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31 results for “serine protease”
Data for Corre et al., Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enterovirus in lake water, ISMEJ 2022
<p>Data for Corre et al., <em>Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enterovirus in lake water</em>, ISMEJ 2022</p> <p>The first file contains all data pertaining to experiments with isolates: collection date, isolation temperature, protease activity measured by 4 different approaches, antiviral effect on E11 and CVA9 (three replicates each); this table corresponds to the data shown in Supplementary Table 2.</p> <p>The second file contains the raw data for all lake water experiments (Figures 1 and 6): information on sample type, antiviral effect (measured in triplicate), presence of a protease inhibitor.</p>
Fig. 6 in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 6. The mortality of the larvae feed on an artficial diet with added dsRNA. (*Student's t-test, n = 3, P <0.05; **Student's t-test, n = 3, P <0.01).
Fig. 4 in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 4. Relatve trypsin gene (Spbtry1) expression levels as determined by qPCR at different tme points. Actn was used as an internal reference gene. (*Student's t-test, n = 3, P <0.05; **Student's t-test, n = 3, P <0.01).
Fig. 5 in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 5. Effect of Spbtry1 RNAi on Leguminivora glycinivorella larval development. (A) The body weight of larvae fed on an artficial diet with added dsRNA at different tme points. (B) Pictures of the larvae showing reduced body size and developmental stage afer 15 days on an artficial diet with added dsRNA. (*Student's t-test, n = 3, P <0.05; **Student's t-test, n = 3, P <0.01).
Fig. 3. A in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 3. A) Relatve Spbtry1 gene expression levels was determined by qPCR (histograms) and RT-PCR (gel pictures) in the synganglion (SY), cutcle (CU), salivary (SA), midgut (MG), ovary (OV), tests (TE), and fat body (FT) in the 3rd instar soybean pod borer larvae. Actn was used as an internal reference gene. (B) Relatve trypsin gene (Spbtry1) expression levels as determined by qPCR (histograms) and RT-PCR (gel pictures) in soybean pod borer eggs (EG), 1st (N1), 2nd (N2), 3rd (N3), 4th (N4) instar larvae and pupae (PU), and adults (AD). Actn was used as an internal reference gene. Relatve Spbtry1 gene expression was analyzed by MJ Optcon Monitor Sofware Version 3.1.
Fig. 2 in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 2. Phylogenetc tree analysis of Spbtry1 and 13 homologues of other lepidopteran trypsin- and chymotrypsin-like serine proteases. The phylogenetc tree analysis was performed using the neighbor-joining algorithm to estmate evolutonary distances in MEGA 6.method at a gap penalty of 10, a gap length penalty of 0.2, and a bootstrap value of 1,000 iteratons.
Conformational Ensembles Reveal the Origins of Serine Protease Catalysis - auxiliary data and code
<p>EnsemblePDB.zip - package version used to create pseudo-ensembles in the paper "Conformational Ensembles Reveal the Origins of Serine Protease Catalysis"</p> <p>serine_protease_ensembles.zip - data and code used to generate and analyze the data presented in the paper "Conformational Ensembles Reveal the Origins of Serine Protease Catalysis"</p>
Docking data for "The evolution of the SARS-CoV-2 spike protein for differential usage of the host transmembrane serine proteases entry pathway"
<p><br>The dataset includes predicted complexes of the SARS-CoV-2 Spike protein (specifically at the S2' cleavage site) with Hepsin and TMPRSS2 proteins. It contains data on three variants: Wuhan, Delta, and Omicron BA.1.</p> <p><strong>Compressed folders:</strong></p> <p>-357596-DeltaHepsin.tgz</p> <p>-357597-DeltaTMPRSS2.tgz</p> <p>-360039-WuhanHepsin.tgz</p> <p>-360042-TMPRSSWuhan.tgz</p> <p>-392981-TMPRSS-BA1_all.tgz</p> <p>-392982-Hepsin-BA-all.tgz</p> <p><strong>Each compressed folder contains the following:</strong></p> <p>-Initial structures in pdb format</p> <p>-Output complexes in pdb format</p> <p>-Clusters in pdb format</p> <p>-Protocols</p> <p>-Parameters</p> <p>-Scoring files</p> <p> </p> <p><strong>Protein-protein docking </strong><br>Molecular docking between the SARS-CoV-2 S protein of Wuhan, Delta (PDB: 7W92, [DOI: 10.1038/s41467-022-28528-w]), and BA.1 (PDB: 7XO5, [DOI: 10.1038/s41422-022-00672-4]) and the human proteases TMPRSS2 (PDB: 8HD8, [DOI: 10.1038/s41467-023-42527-5]) and Hepsin (PDB: 1Z8G, [DOI: 10.1042/BJ20041955]) was performed using the HADDOCK v2.5-2024.03 webserver ([DOI: 10.1021/ja026939x], [DOI: 10.1016/j.jmb.2015.09.014]). Missing loops in the protein structures were reconstructed using Modeller v10.5 ([DOI: 10.1006/jmbi.1993.1626]). Every heteroatom was removed from the reference structures. The relaxed atomistic coordinates for each S protein variant were derived via all-atom molecular dynamics (MD) simulations. These simulations were performed using AMBER22 with the FF19SB force fields and the pmemd.cuda module for enhanced performance ([DOI: 10.1021/acs.jcim.3c01153], [DOI: 10.1021/jz501780a], [DOI:10.1021/ct400314y]). For the Wuhan variant the S protein was retrieved from our previous modeling study [DOI: 10.1039/D0NR03969A] where for Delta and BA.1, ecah S protein was placed in a dodecahedral box, extending 20 Å beyond the solute in every cartesian direction, and solvated with the four-site OPC water model ([DOI: 10.1021/jz501780a]). The systems were neutralized with counterions, specifically one Cl− ion for the Delta variant and three Cl- ions for the BA.1 variant. To remove local clashes, a geometric optimization was performed using the steepest descent algorithm for 5000 cycles. The MD equilibration process consisted of several stages. First, temperature equilibration in the NVT ensemble was performed by gradually increasing the temperature through steps of 150, 200, 250, 300, and finally 310 K, each lasting 200 ps. During this phase, position restraints were applied to the heavy atoms of the proteins, with progressively decreasing spring constants of 5.0, 4.0, 3.0, and 1.0 kcal mol−1 Å−2, facilitating gradual relaxation. This was followed by a 1 ns equilibration at 310 K in the NPT ensemble without restraints. For production MD, the simulations were run in the NPT ensemble with periodic boundary conditions and Particle Mesh Ewald (PME) method ([DOI: 10.1063/5.0040966], [DOI: 10.1021/ct9001015]) using a grid spacing of 1.0 Å for long-range electrostatics. Non-bonded interactions were modeled with a Lennard-Jones potential using a 9Å cutoff. Temperature control was maintained using Langevin dynamics ([DOI: 10.1021/ct800573m]) with a collision frequency of 4.0 ps−1, and pressure control was managed by the Monte Carlo barostat ([DOI: 10.1016/j.cplett.2003.12.039]) with a 2.0 ps relaxation time at 1 bar. Bond constraints on hydrogen atoms were applied using the SHAKE algorithm ([DOI: 10.1016/0021-9991(77)90098-5]), and the hydrogen mass repartitioning scheme was applied via ParmEd ([DOI: 10.1371/journal.pcbi.1005659]), enabling a 4 fs integration time step ([DOI: 10.1021/ct5010406]). Each protein complex was simulated for a total of 20 ns. For the Wuhan variant, the 3D coordinates were retrieved from [DOI: 10.5281/zenodo.3817446].<br>The active interaction region on the spike protein was defined as the cleavage site (residues P809-R815). For TMPRSS2 and Hepsin, the active sites were defined based on their catalytic residues: H296, D345, D435, S441, S460, and G462 for TMPRSS2, and H203, D257, D347, A348, and S353 for Hepsin. These specific regions were selected to guide the docking process and maximize biologically relevant interactions. Docking clusters were analyzed by selecting those with the lowest interaction energies for further structural analysis. To evaluate binding accuracy, native contacts between the S protein and proteases were computed using the contact map analysis based on the OV+rCSU method ([DOI: 10.12693/APhysPolA.145.S9, 10.1021/acs.jctc.6b00986]), which allows for a precise identification of critical stabilizing interactions, both specific and non-specifics. High-frequency contacts, defined as those appearing in over 70% of the generated models, were highlighted as key determinants of protein-protein recognition, providing insight into the most stable and consistent interactions across docking configurations.</p>
Upamostat, a Serine Protease Inhibitor, or Placebo for Treatment of COVID-19 Disease
ClinicalTrials.gov study NCT04723537. IPD Sharing: NO. Countries: 2. Publications: 2.
Data from: Temperature and sex related effects of serine protease alleles on larval development in the Glanville fritillary butterfly
The body reserves of adult Lepidoptera are accumulated during larval development. In the Glanville fritillary butterfly, larger body size increases female fecundity, but in males fast larval development and early eclosion, rather than large body size, increase mating success and hence fitness. Larval growth rate is highly heritable, but genetic variation associated with larval development is largely unknown. By comparing the Glanville fritillary population living in the Åland Islands in northern Europe with a population in Nantaizi in China, within the source of the post-glacial range expansion, we identified candidate genes with reduced variation in Åland, potentially affected by selection under cooler climatic conditions than in Nantaizi. We conducted an association study of larval growth traits by genotyping the extremes of phenotypic trait distributions for 23 SNPs in 10 genes. Three genes in clip-domain serine protease family were associated with larval growth rate, development time and pupal weight. Additive effects of two SNPs in the prophenoloxidase-activating proteinase-3 (ProPO3) gene, related to melanization, showed elevated growth rate in high temperature but reduced growth rate in moderate temperature. The allelic effects of the vitellin-degrading protease precursor gene on development time were opposite in the two sexes, one genotype being associated with long development time and heavy larvae in females but short development time in males. Sexually antagonistic selection is here evident in spite of sexual size dimorphism.
Rosetta Loop Modeling Data for "A Systematic Approach for Evaluating the Role of Surface-Exposed Loops in Trypsin-like Serine Proteases: Analysis of the 170 loop in Coagulation Factor VIIa"
<p>Rosetta Loop Modeling data for the publication "A Systematic Approach for Evaluating the Role of Surface-Exposed Loops in Trypsin-like Serine Proteases: Analysis of the 170 loop in Coagulation Factor VIIa." See the included readme.txt for more details. Please cite the paper if you use these data.</p>
Serine Proteases in Gastrointestinal Function and Irritable Bowel Syndrome (IBS)
ClinicalTrials.gov study NCT01072916. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Temperature and sex related effects of serine protease alleles on larval development in the Glanville fritillary butterfly
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Data from: Phylogentic analysis of serine proteases from Russell's viper (Daboia russelli siamensis) and Agkistrodon piscivorus leucostoma venom
Serine proteases are widely found in snake venoms. They have variety of functions including contributions to hemostasis. In this study, five serine protease were cloned and characterized from two different cDNA libraries. Factor V activator (RVV-V), alpha fibrinogenase (RVAF) and beta fibrinogenase (RVBF) from Russell's viper (Daboia russelli siamensis), and plasminogen activator (APL-PA) and protein C activator (APL-C) from Agkistrodon piscivorus leucostoma. The snake venom serine proteases were clustered in phylogenetic tree according to their functions. KA/KS values suggested that accelerated evolution has occurred in the mature protein-coding regions in cDNAs of snake venom serine proteases.
Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales
Background: Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales. Results: A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales. Conclusions: Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future.
Fig. 1 in RNA interference mediated serine protease gene (Spbtry1) knockdown affects growth and mortality in the soybean pod borer (Lepidoptera: Olethreutidae)
Fig. 1. Nucleotde and deduced amino acid sequences of Spbtry1 cDNA cloned from Leguminivora glycinivorella. The numbers on the lef and right refer to the amino acid sequence. The putatve signal peptde of 17 amino acids is in bold and the cleavage site is indicated by an arrow. The cleavage site for the putatve propeptde removal is indicated by an arrowhead. The stop codon TAA is indicated by an asterisk. The putatve polyadenylaton signal (AATAA) is underlined. The putatve serine protease conserved motf (GDSGGPL) is boxed. The 3 amino acid residues (His72, Asp118, and Ser216) of the catalytc triad for serine protease actvity are indicated with white letters on a gray background. GenBank accession no. JQ340915.
Additional data "The early communication stages between serine proteases and enterovirus capsids in the race for viral disintegration" Corre et al.2023
<p>The deposited files contain the SI videos.</p>
Data from: Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales
Open the record for dataset details and reuse information.
Data from: Phylogentic analysis of serine proteases from Russell’s viper (Daboia russelli siamensis) and Agkistrodon piscivorus leucostoma venom
Open the record for dataset details and reuse information.
Single cell sequencing identifies serine proteases as regulators of myofibroblast differentiation
GEO Series GSE156326. Homo sapiens; Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
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