How to find simple and accurate rules for viral protease cleavage specificities

<p>Abstract</p> <p>Background</p> <p>Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New methods are being developed that produce large amounts of cleavage information for individual proteases and some have been applied to extract cleavage rules from data. However, the hitherto proposed methods for extracting rules have been neither easy to understand nor very accurate. To be practically useful, cleavage rules should be accurate, compact, and expressed in an easily understandable way.</p> <p>Results</p> <p>A new method is presented for producing cleavage rules for viral proteases with seemingly complex cleavage profiles. The method is based on orthogonal search-based rule extraction (OSRE) combined with spectral clustering. It is demonstrated on substrate data sets for human immunodeficiency virus type 1 (HIV-1) protease and hepatitis C (HCV) NS3/4A protease, showing excellent prediction performance for both HIV-1 cleavage and HCV NS3/4A cleavage, agreeing with observed HCV genotype differences. New cleavage rules (consensus sequences) are suggested for HIV-1 and HCV NS3/4A cleavages. The practical usability of the method is also demonstrated by using it to predict the location of an internal cleavage site in the HCV NS3 protease and to correct the location of a previously reported internal cleavage site in the HCV NS3 protease. The method is fast to converge and yields accurate rules, on par with previous results for HIV-1 protease and better than previous state-of-the-art for HCV NS3/4A protease. Moreover, the rules are fewer and simpler than previously obtained with rule extraction methods.</p> <p>Conclusion</p> <p>A rule extraction methodology by searching for multivariate low-order predicates yields results that significantly outperform existing rule bases on out-of-sample data, but are more transparent to expert users. The approach yields rules that are easy to use and useful for interpreting experimental data.</p

Biosynthesis, Processing, and Sorting of Human Neutrophil Granule Proteins. Focus on Cathepsin G, Proteinase 3, and Azurocidin

The neutrophil granulocyte contains a number of multifunctional proteins stored in different subsets of granules. The azurophil granules, synthesized early during differentiation, harbour leukocyte elastase, cathepsin G, proteinase 3, and azurocidin; the members of the serprocidin family. In order to study the biosynthesis, processing, and intracellular sorting of the proteins, human cDNA encoding the latter three proteins, in their preproform, was stably transfected to two hematopoietic rodent cell lines (RBL-1 and 32Dcl3). To investigate the importance of distinct protein motifs, mutations were made in the cDNAs prior to transfection. Cathepsin G lacking functional glycosylation site was normally activated and sorted to granules. Similarly, cathepsin G, lacking both functional catalytic site and amino-terminal propeptide, was stably transfected to both cell lines. However, preterm activation of catalytically active cathepsin G lead to impaired cell survival. Proteinase 3 was expressed and stored in a form that allowed specific recognition by human cANCA-sera from patients with Wegener's granulomatosis. The amino-terminal heptapropeptide of azurocidin was shown to be removed in a stepwise manner involving at least two different enzymes. All serprocidins acquired high-mannose oligosaccharides that were converted into complex forms. Finally, the biosynthetic windows of several neutrophil granule proteins, including myeloperoxidase, lysozyme, cathepsin D, and all four serprocidins, were characterized in an experimental in vitro model for differentiation of human bone marrow progenitor cells into neutrophils

Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: an overview

HIV-1 protease has a broad and complex substrate specificity, which hitherto has escaped a simple comprehensive definition. This, and the relatively high mutation rate of the retroviral protease, makes it challenging to design effective protease inhibitors. Several attempts have been made during the last two decades to elucidate the enigmatic cleavage specificity of HIV-1 protease and to predict cleavage of novel substrates using bioinformatic analysis methods. This review describes the methods that have been utilized to date to address this important problem and the results achieved. The data sets used are also reviewed and important aspects of these are highlighted

Comprehensive Bioinformatic Analysis of the Specificity of Human Immunodeficiency Virus Type 1 Protease

Rapidly developing viral resistance to licensed human immunodeficiency virus type 1 (HIV-1) protease inhibitors is an increasing problem in the treatment of HIV-infected individuals and AIDS patients. A rational design of more effective protease inhibitors and discovery of potential biological substrates for the HIV-1 protease require accurate models for protease cleavage specificity. In this study, several popular bioinformatic machine learning methods, including support vector machines and artificial neural networks, were used to analyze the specificity of the HIV-1 protease. A new, extensive data set (746 peptides that have been experimentally tested for cleavage by the HIV-1 protease) was compiled, and the data were used to construct different classifiers that predicted whether the protease would cleave a given peptide substrate or not. The best predictor was a nonlinear predictor using two physicochemical parameters (hydrophobicity, or alternatively polarity, and size) for the amino acids, indicating that these properties are the key features recognized by the HIV-1 protease. The present in silico study provides new and important insights into the workings of the HIV-1 protease at the molecular level, supporting the recent hypothesis that the protease primarily recognizes a conformation rather than a specific amino acid sequence. Furthermore, we demonstrate that the presence of 1 to 2 lysine residues near the cleavage site of octameric peptide substrates seems to prevent cleavage efficiently, suggesting that this positively charged amino acid plays an important role in hindering the activity of the HIV-1 protease

Kostmann disease and other forms of severe congenital neutropenia

Congenital neutropenia with autosomal recessive inheritance was first described by the Swedish paediatrician Rolf Kostmann who coined the term ‘infantile genetic agranulocytosis’. The condition is now commonly referred to as Kostmann disease. These patients display a maturation arrest of the myelopoiesis in the bone marrow and reduced neutrophil numbers and suffer from recurrent, often life-threatening infections. The molecular mechanism underlying congenital neutropenia has been intensively investigated, and mutations in genes that impinge on programmed cell death have been identified. The present review provides an overview of these studies

Biosynthetic profiles of neutrophil serine proteases in a human bone marrow-derived cellular myeloid differentiation model

Background and Objectives. Human leukocyte elastase, proteinase 3 and cathepsin G are neutrophil granule proteins belonging to the hematopoietic serine protease superfamily. In addition to their established roles in inflammation, they have recently been implicated as regulators of granulopoiesis and mediators of apoptosis. We set out to characterize the individual biosynthetic profiles of these proteins in a neutrophil differentiation model. Design and Methods. Bone marrow-derived CD34(+)CD38(+) hematopoietic progenitor cells from 21 healthy human volunteers were cultured in vitro in the presence of recombinant human granulocyte colony-stimulating factor (G-CSF). Biosynthetic radiolabeling was performed in cells from 13 subjects after various periods of differentiation induction. Following protein extraction, the proteins were specifically immunoprecipitated from cell lysates and media and run in gel electrophoresis. Biosynthetic profiles of azurophil granule proteins, in particular members of the neutrophil serine protease family, were examined during myeloid differentiation. Results. The onset of synthesis of myeloperoxidase, lysozyme, leukocyte elastase, and proteinase 3 occurred early after differentiation induction with G-CSF, while synthesis of cathepsin G, azurocidin, and bactericidal/permeability-increasing protein was detected somewhat later. Cathepsin G and proteinase 3 were retained intracellularly relatively efficiently, while leukocyte elastase and lysozyme were secreted to a greater extent. Cell morphology and positive immunocytochemistry for lactoferrin as well as flow cytometric analysis of selected surface antigens confirmed neutrophil-like maturation. Interpretation and Conclusions. We demonstrate that azurophil granule proteins, including proforms of human leukocyte elastase, proteinase 3 and cathepsin G, are constitutively secreted to various degrees during in vitro myeloid differentiation of human hematopoietic progenitor cells, in addition to being stored intracellularly in active forms. These findings suggest protein-specific sorting mechanisms and may have implications for the regulation of granulopoiesis

Characterization of the processing and granular targeting of human proteinase 3 after transfection to the rat RBL or the murine 32D leukemic cell lines

Proteinase 3 (PR3) is a neutrophil serine protease stored in the azurophil granules of the promyelocyte and its successors. The protease has been identified as an autoantigen for anti-neutrophil cytoplasmic autoantibodies (ANCA) occurring in patients with Wegener's granulomatosis. To characterize the biosynthesis and processing of human PR3 in a transgenic cellular model, cDNA encoding human pre-proproteinase 3 cloned from U-937 cells was transfected to the rat basophilic/mast cell line RBL-1 and the murine myeloblast-like cell line 32D c13. The stable expression of transgenic proteinase 3 was characterized by biosynthetic labeling, followed by immunoprecipitation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and fluorography. After pulse labeling for 30 min two proforms of PR3 (32 and 35 kDa), differing in carbohydrate content but with protein cores of identical size, were demonstrated. Chase of the label resulted in a processed 32-kDa form clearly visible in RBL, but only faintly in 32D cells, probably indicating delayed intracellular transfer in the latter cell line. Partial digestion with N-glycosidase F showed that both potential N-glycosylation sites on PR3 were occupied and conversion of the oligosaccharide side chains into complex forms was demonstrated by acquisition of resistance to endoglycosidase H. Translocation of PR3 to granules was shown by subcellular fractionation and immunocytochemistry. Enzymatic activation of PR3 was suggested by affinity to diisopropylfluorophosphate and removal of an amino-terminal propeptide. Cells transfected with PR3 showed positive immunofluorescence for ANCA-containing sera from patients with Wegener's granulomatosis. Our results show that human PR3 transfected to RBL or 32D cells is synthesized as a 29-kDa protein core glycosylated on two distinct sites. Oligosaccharide trimming and proteolytic processing occur and the protein is targeted for granular storage in a form antigenic for ANCA