F2 kringle domain of its partner. This interaction suggests a new model for prothrombin organization.

Blood coagulation proteins and urolithiasis are linked: crystal matrix protein is the F1 activation peptide of human prothrombin.

To determine the relationship between prothrombin and crystal matrix protein (CMP). CMP is the predominant protein found in the organic matrix of calcium oxalate (CaOx) crystals generated from human urine and is a 31 kDa glycoprotein, whose N-terminal amino acid sequence shares homology with human prothrombin. CaOx crystallization was induced in ultrafiltered (UF) human urine containing either plasma or serum derived from the same healthy donor, by the addition of sodium oxalate. The crystals were demineralized and the resulting protein extracts analysed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting, using antibodies raised against human prothrombin and the C-terminus of prothrombin fragment 1 + 2 (F1 + 2). Prothrombin was detected in extracts of crystals precipitated from the UF urine in the presence of plasma, while CMP was completely absent. Crystals precipitated from UF urine supplemented with serum contained relatively large amounts of F1 + 2 and a protein with the same electrophoretic mobility as CMP. Analysis of a standard preparation of F1 + 2 which also contained prothrombin fragment 1 (F1) as a minor contaminant, showed a protein with electrophoretic and staining properties comparable to CMP. CMP is a urinary form of F1, a degradation product of prothrombin possessing the domain rich in gamma-carboxyglutamic acid, which may have undergone some molecular modification either before or after its release into the urine.

Calcium oxalate crystal matrix extract: the most potent macromolecular inhibitor of crystal growth and aggregation yet tested in undiluted human urine in vitro.

Demineralization of calcium oxalate (CaOx) crystals precipitated from human urine in vitro yields an organic crystal matrix extract (CME) consisting predominantly of a single protein which we originally named crystal matrix protein but have subsequently shown to be a urinary form of prothrombin activation peptide fragment 1 (F1). The aim of this study was to determine whether CME is a promoter or inhibitor of CaOx crystallization. The effect of CME on CaOx crystal growth and aggregation was tested using a standard seeded crystallization system, and its effect quantified by use of particle size analysis and a computer model. In addition, the effect of CME on the crystallization of CaOx was tested in undiluted, ultrafiltered human urine using Coulter Counter analysis and scanning electron microscopy. It was shown that CME is a potent inhibitor of CaOx crystal growth and aggregation in a seeded metastable solution. However, of greater significance is that at a concentration of 10 mg/l it completely reversed the formation of large crystalline aggregates that form upon the removal of urinary macromolecules from undiluted urine. It was concluded that CME is the most potent macromolecular urinary inhibitor yet to be tested in urine in vitro. By preventing the aggregation of newly formed crystals, the components of CME may significantly reduce the probability of particle retention in vivo and therefore the occurrence of urolithiasis.

Activation-induced exposure of the thrombin anion-binding exosite. Interactions of recombinant mutant prothrombins with thrombomodulin and a thrombin exosite-specific antibody.

The activation of serine protease zymogens involves conformational changes that increase the affinity of substrate binding and the activity of the catalytic center. The activation of prothrombin is particularly complex and requires several cleavages in the proenzyme region in addition to the conserved activation cleavage after Arg320. To understand how these cleavages lead to the exposure of the thrombin anion-binding exosite, a major macromolecular recognition site, interactions of recombinant human prothrombin derivatives with thrombomodulin, and an exosite-specific antibody were studied by competition binding and immunoprecipitation. By either method, the anion-binding exosite is not functional on prethrombin 2, which is cleaved after Arg271 and lacks fragment 1.2, nor on meizothrombin, which is cleaved only after Arg320. In contrast, the exosite is fully exposed on meizothrombin des-F1, which is cleaved after both Arg320 and Arg155 and therefore lacks amino-terminal fragment 1 (F1). Thus, two events are required to create the exosite. First, cleavage after Arg320 causes conformational changes that are much more extensive than those accompanying the activation of trypsinogen. Second, removal of amino-terminal F1 is necessary, perhaps to relieve steric hindrance. These results indicate that the F1 fragment regulates access to the thrombin exosite. The properties of meizothrombin des-F1 suggest that this prothrombin derivative could have a biological function.