Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for both docking pose prediction and affinity ranking, and in D3R-GC4 for binding affinity ranking. The difficulties posed by CatS inhibitors in D3R mainly come from three aspects: large size, high flexibility and similar chemical structures. We have participated in GC4; our best submitted model, which employs a similarity-based alignment docking and Vina scoring protocol, yielded Kendall's τ of 0.23 for 459 binders in GC4. In our further explorations with machine learning, by curating a CatS specific training set, adopting a similarity-based constrained docking method as well as an arm-based fragmentation strategy which can describe large inhibitors in a locality-sensitive fashion, our best structure-based ranking protocol can achieve Kendall's τ of 0.52 for all binders in GC4. In this exploration process, we have demonstrated the importance of training data, docking approaches and fragmentation strategies in inhibitor-ranking protocol development with machine learning.

The role of the silicatein-alpha interactor silintaphin-1 in biomimetic biomineralization.

Biosilicification in sponges is initiated by formation of proteinaceous filaments, predominantly consisting of silicateins. Silicateins enzymatically catalyze condensation of silica nanospheres, resulting in symmetric skeletal elements (spicules). In order to create tailored biosilica structures in biomimetic approaches it is mandatory to elucidate proteins that are fundamental for the assembly of filaments. Silintaphin-1 is a core component of modularized filaments and also part of a spicule-enfolding layer. It bears no resemblance to other proteins, except for the presence of an interaction domain that is fundamental for its function as scaffold/template. In the presence of silicatein silintaphin-1 facilitates the formation of in vitro filaments. Also, it directs the assembly of gamma-Fe(2)O(3) nanoparticles and surface-immobilized silicatein to rod-like biocomposites, synthetic spicules. Thus, silintaphin-1 will contribute to biomimetic approaches that pursue a controlled formation of patterned biosilica-based materials. Its combination with gamma-Fe(2)O(3) nanoparticles and immobilized silicatein will furthermore inspire future biomedical applications and clinical diagnostics.

Molecular control of serial module formation along the apical-basal axis in the sponge Lubomirskia baicalensis: silicateins, mannose-binding lectin and mago nashi.

The freshwater sponge Lubomirskia baicalensis (from Lake Baikal) is characterized by a body plan composed of serial modules which are arranged along an apical-basal axis. In shallow water, the sponge occurs only encrusting, while in deeper environment (>3 m), this species forms branches and grows in an arborescent manner. Each module is stabilized by bundles of spined oxeas (amphioxeae spicules). The spicules are surrounded by an organic matrix. cDNAs for structural proteins (silicatein and mannose-binding lectin (MBL)) as well as for one regulatory protein (mago nashi) were isolated from L. baicalensis. Surprisingly the silicatein alpha molecule exists in several, at least four, isoforms (a1 to a4). Expression studies revealed that the steady-state levels of transcripts for the silicateins, the mannose-binding lectin, and mago nashi are highest at the top of the branches, while only very low levels are found in cells at the base. Based on in situ hybridization studies, evidence is presented that the spicule formation (1) starts and is completed inside of the bundles, and (2) occurs together with the mannose-binding lectin from the surfaces of the bundles. The data suggest that the modules are sequentially formed. It is speculated that the expression of the silicateins and the mannose-binding lectin might be (partially) controlled by mago nashi.

Fractal intermediates in the self-assembly of silicatein filaments.

Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges; they are the constituents of macroscopic protein filaments that are found occluded within the silica needles made by Tethya aurantia. Self-assembly of the silicatein monomers and oligomers is shown to form fibrous structures by a mechanism that is fundamentally different from any previously described filament-assembly process. This assembly proceeds through the formation of diffusion-limited, fractally patterned aggregates on the path to filament formation. The driving force for this self-assembly is suggested to be entropic, mediated by the interaction of hydrophobic patches on the surfaces of the silicatein subunits that are not found on highly homologous congeners that do not form filaments. Our results are consistent with a model in which silicatein monomers associate into oligomers that are stabilized by intermolecular disulfide bonds. These oligomeric units assemble into a fractal network that subsequently condenses and organizes into a filamentous structure. These results represent a potentially general mechanism for protein fiber self-assembly.

Mineralization of SaOS-2 cells on enzymatically (silicatein) modified bioactive osteoblast-stimulating surfaces.

There is a demand for novel bioactive supports in surgery, orthopedics, and tissue engineering. The availability of recombinant silica-synthesizing enzyme (silicatein) opens new possibilities for the synthesis of silica-containing bioactive surfaces under ambient conditions that do not damage biomolecules like proteins. Here it is shown that growth of human osteosarcoma SaOS-2 cells on cluster plates precoated with Type 1 collagen is not affected by additional coating of the plates with the recombinant silicatein and incubation with its enzymatic substrate, tetraethoxysilane (TEOS). However, the enzymatic modification of the plates by biosilica deposition on the protein-coated surface caused a marked increase in calcium phosphate formation of SaOS-2 cells as revealed by alizarin red-S staining to quantify calcium mineral content. The increased occurrence of calcium-phosphate nodules on the modified surface was also observed by scanning electron microscopy. These results suggest that by supporting calcium-phosphate deposition in vitro, biosilica (silicatein)-modified surfaces are potentially bioactive in vivo, by stimulating osteoblast mineralization function.

Structural characterization of siliceous spicules from marine sponges.

Siliceous sponges, one of the few animal groups involved in a biosilicification process, deposit hydrated silica in discrete skeletal elements called spicules. A multidisciplinary analysis of the structural features of the protein axial filaments inside the spicules of a number of marine sponges, belonging to two different classes (Demospongiae and Hexactinellida), is presented, together with a preliminary analysis of the biosilicification process. The study was carried out by a unique combination of techniques: fiber diffraction using synchrotron radiation, scanning electron microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetric (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular modeling. From a phylogenetic point of view, the main result is the structural difference between the dimension and packing of the protein units in the spicule filaments of the Demospongiae and the Hexactinellida species. Models of the protein organization in the spicule axial filaments, consistent with the various experimental evidences, are given. The three different species of demosponges analyzed have similar general structural features, but they differ in the degree of order. The structural information on the spicule axial filaments can help shed some light on the still unknown molecular mechanisms controlling biosilicification.

Immunolocalization of cysteine proteinases (cathepsins) and cysteine proteinase inhibitors (salarin and salmon kininogen) in Atlantic salmon, Salmo salar.

Tissue localization of cysteine proteinases (cathepsins) and their inhibitors (salarin, salmon kininogen) was performed in tissues of the Atlantic salmon. In skin, both epidermis and dermis were strongly stained by antisera against salarin and salmon kininogen. In epidermis the intercellular space seemed to be heavily stained (salarin). In kidney, the inhibitors were mainly localized to the interstitial capillaries. Also, some epithelial cells of the tubules (salarin) and some cells of the interstitium were stained. Mostly, the staining had a diffuse cytoplasmic localization. In the liver some hepatocytes were strongly positive for salarin and salmon kininogen. Purified fish cysteine proteinase inhibitors were not found to inhibit the growth of fish pathogenic bacteria and viruses. In the trunk kidney cathepsins B and L were localized in epithelial cells of the tubules (proximal part) and in cells of the interstitium. Mostly, the staining showed a prominent lysosomal localization. In head kidney large macrophage-like cells were positively stained for cathepsin B. The staining was localized to granula/vacuoles in the cytoplasm. In the liver, some hepatocytes were strongly stained and some were less strongly positive for cathepsin B and L. Mostly, the hepatocytes showed lysosomal staining. Cathepsin L was found in some big macrophage-like cells in the spleen. Mucosal epithelial cells of the esophagus and intestine seemed to be strongly stained for cathepsin B and L. The results show that cathepsins and their inhibitors are specifically and widely distributed in the Atlantic salmon skin indicating that they perform some biologically important and specific but so far unknown functions.

Expression of cathepsin K mRNA and protein in odontoclasts after experimental tooth movement in the mouse maxilla by in situ hybridization and immunoelectron microscopy.

This study demonstrated the simultaneous expression of cathepsin K (CK) mRNA by in situ hybridization and CK protein by immunoelectron microscopy in odontoclasts in mouse maxillae after experimental tooth movement. On the pressure side (the area under pressure during tooth movement), CK mRNA was detected in odontoclasts in resorption lacunae in the tooth root, in osteoclasts in bone resorption lacuane, and in fibroblasts in the periodontal ligament. Using electron microscopy, CK protein was detected at the apex of odontoclasts, intracellularly in vesicles and granules, and extracellularly in irregularly shaped vacuoles (extracellular spaces), on the plasma membrane of the ruffled border, and on and between typical striated type I collagen fibrils in the lacunae. These vesicles and granules appeared to fuse with irregular vacuoles containing CK-positive fragmented fibril-like structures close to the ruffled border. In the basolateral portion of odontoclasts, small amounts of CK-positive rough endoplasmic reticulum (ER) were found. CK-positive intracellular vacuoles (not extracellular spaces) also appeared to fuse with the vesicles and granules. However, these fused organelles rarely contained fragmented fibril-like structures. They are probably endolysosomes. The distribution of CK in odontoclasts was similar to that previously seen in osteoclasts. Furthermore, CK-positive fibril-like structures were found in the vacuoles of fibroblasts. These results indicated that during tooth movement CK is synthesized in odontoclasts on the pressure side and secreted into the tooth resorption lacunae. Therefore, CK may take part in the degradation of the dentin matrix (type I collagen fibrils and non-collagenous protein) of the tooth root, and in the subsequent intracellular degradation of endocytosed fragmented fibril-like structures in endolysosomes.

Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro.

Nanoscale control of the polymerization of silicon and oxygen determines the structures and properties of a wide range of siloxane-based materials, including glasses, ceramics, mesoporous molecular sieves and catalysts, elastomers, resins, insulators, optical coatings, and photoluminescent polymers. In contrast to anthropogenic and geological syntheses of these materials that require extremes of temperature, pressure, or pH, living systems produce a remarkable diversity of nanostructured silicates at ambient temperatures and pressures and at near-neutral pH. We show here that the protein filaments and their constituent subunits comprising the axial cores of silica spicules in a marine sponge chemically and spatially direct the polymerization of silica and silicone polymer networks from the corresponding alkoxide substrates in vitro, under conditions in which such syntheses otherwise require either an acid or base catalyst. Homology of the principal protein to the well known enzyme cathepsin L points to a possible reaction mechanism that is supported by recent site-directed mutagenesis experiments. The catalytic activity of the "silicatein" (silica protein) molecule suggests new routes to the synthesis of silicon-based materials.

pH-induced conformational transitions of the propeptide of human cathepsin L. A role for a molten globule state in zymogen activation.

Synthesis of proteases as inactive zymogens is a very important mechanism for the regulation of their activity. For lysosomal proteases proteolytic cleavage of the propeptide is triggered by the acidic pH. By using fluorescence, circular dichroism, and NMR spectroscopy, we show that upon decreasing the pH from 6.5 to 3 the propeptide of cathepsin L loses most of the tertiary structure, but almost none of the secondary structure is lost. Another partially structured intermediate, prone to aggregation, was identified between pH 6.5 and 4. The conformation, populated below pH 4, where the activation of cathepsin L occurs, is not completely unfolded and has the properties of molten globule, including characteristic binding of the 1-anilinonaphthalene-8-sulfonic acid. This pH unfolding of the propeptide parallels a decrease of its affinity for cathepsin L and suggests the mechanism for the acidic zymogen activation. Addition of anionic polysaccharides that activate cathepsin L already at pH 5.5 unfolds the tertiary structure of the propeptide at this pH. Propeptide of human cathepsin L which is able to fold independently represents an evolutionary intermediate in the emergence of novel inhibitors originating from the enzyme proregions.