scholarly journals PINIR: a comprehensive information resource for Pin-II type protease inhibitors

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nikhilesh K. Yadav ◽  
Nidhi S. Saikhedkar ◽  
Ashok P. Giri
Keyword(s):  
Protease Inhibitors ◽  
Disulfide Bond ◽  
Protein Sequences ◽  
Biochemical Properties ◽  
Information Resource ◽  
Alternative Processing ◽  
Comprehensive Information ◽  
Reactive Center ◽  
Signature Sequences ◽  
Species Specific

Abstract Background Serine protease inhibitors belonging to the Potato type-II Inhibitor family Protease Inhibitors (Pin-II type PIs) are essential plant defense molecules. They are characterized by multiple inhibitory repeat domains, conserved disulfide bond pattern, and a tripeptide reactive center loop. These features of Pin-II type PIs make them potential molecules for protein engineering and designing inhibitors for agricultural and therapeutic applications. However, the diversity in these PIs remains unexplored due to the lack of annotated protein sequences and their functional attributes in the available databases. Results We have developed a database, PINIR (Pin-II type PIs Information Resource), by systematic collection and manual annotation of 415 Pin-II type PI protein sequences. For each PI, the number and position for signature sequences are specified: 695 domains, 75 linkers, 63 reactive center loops, and 10 disulfide bond patterns are identified and mapped. Database analysis revealed novel subcategories of PIs, species-correlated occurrence of inhibitory domains, reactive center loops, and disulfide bond patterns. By analyzing linker regions, we predict that alternative processing at linker regions could generate PI variants in the Solanaceae family. Conclusion PINIR (https://pinir.ncl.res.in) provides a web interface for browsing and analyzing the protein sequences of Pin-II type PIs. Information about signature sequences, spatio-temporal expression, biochemical properties, gene sequences, and literature references are provided. Analysis of PINIR depicts conserved species-specific features of Pin-II type PI protein sequences. Diversity in the sequence of inhibitory domains and reactive loops directs potential applications to engineer Pin-II type PIs. The PINIR database will serve as a comprehensive information resource for further research into Pin-II type PIs.

scholarly journals Biochemical characterization of specific Alanine Decarboxylase (AlaDC) and its ancestral enzyme Serine Decarboxylase (SDC) in tea plants (Camellia sinensis)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Peixian Bai ◽  
Liyuan Wang ◽  
Kang Wei ◽  
Li Ruan ◽  
Liyun Wu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Camellia Sinensis ◽  
Biochemical Characterization ◽  
Specific Activity ◽  
Protein Sequences ◽  
Biochemical Properties ◽  
High Similarity ◽  
New Gene ◽  
Tea Plants

Abstract Background Alanine decarboxylase (AlaDC), specifically present in tea plants, is crucial for theanine biosynthesis. Serine decarboxylase (SDC), found in many plants, is a protein most closely related to AlaDC. To investigate whether the new gene AlaDC originate from gene SDC and to determine the biochemical properties of the two proteins from Camellia sinensis, the sequences of CsAlaDC and CsSDC were analyzed and the two proteins were over-expressed, purified, and characterized. Results The results showed that exon-intron structures of AlaDC and SDC were quite similar and the protein sequences, encoded by the two genes, shared a high similarity of 85.1%, revealing that new gene AlaDC originated from SDC by gene duplication. CsAlaDC and CsSDC catalyzed the decarboxylation of alanine and serine, respectively. CsAlaDC and CsSDC exhibited the optimal activities at 45 °C (pH 8.0) and 40 °C (pH 7.0), respectively. CsAlaDC was stable under 30 °C (pH 7.0) and CsSDC was stable under 40 °C (pH 6.0–8.0). The activities of the two enzymes were greatly enhanced by the presence of pyridoxal-5′-phosphate. The specific activity of CsSDC (30,488 IU/mg) was 8.8-fold higher than that of CsAlaDC (3467 IU/mg). Conclusions Comparing to CsAlaDC, its ancestral enzyme CsSDC exhibited a higher specific activity and a better thermal and pH stability, indicating that CsSDC acquired the optimized function after a longer evolutionary period. The biochemical properties of CsAlaDC might offer reference for theanine industrial production.

scholarly journals A cellular endolysosome-modulating pore-forming protein from a toad is negatively regulated by its paralog under oxidizing conditions

2020 ◽  
Vol 295 (30) ◽  
pp. 10293-10306 ◽  
Author(s):  
Qiquan Wang ◽  
Xianling Bian ◽  
Lin Zeng ◽  
Fei Pan ◽  
Lingzhen Liu ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Cell Biology ◽  
Biochemical Properties ◽  
Bacterial Toxin ◽  
Cell Physiology ◽  
Dependent Manner ◽  
Membrane Pore ◽  
Intracellular Vesicles

Endolysosomes are key players in cell physiology, including molecular exchange, immunity, and environmental adaptation. They are the molecular targets of some pore-forming aerolysin-like proteins (ALPs) that are widely distributed in animals and plants and are functionally related to bacterial toxin aerolysins. βγ-CAT is a complex of an ALP (BmALP1) and a trefoil factor (BmTFF3) in the firebelly toad (Bombina maxima). It is the first example of a secreted endogenous pore-forming protein that modulates the biochemical properties of endolysosomes by inducing pore formation in these intracellular vesicles. Here, using a large array of biochemical and cell biology methods, we report the identification of BmALP3, a paralog of BmALP1 that lacks membrane pore-forming capacity. We noted that both BmALP3 and BmALP1 contain a conserved cysteine in their C-terminal regions. BmALP3 was readily oxidized to a disulfide bond-linked homodimer, and this homodimer then oxidized BmALP1 via disulfide bond exchange, resulting in the dissociation of βγ-CAT subunits and the elimination of biological activity. Consistent with its behavior in vitro, BmALP3 sensed environmental oxygen tension in vivo, leading to modulation of βγ-CAT activity. Interestingly, we found that this C-terminal cysteine site is well conserved in numerous vertebrate ALPs. These findings uncover the existence of a regulatory ALP (BmALP3) that modulates the activity of an active ALP (BmALP1) in a redox-dependent manner, a property that differs from those of bacterial toxin aerolysins.

scholarly journals High light induces species specific changes in the membrane lipid composition of Chlorella

2020 ◽  
Vol 477 (13) ◽  
pp. 2543-2559
Author(s):  
Janka Widzgowski ◽  
Alexander Vogel ◽  
Lena Altrogge ◽  
Julia Pfaff ◽  
Heiko Schoof ◽  
...  
Keyword(s):  
Cell Membranes ◽  
De Novo ◽  
Algal Cell ◽  
Isotopic Labeling ◽  
Biochemical Properties ◽  
Membrane Lipid ◽  
Light Conditions ◽  
Hydrophobic Barrier ◽  
Glycerolipid Composition ◽  
Species Specific

Algae have evolved several mechanisms to adjust to changing environmental conditions. To separate from their surroundings, algal cell membranes form a hydrophobic barrier that is critical for life. Thus, it is important to maintain or adjust the physical and biochemical properties of cell membranes which are exposed to environmental factors. Especially glycerolipids of thylakoid membranes, the site of photosynthesis and photoprotection within chloroplasts, are affected by different light conditions. Since little is known about membrane lipid remodeling upon different light treatments, we examined light induced alterations in the glycerolipid composition of the two Chlorella species, C. vulgaris and C. sorokiniana, which differ strongly in their ability to cope with different light intensities. Lipidomic analysis and isotopic labeling experiments revealed differences in the composition of their galactolipid species, although both species likely utilize galactolipid precursors originated from the endoplasmic reticulum. However, in silico research of de novo sequenced genomes and ortholog mapping of proteins putatively involved in lipid metabolism showed largely conserved lipid biosynthesis pathways suggesting species specific lipid remodeling mechanisms, which possibly have an impact on the response to different light conditions.

scholarly journals Solution structure of sperm lysin yields novel insights into molecular dynamics of rapid protein evolution

2018 ◽  
Vol 115 (6) ◽  
pp. 1310-1315 ◽  
Author(s):  
Damien B. Wilburn ◽  
Lisa M. Tuttle ◽  
Rachel E. Klevit ◽  
Willie J. Swanson
Keyword(s):  
Protein Evolution ◽  
Solution Structure ◽  
Biochemical Characterization ◽  
Purifying Selection ◽  
Biochemical Properties ◽  
Targeted Mutagenesis ◽  
High Definition ◽  
Binding Interface ◽  
Accelerated Evolution ◽  
Species Specific

Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins that are part of systems under arms race dynamics often evolve at unparalleled rates that can produce atypical biochemical properties. In the marine mollusk abalone, lysin and vitelline envelope receptor for lysin (VERL) are a pair of rapidly coevolving proteins that are essential for species-specific interactions between sperm and egg. Despite extensive biochemical characterization of lysin—including crystal structures of multiple orthologs—it was unclear how sites under positive selection may facilitate recognition of VERL. Using a combination of targeted mutagenesis and multidimensional NMR, we present a high-definition solution structure of sperm lysin from red abalone (Haliotis rufescens). Unapparent from the crystallography data, multiple NMR-based analyses conducted in solution reveal clustering of the N and C termini to form a nexus of 13 positively selected sites that constitute a VERL binding interface. Evolutionary rate was found to be a significant predictor of backbone flexibility, which may be critical for lysin bioactivity and/or accelerated evolution. Flexible, rapidly evolving segments that constitute the VERL binding interface were also the most distorted regions of the crystal structure relative to what was observed in solution. While lysin has been the subject of extensive biochemical and evolutionary analyses for more than 30 years, this study highlights the enhanced insights gained from applying NMR approaches to rapidly evolving proteins.

SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files

2020 ◽  
Author(s):  
Ahmed Hafez ◽  
Ricardo Futami ◽  
Amir Arastehfar ◽  
Farnaz Daneshnia ◽  
Ana Miguel ◽  
...  
Keyword(s):  
Protein Sequences ◽  
Software Tool ◽  
Primer Design ◽  
Reference Sequence ◽  
Supplementary Information ◽  
Interactive Software ◽  
Rna Sequences ◽  
Content Mining ◽  
Species Specific ◽  
Flexible Application

Abstract Motivation Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis. Result SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets. Availabilityand implementation SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Trypsin-specific inhibitors from the basidiomycete Clitocybe nebularis with regulatory and defensive functions

Microbiology ◽  
2009 ◽  
Vol 155 (12) ◽  
pp. 3971-3981 ◽  
Author(s):  
Petra Avanzo ◽  
Jerica Sabotič ◽  
Sabina Anžlovar ◽  
Tatjana Popovič ◽  
Adrijana Leonardi ◽  
...  
Keyword(s):  
Protease Inhibitor ◽  
Serine Protease ◽  
Protease Inhibitors ◽  
Physiological Role ◽  
Serine Protease Inhibitor ◽  
Biochemical Properties ◽  
High Yield ◽  
Cdna Sequences ◽  
Predatory Insects ◽  
Endogenous Proteases

We have isolated serine protease inhibitors from the basidiomycete Clitocybe nebularis, CnSPIs, using trypsin affinity chromatography. Full-length gene and cDNA sequences were determined for one of them, named cnispin, and the recombinant protein was expressed in Escherichia coli at high yield. The primary structure and biochemical properties of cnispin are very similar to those of the Lentinus edodes serine protease inhibitor, until now the only member of the I66 family of protease inhibitors in the MEROPS classification. Cnispin is highly specific towards trypsin, with K i in the nanomolar range. It also exhibited weaker inhibition of chymotrypsin and very weak inhibition of subtilisin and kallikrein; other proteases were not inhibited. Inhibitory activity against endogenous proteases from C. nebularis revealed a possible regulatory role for CnSPIs in the endogenous proteolytic system. Another possible biological function in defence against predatory insects was indicated by the deleterious effect of CnSPIs on the development of larvae of Drosophila melanogaster. These findings, together with the biochemical and genetic characterization of cnispin, suggest a dual physiological role for this serine protease inhibitor of the I66 MEROPS family.

Relative Affinity of Plasmin for the α1-Macroglobulin, Cl Inactivator and α1-Antitrypsin Inhibitors

1975 ◽  
Author(s):  
Peter C. Harpel
Keyword(s):  
Complex Formation ◽  
Protease Inhibitors ◽  
Disulfide Bond ◽  
Light Chain ◽  
Binding Sites ◽  
Gel Electrophoresis ◽  
Molar Ratio ◽  
Molar Ratios ◽  
Relative Affinity ◽  
Quantitative Contribution

The quantitative contribution of three major plasma protease inhibitors in binding plasmin has been studied. Mixtures of plasmin and each of the purified inhibitors were analyzed by SDS-acrylamide gel electrophoresis. Plasmin remained bound to its inhibitors in the presence of SDS and urea. A 1 : 1 molar ratio for complex formation was established, and treatment of the complexes with a disulfide bond reducing agent showed that the light chain of plasmin contained the binding sites for both CĪ inactivator and α-antitrysin. Limited degradation of all three inhibitors by plasmin was observed, and the altered inhibitor remained complexed to the enzyme. The competitive binding of 125I plasmin to mixtures of these inhibitors was followed by sucrose density ultracentrifugation and by SDS-gel electrophoresis. In mixtures containing physiologic molar ratios of enzyme and inhibitors, over 80% of the bound plasmin was complexed to the α2-macroglobufui (α2M). No evidence for an exchange of plasmin between the inhibitors was obtained.

scholarly journals Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0124617 ◽  
Author(s):  
Jorge Duitama ◽  
Alexander Silva ◽  
Yamid Sanabria ◽  
Daniel Felipe Cruz ◽  
Constanza Quintero ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Marker Assisted Selection ◽  
Information Resource ◽  
Whole Genome ◽  
Rice Cultivars ◽  
Comprehensive Information

scholarly journals Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

2021 ◽  
Vol 118 (15) ◽  
pp. e2016239118
Author(s):  
Alexander Rives ◽  
Joshua Meier ◽  
Tom Sercu ◽  
Siddharth Goyal ◽  
Zeming Lin ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Amino Acids ◽  
Unsupervised Learning ◽  
Tertiary Structure ◽  
State Of The Art ◽  
Sequence Data ◽  
Protein Sequences ◽  
Representation Learning ◽  
Biological Properties ◽  
Biochemical Properties

In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.

scholarly journals Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

2019 ◽  
Author(s):  
Alexander Rives ◽  
Joshua Meier ◽  
Tom Sercu ◽  
Siddharth Goyal ◽  
Zeming Lin ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Amino Acids ◽  
Unsupervised Learning ◽  
Tertiary Structure ◽  
State Of The Art ◽  
Sequence Data ◽  
Protein Sequences ◽  
Representation Learning ◽  
Biological Properties ◽  
Biochemical Properties

In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure, and improving state-of-the-art features for long-range contact prediction.

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