Sequence-derived structural features driving proteolytic processing

Proteolytic signaling, or regulated proteolysis, is an essential part of many important pathways such as Notch, Wnt, and Hedgehog. How the structure of the cleaved substrate regions influences the efficacy of proteolytic processing remains underexplored. Here, we analyzed the relative importance in proteolysis of various structural features derived from substrate sequences using a dataset of more than 5000 experimentally verified proteolytic events captured in CutDB. Accessibility to the solvent was recognized as an essential property of a proteolytically processed polypeptide chain. Proteolytic events were found nearly uniformly distributed among three types of secondary structure, although with some enrichment in loops. Cleavages in α-helices were found to be relatively abundant in regions apparently prone to unfolding, while cleavages in β-structures tended to be located at the periphery of β-sheets. Application of the same statistical procedures to proteolytic events divided into separate sets according to the catalytic classes of proteases proved consistency of the results and confirmed that the structural mechanisms of proteolysis are universal. The estimated prediction power of sequence-derived structural features, which turned out to be sufficiently high, presents a rationale for their use in bioinformatic prediction of proteolytic events.

[Draft macronuclear genome of a ciliate Euplotes crassus]

Basic bioinformatical analysis of the draft Euplotes crassus macronuclear genome and transcriptome suggests that more than a quarter of E. crassus genes contain several exons. A large fraction of all introns is formed by "tiny" introns having length 20-30 bp. Analysis of the transcriptome revealed 63 possible cases of alternative splicing, and also 14 introns with non-standard splicing sites. About 2000 hypothetical genes do not have homologs in other ciliates, and since most of them have the closest homologs in bacterial genomes, they are likely an artifact of the sample preparation. Comparison of the E. crassus genome to the genomes of other ciliates showed an expansion of the same gene families, responsible for the free-living heterotrophic lifestyle.

[Intraoperative assessment of blood flow along coronary and internal thoracic arteries before and after myocardial revascularization]

The article deals with intraoperative assessment of the blood flow in the coronary arteries and internal thoracic artery before and after myocardial revascularization. This is accompanied and followed by ultrasonographic characteristics of the coronary blood flow before and after surgical intervention, as well as competence of anastomoses and functional state of revascularization depending on the degree of the atherosclerotic lesion and the diameter of coronary arteries. The average linear and volumetric velocities of the blood flow in the coronary arteries were found to depend upon the degree of the lesion of coronary arteries, the diameter and capacity of the coronary bed. The work was based on studying a total of forty-eight patients presenting with coronary artery disease and subjected to myocardial revascularization using the internal thoracic artery (ITA). Also determined was efficacy of myocardial revascularization in different diameters of the coronary arteries and parameters of the ITA blood flow.

[Outcomes of surgical management of elderly and aged patients with complicated forms of coronary artery disease]

The article is dedicated to comparative analysis of surgical management of elderly and aged patients presenting with complicated forms of coronary artery disease (CAD). Suggested herein is an algorithm of concerning the choice of methods aimed at surgical correction of postinfarction aneurysms of the right ventricle of the heart and postinfarction ruptures of the interventricular septum in these patients, depending on the morphological structure of the right-ventricular postinfarction aneurysms and postinfarction ruptures of the interventricular septum, followed by determining the incidence rate of using "complete" and "incomplete" myocardial revascularization in elderly and aged patients with complicated forms of CAD depending on peculiarities of the coronary blood flow. Also considered herein is efficacy of preventing rethrombosis following correction of right-ventricular postinfarction aneurysms and thrombectomy. The article is based on studying a total of forty-two 60-to-78-year-old patients with CAD. The measures taken made it possible to decrease postoperative lethality and postoperative complications rate in the patients concerned.

Applying hybrid reasoning to mine for associative features in biological data

We develop the means to mine for associative features in biological data. The hybrid reasoning schema for deterministic machine learning and its implementation via logic programming is presented. The methodology of mining for correlation between features is illustrated by the prediction tasks for protein secondary structure and phylogenetic profiles. The suggested methodology leads to a clearer approach to hierarchical classification of proteins and a novel way to represent evolutionary relationships. Comparative analysis of Jasmine and other statistical and deterministic systems (including Explanation-Based Learning and Inductive Logic Programming) are outlined. Advantages of using deterministic versus statistical data mining approaches for high-level exploration of correlation structure are analyzed.

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein and characterization of regulatory mutations. Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. RegTransBase is available at .

Identification and characterization of LRP8 (apoER2) in human blood platelets

Recently, we reported that apoE inhibits platelet reactivity by stimulating NO release and postulated apoE-receptor activation of intracellular NO synthase (eNOS). Here, we implicate a low density lipoprotein receptor (LDL-R) family member by studying ligand requirements using purified apoE isoforms, synthetic peptides, and the receptor antagonist, receptor-associated protein (RAP). Then, using a homology cloning approach and degenerate PCR primers to amplify the conserved Cys-rich binding domain of the LDL-R family, this receptor was identified as LRP8 (formerly termed, apoER2), a newly described brain protein with several splice variants. Immunoprecipitation of platelet membranes with anti-peptide antisera confirmed protein expression, while analysis of RNA from platelets and two megakaryocytic cell lines (Meg-01 and HEL) disclosed that the major LRP8 transcript lacked binding repeats 4-6 (LRP8delta4-6) but contained the full-length cytoplasmic tail. Sequence analysis of cytoplasmic LRP8 revealed several peptide motifs with potential for cellular signaling and we propose this as a rational mechanism through which apoE inhibits platelet aggregation.

Effects of peroxynitrite on plasma components of the reverse cholesterol transport pathway

Elimination of cholesterol from arterial tissue, crucial in limiting atherogenesis, may be achieved via high-density lipoprotein (HDL)-mediated reverse cholesterol transport (RCT); components of this pathway can be modulated by oxidative stress. Here we have examined the relations between cholesterol efflux, esterification and transfer in human plasma treated with the powerfully reactive nitrogen species, peroxynitrite. Cellular cholesterol efflux to whole plasma, or to peroxynitrite-modified HDL3, was relatively insensitive to peroxynitrite, as was the transfer of esterified cholesterol. However, plasma cholesterol esterification, via lecithin:cholesterol acyltransferase (LCAT), was markedly inhibited, both directly and indirectly, by peroxynitrite treatment, implying inefficient RCT follows HDL sequestration of cellular cholesterol.

Characterization of mocarhagin, a cobra venom metalloproteinase from Naja mocambique mocambique, and related proteins from other Elapidae venoms

Mocarhagin, a cobra venom metalloproteinase from Naja mocambique mocambique, has previously been shown to cleave selectively two mucin-like substrates on platelets and neutrophils within anionic amino acid sequences containing sulfated tyrosines. We now show that purified mocarhagin has haemagglutinin activity, and a similar profile for inhibition of mocarhagin-dependent haemagglutination and proteolysis suggests that the lectin-like domain may account for its substrate specificity. In addition, immunologically and functionally related proteins were detected in other Elapidae venoms.

Deficiency of P-selectin in a patient with grey platelet syndrome

Patient B.G. is a 29-yr-old female with a lifelong bleeding disorder characterized clinically by a highly increased bleeding time, menorrhagias, long-lasting bleeding after cuts and tooth extractions and large post-traumatic haematomas. Her coagulation tests were within normal range, platelet count was 140,000-160,000 per microliters, but platelet function was impaired as demonstrated by the absence of collagen-induced aggregation, although no abnormalities were detected in aggregation response to ADP and ristocetin. Morphologically her platelets were characterized by gigantic size-average profile area was about 2.5 times higher than that of control donors, and severe deficiency of alpha-granules-only 16% of their number in control donors. These features taken together indicated the diagnosis of grey platelet syndrome. As has been shown by quantitative immunoblotting, patient's platelets contained small amounts of alpha-granule membrane protein P-selectin-about 15% of that in control donors. The content of plasma membrane glycoproteins IIb-IIIa and Ib was not reduced, suggesting the specific deficiency of alpha-granule membrane protein. Thus, B.G. is the second patient described in the literature (see also Lages et al, J Clin Invest 1991: 87: 919-929) with combined deficiency of alpha-granules and P-selectin.

Interactions of CD80 and CD86 with CD28 and CTLA4

CD80 and CD86 are cell surface glycoproteins expressed on a variety of professional APCs. They have attracted much attention due to their function as potent costimulators of T lymphocyte function through their interaction with CD28 and possibly CTLA4. Because inhibitors of this interaction may have therapeutic relevance in human autoimmune disease, we investigated the properties of linear peptides derived from conserved regions of CTLA4 and CD80 known to be essential for binding. None of these peptides were sufficient to bind ligand, nor did they act as potent competitive inhibitors. Conformationally constrained versions of the CTLA4 motif were also inactive. These results suggested that other parts of the proteins are important in determining binding, so a series of modified CD80 and CD86 molecules were constructed in an attempt to identify other binding determinants. Insertion of two residues between the two Ig domains of CD80 resulted in decreased affinity for CTLA4, but a similar mutation in CD86 was without effect. We also identified another asymmetry between CD80 and CD86 in that the V domain of CD86 but not that of CD80 is sufficient for CTLA4 binding. The CD86-V domain appears to have CTLA4 binding properties equivalent to that of intact CD86. These data illustrate a fundamental difference between these costimulatory molecules and suggest a mechanism by which they may be differentially recognized by receptors on the T cell surface.

Interactions of CD80 and CD86 with CD28 and CTLA4

CD80 and CD86 are cell surface glycoproteins expressed on a variety of professional APCs. They have attracted much attention due to their function as potent costimulators of T lymphocyte function through their interaction with CD28 and possibly CTLA4. Because inhibitors of this interaction may have therapeutic relevance in human autoimmune disease, we investigated the properties of linear peptides derived from conserved regions of CTLA4 and CD80 known to be essential for binding. None of these peptides were sufficient to bind ligand, nor did they act as potent competitive inhibitors. Conformationally constrained versions of the CTLA4 motif were also inactive. These results suggested that other parts of the proteins are important in determining binding, so a series of modified CD80 and CD86 molecules were constructed in an attempt to identify other binding determinants. Insertion of two residues between the two Ig domains of CD80 resulted in decreased affinity for CTLA4, but a similar mutation in CD86 was without effect. We also identified another asymmetry between CD80 and CD86 in that the V domain of CD86 but not that of CD80 is sufficient for CTLA4 binding. The CD86-V domain appears to have CTLA4 binding properties equivalent to that of intact CD86. These data illustrate a fundamental difference between these costimulatory molecules and suggest a mechanism by which they may be differentially recognized by receptors on the T cell surface.

Detection of an epitope specific for the dissociated form of glycoprotein IIIa of platelet membrane glycoprotein IIb-IIIa complex and its expression on the surface of adherent platelets

Glycoproteins (GPs) IIb and IIIa form a Ca(2+)-dependent complex in platelet membrane and change their conformation upon platelet activation and dissociation of the complex. A new anti-GPIIIa monoclonal antibody (mAb), CRC54, is described which could distinguish different conformational states of GPIIIa. This antibody (i) precipitated GPIIb-IIIa from platelet Triton X-100-lysate, (ii) recognized the GPIIIa band in Western blotting of platelet SDS-lysate, and (iii) did not react with platelets from a Glanzmann's thrombasthenia patient lacking GPIIb-IIIa. Immunoblotting of chymotryptic digestion products of purified GPIIb-IIIa has shown that CRC54 epitope is located within residues 1-100 at the N-terminus of GPIIIa. CRC54 bound weakly to platelets in the presence of Ca2+ and Mg2+, 2.34 +/- 0.28 x 10(3) molecules per platelet at saturation. The same level of binding was observed without any divalent cations in the medium. However, binding of CRC54 was increased by several times after treatment of platelets with EDTA, 10.04 +/- 0.28 x 10(3) molecules per platelet. Increase of CRC54 binding correlated with the dissociation of GPIIb-IIIa complex which was followed by the decrease of the binding of another mAb, CRC64, directed against complex-specific epitope of GPIIb-IIIa. Binding of CRC54 to platelets was changed neither by platelet activation in suspension with thrombin or ADP nor by the occupancy of GPIIb-IIIa ligand binding site with GRGDSR peptide. However, binding was significantly stimulated by platelet adhesion to polystyrene plastic. As measured using 51Cr-labelled platelets, binding of 125I-CRC54 to adherent platelets in the presence of divalent cations was about 4 times higher than to platelets in suspension, 8.68 +/- 0.48 x 10(3) per platelet. This increase was not due to the dissociation of GPIIb-IIIa since complex-specific antibody CRC64 still bound effectively to the surface of adherent platelets. The data obtained indicated that: (1) CRC54 recognized an epitope specific for the dissociated form of GPIIIa; (2) the CRC54-reactive epitope of GPIIIa is also expressed on the surface of adherent platelets.

[The immunodiagnosis of thrombocyte membrane glycoprotein deficiencies: Glanzmann's thrombasthenia, Bernard-Soulier syndrome and GMP-140 protein deficiency]

Immunological methods were developed for the diagnosis of platelet membrane glycoprotein (GP) deficiencies. The number of membrane GP on platelet surface was determined as the binding of 125I-labeled monoclonal antibodies (mAB) directed against individual platelet GP. Total amount of GP in platelet lysate was assessed by immunoblotting with specific polyclonal antibodies. Methods were applied for patients with different thrombocytopathies. Binding of mAB VM16a, directed against GP IIb-IIIa was strongly decreased in patients with Glanzmann's thrombasthenia (0.5-14.5% of normal) and binding of anti-GP Ib mAB VM16d--in patient with Bernard-Soulier syndrome (0.5% of control) indicating the deficiencies of corresponding GP. In patient with gray platelet syndrome binding of both antibodies was not decreased but even increased. It was shown by immunoblotting that platelets from the patient with gray platelet syndrome contained normal amount of GP IIa, but strongly decreased amount of GMP-140 (14.5% of control)--membrane GP of platelet--granules.

A monoclonal antibody, VM64, reacts with a 130 kDa glycoprotein common to platelets and endothelial cells: heterogeneity in antibody binding to human aortic endothelial cells

A new monoclonal antibody (mAb), VM64, reacts with a common antigen on the surface of human platelets and vascular endothelial cells (EC). Under nonreduced conditions it recognized in immunoblotting a protein of 130 kDa both in platelets and EC. VM64 precipitated the same 130 kDa protein from the lysate of surface radioiodinated platelets. Electrophoretic mobility of this protein was not altered by reduction and differed from the bands precipitated by reference mAb against platelet glycoproteins (GP) Ia-IIa, Ib, IIb-IIIa and GMP130. VM64 binding to platelets and EC was specific and saturable. The number of binding sites on platelets was 9.9 +/- 3.5 x 10(3) per platelet and on the surface of EC monolayer -2.40 +/- 0.32 x 10(6) per cell. VM64 also binds to platelets from Glanzmann's thrombasthenia patients which lack GPIIb-IIIa. VM64 did not affect platelet aggregation induced by ADP, collagen, thrombin and ristocetin. In the monolayers of EC from umbilical vein and human aorta, VM64 stained the area at the periphery of the cells adjacent to the cell-cell boundaries. In preconfluent cultures preferential staining was observed at the active leading margins of the cells. Unlike EC cultures from umbilical vein, where all cells were positively stained, in aortic EC cultures some unstained or poorly stained cells were constantly present, indicating a heterogeneity of EC population related to the expression of VM64 antigen. The biochemical characteristics of VM64 antigen, its presence both on platelets and EC and typical distribution on the surface of EC suggested that this antigen is identical to PECAM (CD31) protein.

Characterization of an antiglycoprotein Ib monoclonal antibody that specifically inhibits platelet-thrombin interaction

Platelet glycoprotein Ib (GPIb) acts as a high-affinity thrombin binding site and as a receptor for von Willebrand Factor (vWF). A new anti-GPIb monoclonal antibody (mAB) VM16d was produced that specifically inhibited platelet-thrombin but not platelet-vWF interaction. The epitope for VM16d was located within the 45 kDa N-terminal region of the alpha-chain of GPIb. VM16d inhibited platelet aggregation induced by low dose thrombin (0.05 U/ml) but did not affect platelet aggregation induced by ristocetin, bovine vWF, ADP or collagen. The same inhibitory effects on thrombin-induced platelet aggregation were observed with the whole IgG molecule of VM16d and its F(ab')2 and F(ab') fragments. VM16d also inhibited 14C-serotonin secretion induced by low dose thrombin and binding of 125I-thrombin but not ristocetin-dependent binding of 125I-vWF to platelets. These data indicate that the high-affinity thrombin binding site is located on the N-terminal 45 kDa domain of GPIb and that it is topographically separated from the vWF binding site.

[Inhibition of Fc-receptor dependent platelet aggregation by monoclonal antibodies against the glycoprotein IIb-IIIa complex]

A murine monoclonal antibody (MoAb) VM16a specifically binding to human platelets has been produced. Approximately 56,000 molecules of VM16a bound per platelet at saturation (Kd = 7.9 nM) but no binding to platelets from Glanzmann's thrombasthenia patients was detected. VM16a precipitated two proteins with molecular masses corresponding to those of glycoproteins (GP) IIb and IIIa from solubilized surface-labelled platelets. However, after dissociation of the GPIIb--IIIa complex with EDTA VM16a did not bind to platelets and precipitated nothing from their lysate, thus evidencing that its determinant is complex-dependent. VM16a had no effect on ADP-, thrombin- and ristocetin-induced platelet aggregation but inhibited the aggregation induced by collagen. This inhibitory effect was more pronounced in the presence of plasma. VM16a completely blocked the Fc-receptor-mediated aggregation induced by aggregated human IgG, aggregated murine IgG1 and the previously described MoAb VM58. F(ab')2 fragments of VM16a were also able to inhibit this aggregation by decreasing the rate of aggregation induced by aggregated IgG and by extending the lag phase of VM58-induced aggregation. These results suggest that the platelet Fc-receptor may be topographically associated with the GPIIb-IIIa complex.

Visualization of apo B, fibrinogen/fibrin, and fibronectin in the intima of normal human aorta and large arteries and during atherosclerosis

Apolipoprotein B (apo B), fibrinogen/fibrin, blood platelets, factor VIII-related antigen of the blood coagulation system, and smooth muscle cells (SMC) were identified in the intima of normal and atherosclerotic human aorta and large arteries by the indirect immunofluorescence technique. Fibrinogen/fibrin was revealed by a monoclonal antibody (monAb) against the C-terminal region of human fibrinogen A alpha-chain. Fibronectin was visualized by monAb to the cellular form and against an epitope shared by different fibronectin subunit variants. In normal intima, fatty streaks, small amounts of fibrinogen/fibrin together with large amounts of apo B were observed. Fibronectin detected by two types of monAb was not found in extracellular matrix (ECM), whereas cellular fibronectin encircled SMC. According to the data obtained, fibrinogen/fibrin accumulates in plaques as a result of intramural thrombus incorporation, blood insudation, intramural haemorrhage, and in or around cells, apparently macrophages.

[Determination of antithrombocyte antibodies in the blood serum of patients with idiopathic thrombocytopenic purpura by an immunoenzyme method]

Enzyme-linked immunosorbent assay (ELISA) was developed for determination of serum antiplatelet antibodies. Platelets obtained from healthy donors of blood group 0(1) were washed off plasma and sedimented on the bottom of microtest wells. After washing off unattached platelets and blocking of plastic with albumin platelets were incubated with sera under investigation and binding of serum antibodies was detected using antihuman immunoglobulin antibodies conjugated with peroxidase. Ten patients with idiopathic thrombocytopenic purpura (ITP). 1 patient with systemic lupus erythematosus. 1 patient with red blood cell aplasia and 9 healthy donors (negative control) were studied by ELISA. Serum antibodies which effectively bound to platelets were detected in 5 patients with ITP, in patient with lupus erythematosus and in patient with red blood cell aplasia.