Dependence of the rate of thrombin/antithrombin III reaction upon the turnover rate of a catalytic amount of heparin

Commercially available heparin preparations slightly enhanced the rate of thrombin/antithrombin (AT) III reaction at pH 6.05 in the absence of NaCl. However, this accelerative activity was significantly lower than that induced by heparin with high affinity for AT III (HA-heparin), probably due to the formation of the binary complexes of HA-heparin-AT III as well as that composed of thrombin and heparin with low affinity for AT III (LA-heparin). The HA-heparin-catalyzed thrombin/AT III reaction was faster in the presence of 0.1 M NaCl at pH 6.05 than that in the absence of the salt. LA-heparin and dextran sulfate (DS) were also found to accelerate the thrombin/AT III reaction rate, but neither substance catalyzed the formation of the complex in the presence of 0.1 M NaCl at pH 7.4. LA-heparin was also confirmed to compete with HA-heparin for enhancement of the thrombin/AT III reaction. Thus, it appears that AT III tends to form a ternary complex with the thrombin-DS or thrombin-LA-heparin complex, even in the presence of 0.1 M NaCl, whereas factor Xa reacts with the AT III-DS or AT III-LA-heparin complex. These results indicate that HA-heparin is the only substance having the ability to catalyze the thrombin/AT III reaction, and that its turnover rate is markedly elevated in the presence of strongly electropositive and electronegative ions because of the decreased affinity of the enzyme for heparin under such conditions.     

Role of crosslinked protein in lung injury following total body irradiation and bone marrow transplantation

The aberrant protein crosslinks formation during lung injury as results total body irradiation (TBI) and bone marrow transplantation (BMT) therapy has been examined as apossible contributory factor in organ or tissue pathogenesis. Female C3HeB/ FeJ mice were used for an experimental animal. Carbon monoxide uptake (V(CO)) was measured at 1, 2, 3, 4 and 5 months after TBI at respective doses of 12, 14, 16 and 18 Gy 16 h prior to syngeneic BMT. Also as a measure of aberrant protein crosslinking in the inured tissues, transglutaminase (TGase)-activities and crosslinked protein were examined along with thrombin, a protease known to activate TGases. Reductions of VCO were detected following TBI and BMT. Activities of thrombin and TGase 1, and crosslinked protein in bronchoalveolar lavage (BAL) fluid of the mice 1 wk after TBI at 12 Gy and BMT were identified and found to be elevated in the treated animals. These findings suggest that elevated levels of crosslinked proteins and TGase I in the bronchoalveolar larvage during the lung injury could have enhanced the organ pathogenesis following TBI and BMT.     

Synergistic effect of antithrombin III, activated protein C and heparin on the inhibition of the tissue thromboplastin-mediated coagulation

The synergistic effect of antithrombin III (ATIII), activated protein C (APC) and heparin on the tissue thromboplastin (TP)-mediated coagulation cascade was studied. APC prolonged the activated partial thromboplastin time of human plasma with increasing APC concentration but affected the prothrombin time only slightly. Neither ATIII nor heparin prolonged the prothrombin time by itself, while a mixture of APC and heparin strongly inhibited the coagulation. When the effects of APC, heparin and ATIII on the TP-mediated coagulation were examined with a solution consisting of prothrombin, factor V, factor VII, factor X and fibrinogen at physiological concentrations, the coagulation time was prolonged only slightly by the APC-heparin or ATIII-heparin mixture. However, the coagulation time was prolonged markedly by simultaneous addition of APC, ATIII and heparin to the solution. Inhibition of thrombin activity by the ATIII-APC-heparin mixture was weak as compared with that by the ATIII-heparin mixture after a 1-min incubation, but after a 2-min incubation the inhibitory activities were equal. Suppression of thrombin activity by the ATIII-APC-heparin mixture was supposed to be due to the inhibition of the interaction between ATIII and heparin on thrombin by APC because the APC-ATIII-heparin complex was detected by crossed immuno-electrophoresis but not by sodium dodecyl sulfate (SDS)-polyacrylamide electrophoresis. When the inhibitory effect of APC alone or the APC-heparin mixture on the platelet prothrombin converting activity (PPCA) was examined, heparin accelerated the PPCA inhibition by APC.(ABSTRACT TRUNCATED AT 250 WORDS)     

Aptamer-capped nanocrystal quantum dots: a new method for label-free protein detection

We demonstrate that aptamer-capped near-infrared PbS quantum dots (QDs) can detect a target protein based on selective charge transfer. The water-soluble QDs are synthesized with the thrombin-binding aptamer, which retains the secondary quadruplex structure necessary for binding to thrombin. These QDs have diameters of 3-6 nm and fluoresce around 1050 nm. When the aptamer-functionalized QD binds to its target, a fluorescence quenching occurs due to charge transfer from amine groups on the protein to the QD. Thrombin is detected within 1 min with a detection limit of approximately 1 nM. This selective detection is observed even in the presence of high background concentrations of interfering negatively or positively charged proteins, suggesting that aptamer-capped QDs could be useful for label-free protein assays.     

Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate

Two routes for the de novo biosynthesis of pyridoxal-5'-phosphate (PLP) have been discovered and reconstituted in vitro. The most common pathway that organisms use is dependent upon the activity of just two enzymes, known as Pdx1 (YaaD) and Pdx2 (YaaE) in bacteria. Pdx2 has been shown to have glutaminase activity and most likely channels ammonia to the active site of the PLP synthase subunit, Pdx1, where ribose-5-phosphate (R5P), glyceraldehyde-3-phosphate (G3P), and ammonia are condensed in a complex series of reactions. In this report we investigated the early steps in the mechanism of PLP formation. Under pre-steady-state conditions, a chromophoric intermediate (I320) is observed that accumulates upon addition of only two of the substrates, R5P and glutamine. The intermediate is covalently bound to the protein. We synthesized C5 monodeuterio (pro-R, pro-S) and dideuterio R5P and showed that there is a primary kinetic isotope effect on the formation of this intermediate using the pro-R but not the pro-S labeled isomer. Furthermore, it was shown that the phosphate unit of R5P is eliminated rather than hydrolyzed in route to intermediate formation and also that there is an observed C5-deuterium kinetic isotope effect on this elimination step. Interestingly, it was observed that the formation of the intermediate could be triggered in the absence of Pdx2 by the addition of high concentrations of NH4Cl to a preincubated solution of Pdx1 and R5P. The formation of I320 was also monitored using high-resolution electrospray ionization Fourier transform mass spectrometry and revealed a species of mass 34,304 Da (Pdx1 + 95 Da). These results allow us to narrow the mechanistic possibilities for the complex series of reactions involved in PLP formation.     

Change of viscoelastic property and morphology of fibrin affected by antithrombin III and heparin: QCM-Z and AFM study

Viscoelastic property and morphology of fibrin, which is caused by the enzymatic action of thrombin on fibrinogen, was studied quantitatively as a function of antithrombin III (AT) and heparin concentration by adding fibrinogen, heparin, AT, and thrombin, sequentially. A quartz crystal microbalance with impedance analysis (QCM-Z) was used to detect the change of viscoelastic properties as well as the thickness of adsorbed layer during fibrin formation process, while AFM was used to characterize the surface morphology of fibrin layer under the influence of two known anticoagulants. By the addition of fibrinogen initially, a rigid and thin fibrinogen layer with rather smooth surface morphology was formed on the substrate. Then, the addition of thrombin in the absence of AT and heparin, resulted in viscous and thick fibrin gel with textured surface morphology. As an anticoagulant, AT was added before the injection of thrombin, but AT in the absence of heparin showed only marginal effects at higher concentration of AT than that of thrombin. On the contrary, the thick and viscous fibrin layer was altered gradually to more fibrinogen-like layer as the heparin concentration increases at low concentrations of AT, demonstrating the powerful anticoagulant effect by heparin/AT complex. Interestingly, heparin alone without AT was also effective in preventing fibrin formation, influencing the viscoelastic property and morphology of fibrin.     

Separation of antithrombin III variants by micellar electrokinetic chromatography

The characterisation of proteins is still one of the most challenging analytical tasks in modern bioanalysis. Due to the complex structure of proteins, several analytical techniques are often required to get sufficient information. Antithrombin III (AT III), a high-molecular-mass plasma glycoprotein which is an important protease inhibitor and the main modulator of thrombin activity, circulates in plasma in two isoforms, the so-called AT III-alpha (90-95%) and -beta (5-10%). Micellar electrokinetic chromatography was used to analytically separate these AT III variants, which differ in their affinity to the polysaccharide heparin.     

Effect of protein content on the surface activity and viscosity of emulsan

Emulsan, produced byAcinetobacter calcoaceticus RAG-1, consists of a lipoheteropolysaccharide-protein complex. The amount of protein in the complex depends on the purification procedure. Maximum hexadecane-in-water emulsifying activity of emulsan was obtained with preparations containing 8–16 % protein. Neither deproteinized preparations (apoemulsan) nor protein-rich preparations emulsified hexadecane-in-water; however, mixtures of these preparations (containing 10–15 % total protein) were potent emulsifiers.Emulsifying activity was also obtained with a mixture of apoemulsan and polysaccharide-free emulsan protein. The stimulatory role of protein in the activity of emulsan was also demonstrated by pronase treatment of the complex. The presence of protein in the complex was important for lowering interfacial tension between hexadecane and water. Apoemulsan solutions showed _i values of 30 mN/m whereas, emulsan containing more than 6% protein showed values of 13–15 mN/m. Viscosity studies showed that: (i) The higher the protein content in the complex, the lower its intrinsic viscosity, indicating that association of protein with the polysaccharide backbone results in less extended conformation; (ii) the complex appears to be stable between 30 ° and 80 °C; and (iii) mixtures of apoemulsan and emulsan had intrinsic viscosities close to the value predicted from addition of the weight-fraction contribution of the individual components. The synergistic emulsifying activity of emulsan mixtures is explained in terms of surface tension lowering by the protein component and formation of stable interfacial films by the high molecular weight polysaccharide component.Preliminary results of this work were presented at the 5th International Conference on Surface and Colloid Science, Potsdam, N.Y., June 1985.     

Quantitation of femtomolar protein levels via direct readout with the electrochemical proximity assay

We have developed a separation-free, electrochemical assay format with direct readout that is amenable to highly sensitive and selective quantitation of a wide variety of target proteins. Our first generation of the electrochemical proximity assay (ECPA) is composed of two thrombin aptamers which form a cooperative complex only in the presence of target molecules, moving a methylene blue (MB)-conjugated oligonucleotide close to a gold electrode. Without washing steps, electrical current is increased in proportion to the concentration of a specific target protein. By employing a DNA-based experimental model with the aptamer system, we show that addition of a short DNA competitor can reduce background current of the MB peak to baseline levels. As such, the detection limit of aptamer-based ECPA for human thrombin was 50 pM via direct readout. The dual-probe nature of ECPA gave high selectivity and 93% recovery of signal from 2.5 nM thrombin in 2% bovine serum albumin (BSA). To greatly improve the flexibility of ECPA, we then proved the system functional with antibody-oligonucleotide conjugates as probes; the insulin detection limit was 128 fM with a dynamic range of over 4 orders of magnitude in concentration, again with high assay selectivity. ECPA thus allows separation-free, highly sensitive, and highly selective protein detection with a direct electrochemical readout. This method is extremely flexible, capable of detecting a wide variety of protein targets, and is amenable to point-of-care protein measurement, since any target with two aptamers or antibodies could be assayed via direct electrochemical readout.     

合成条件对磷钨杂多酸季铵盐催化剂性能的影响

 采用廉价的季铵盐［C16H33(CH3)3(70%)+C18H37(CH3)3(30%)］N+Cl-(简记为Q+Cl-)代替［C5H5NC16H33］+Cl-作为相转移剂,制备了一种新型的反应控制相转移催化剂,详细考察了制备过程中各因素对催化剂性能的影响,确定了适宜的催化剂制备条件,同时对催化剂的 31P NMR上的各峰进行了归属. 研究结果表明,在1-辛烯环氧化反应中,催化剂各组分在双氧水作用下能够相互转化形成合适比例的多组分复合催化剂,催化活性较高,但任一组分单独作用时催化活性则较低.     

Characterization of protein contributions to cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase by using photolysis in the ternary complex

Protein contributions to the substrate-triggered cleavage of the cobalt-carbon (Co-C) bond and formation of the cob(II)alamin-5'-deoxyadenosyl radical pair in the adenosylcobalamin (AdoCbl)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been studied by using pulsed-laser photolysis of AdoCbl in the EAL-AdoCbl-substrate ternary complex, and time-resolved probing of the photoproduct dynamics by using ultraviolet-visible absorption spectroscopy on the 10(-7)-10(-1) s time scale. Experiments were performed in a fluid dimethylsulfoxide/water cryosolvent system at 240 K, under conditions of kinetic competence for thermal cleavage of the Co-C bond in the ternary complex. The static ultraviolet-visible absorption spectra of holo-EAL and ternary complex are comparable, indicating that the binding of substrate does not labilize the cofactor cobalt-carbon (Co-C) bond by significantly distorting the equilibrium AdoCbl structure. Photolysis of AdoCbl in EAL at 240 K leads to cob(II)alamin-5'-deoxyadenosyl radical pair quantum yields of <0.01 at 10(-6) s in both holo-EAL and ternary complex. Three photoproduct states are populated following a saturating laser pulse, and labeled, P(f), P(s), and P(c). The relative amplitudes and first-order recombination rate constants of P(f) (0.4-0.6; 40-50 s(-1)), P(s) (0.3-0.4; 4 s(-1)), and P(c) (0.1-0.2; 0) are comparable in holo-EAL and in the ternary complex. Time-resolved, full-spectrum electron paramagnetic resonance (EPR) spectroscopy shows that visible irradiation alters neither the kinetics of thermal cob(II)alamin-substrate radical pair formation, nor the equilibrium between ternary complex and cob(II)alamin-substrate radical pair, at 246 K. The results indicate that substrate binding to holo-EAL does not "switch" the protein to a new structural state, which promptly stabilizes the cob(II)alamin-5'-deoxyadenosyl radical pair photoproduct, either through an increased barrier to recombination, a decreased barrier to further radical pair separation, or lowering of the radical pair state free energy, or a combination of these effects. Therefore, we conclude that such a change in protein structure, which is independent of changes in the AdoCbl structure, and specifically the Co-C bond length, is not a basis of Co-C bond cleavage catalysis. The results suggest that, following the substrate trigger, the protein interacts with the cofactor to contiguously guide the cleavage of the Co-C bond, at every step along the cleavage coordinate, starting from the equilibrium configuration of the ternary complex. The cleavage is thus represented by a diagonal trajectory across a free energy surface, that is defined by chemical (Co-C separation) and protein configuration coordinates.     

Highly sensitive detection of protein and small molecules based on aptamer-modified electrochemiluminescence nanoprobe

Amplified optical detection of biomolecules using nanoparticle as the carrier has attracted considerable interest in the scientific community. In this study, a promising aptasensor was developed for highly sensitive detection of protein and small molecules based on the construction of aptamer-modified electrochemiluminescence (ECL) nanoprobe. Specifically, thrombin and ATP serve as the examples for detection. By taking advantage of sandwich binding of two affinity aptamers for high specificity, tris-(2,2'-bipyridyl)ruthenium (TBR)-cysteamine loaded in gold nanoparticle (GNP) as barcodes for signal amplification, and micromagnetic particles (MMPs) based ECL technology for rapid detection, a novel assay for biomolecules quantification was developed. The sandwich complex containing targets could be selectively captured by MMPs and then quantified by ECL intensity. We have demonstrated that the detection limits of human thrombin and ATP are 1 pM and 10 pM, respectively, with high specificity. The proposed technology is expected to become a powerful tool for biomolecule analysis.     

Impedimetric Aptasensor for Thrombin Recognition Based on CD Support

We report an aptamer biosensing array for thrombin detection by measuring the electrochemical impedance upon aptamer‐protein formation at the surface of CD‐trodes (GCDTs) in the presence of the redox couple [Fe(CN)₆]^3?/4?. GCDTs are fabricated from recordable compact discs that contain a fine gold layer. The biosensor is constructed by self‐assembling of a thiol‐modified thrombin binding aptamer (TBA) onto a GCDT surface. The sensor reveals good ligand specificity, recognition in a wide range of thrombin concentrations from 20 nM to 1 µM with a limit of detection of 5 nM.     

Dissecting functional interactions in coagulation protein complexes by use of NMR spectroscopy

The blood coagulation cascade can be considered as a system of well-orchestrated protein activation reactions involving and leading to the formation of large macromolecular assemblies. NMR investigations performed during the last six years have focused on the structural, motional and binding properties of some protein domains and interfaces critical for the formation of these protein complexes, outlining sophisticated intermolecular adaptations. The studied protein domains are either single molecules or covalently-linked heterodimers of the epidermal growth factor (EGF) homology domains, calcium-binding EGF domains and gamma-carboxyglutamic(Gla)-containing domains responsible for calcium-dependent binding to cell membranes. The characterized binding interfaces have included those between thrombin and fibrinogen, between thrombin and thrombomodulin, between factor VIIIa and the cell membrane, between tissue factor and factor VIIa, and most recently between factor Va and prothrombin. The obtained results indicate that the regulation of blood coagulation by protein and low molecular weight cofactors may involve a significant degree of protein folding transitions with changes in molecular and conformational motions coupled to enzymatic activities. This new level of complexity of the molecular processes controlling coagulation may lead to novel strategies for the development of more effective therapeutic anticoagulants.     

Novel class of hybrid natural products derived from lupeol as antimalarial agents

Thirty-four novel hybrid lupeol derivatives (4-18) were prepared and evaluated for antimalarial activity in vitro against Plasmodium falciparum. Three compounds (13d, 16a and 17a) have shown antimalarial activity at lower dose (10 microg mL(-1)) than lupeol.     

Anticoagulatory Substances of Bloodsucking Animals: From Hirudin to Hirudin Mimetics

Bloodsucking animals contain substances in their saliva that specifically interfere with the blood clotting system. These substances are mainly low molecular weight proteins with a molecular mass of between 4 and 50 kDa. Some have become accessible in large quantities with the help of genetic engineering, and as a result their structures and structure—activity relationships have been studied and clinically tested. In the light of what is known about the mode of action of these natural products at the molecular level, new compounds with possible therapeutic effect can be derived. In the last ten years this approach has been tested with the proteinase inhibitor hirudin, obtained from medicinal leeches, and with the thrombin/hirudin complex. The serine protease thrombin plays a central role in the complex pathway of the blood clotting process and its pathophysiological effect finally results in thrombosis. The selectivity of the formation of complexes from hirudin and thrombin lies in the bivalent interaction of the inhibitor with the active site of the enzyme as well as with a substrate recognition site outside of the active site, the so-called fibrin-(ogen) binding site (FBS). The knowledge of this mode of action enabled the synthesis of bifunctional thrombin inhibitors based on hirudin peptides. Hirudin and hirudin mimetics in vivo have been shown to be highly potent anticoagulants for the treatment of arterial and venous thrombosis.     

Molecularly imprinted aptamers of gold nanoparticles for the enzymatic inhibition and detection of thrombin

We prepared thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs) through a molecularly imprinted (MP) approach, which provide highly efficient inhibition activity toward the polymerization of fibrinogen. Au NPs (diameter, 13 nm), 15-mer thrombin-binding aptamer (TBA(15)) with different thymidine linkers, and 29-mer thrombin-binding aptamer (TBA(29)) with different thymidine linkers (Tn) in the presence of thrombin (Thr) as a template were used to prepare MP-Thr-TBA(15)/TBA(29)-Tn-Au NPs. Thrombin molecules were then removed from Au NPs surfaces by treating with 100 mM Tris-NaOH (pH ca. 13.0) to form MP-TBA(15)/TBA(29)-Tn-Au NPs. The length of the thymidine linkers and TBA density on Au NPs surfaces have strong impact on the orientation, flexibility, and stability of MP-TBA(15)/TBA(29)-Tn-Au NPs, leading to their stronger binding strength with thrombin. MP-TBA(15)/TBA(29)-T(15)-Au NPs (ca. 42 TBA(15) and 42 TBA(29) molecules per Au NP; 15-mer thymidine on aptamer terminal) provided the highest binding affinity toward thrombin with a dissociation constant of 5.2 × 10(-11) M. As a result, they had 8 times higher anticoagulant (inhibitory) potency relative to TBA(15)/TBA(29)-T(15)-Au NPs (prepared in the absence of thrombin). We further conducted thrombin clotting time (TCT) measurements in plasma samples and found that MP-TBA(15)/TBA(29)-T(15)-Au NPs had greater anticoagulation activity relative to four commercial drugs (heparin, argatroban, hirudin, and warfarin). In addition, we demonstrated that thrombin induced the formation of aggregates from MP-TBA(15)-T(15)-Au NPs and MP-TBA(29)-T(15)-Au NPs, thereby allowing the colorimetric detection of thrombin at the nanomolar level in serum samples. Our result demonstrates that our simple molecularly imprinted approach can be applied for preparing various functional nanomaterials to control enzyme activity and targeting important proteins.     

Assessing helical protein interfaces for inhibitor design

Structure-based design of synthetic inhibitors of protein-protein interactions (PPIs) requires adept molecular design and synthesis strategies as well as knowledge of targetable complexes. To address the significant gap between the elegant design of helix mimetics and their sporadic use in biology, we analyzed the full set of helical protein interfaces in the Protein Data Bank to obtain a snapshot of how helices that are critical for complex formation interact with the partner proteins. The results of this study are expected to guide the systematic design of synthetic inhibitors of PPIs. We have experimentally evaluated new classes of protein complexes that emerged from this data set, highlighting the significance of the results described herein.     

Activation of cyclic AMP-dependent protein kinase and stimulation of protein phosphorylation in response to adenosine in C-1300 murine neuroblastoma.

DEAE-cellulose chromatography of the 20,000g supernatant fraction of homogenates of C-1300 murine neuroblastoma (clone N2a) yields one major and two minor peaks of cyclic AMP-dependent protein kinase activity. Assessment of the endogenous activation state of the enzyme(s) reveals that the enzyme is fully activated by the treatment of whole cells with adenosine (10 microM) in the presence of the phosphodiesterase inhibitor Ro 20 1724 (0.7 mM). This treatment produces a large elevation in the cyclic AMP content of the cells. The treatment of whole cells with adenosine alone (1-100 microM) or Ro 20 1724 alone (0.1-0.7 mM) produces minimal elevations in cyclic AMP but nevertheless causes significant activations of cyclic AMP-dependent protein kinase. The autophosphorylation of whole homogenates of treated and untreated cells was studied using [gamma-32P] ATP, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Treatments which activate cyclic AMP-dependent protein kinase selectively stimulate the incorporation of 32P into several proteins. This stimulation is most prominent in the 15,000-dalton protein band. The addition of cyclic AMP to phosphorylation reactions containing homogenate of untreated cells stimulates the phosphorylation of the same protein bands. These results indicate that adenosine may have regulatory functions through its effect on the cyclic AMP:cyclic AMP-dependent protein kinase system.     

Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement

Bioisosteres have been defined as structurally different molecules or substructures that can form comparable intermolecular interactions, and therefore, fragments that bind to similar protein structures exhibit a degree of bioisosterism. We present KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints. The binding site fingerprints have been optimized to improve their performance for both intra- and interprotein family comparisons. A range of attributes of the fingerprints was considered in the optimization, including the placement of pharmacophore features, whether or not the fingerprints are fuzzified, and the resolution and complexity of the pharmacophore fingerprints (2-, 3-, and 4-point fingerprints). Fuzzy 3-point pharmacophore fingerprints were found to represent the optimal balance between computational resource requirements and the identification of potential replacements. The complete PDB was converted into a database comprising almost 300?000 optimized fingerprints of local binding sites together with their associated ligand fragments. The value of the approach is demonstrated by application to two crystal structures from the Protein Data Bank: (1) a MAP kinase P38 structure in complex with a pyridinylimidazole inhibitor ( 1A9U ) and (2) a complex of thrombin with melagatran ( 1K22 ). Potentially valuable bioisosteric replacements for all subpockets of the two studied protein are identified.