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Insights from the in silico structural, functional and phylogenetic characterization of canine lysyl oxidase protein.

ABSTRACT: BACKGROUND:Lysyl oxidase is an extracellular regulatory enzyme with an imperative role in interlinking of collagen and elastin by oxidizing lysine residues. Lysyl oxidase has been implicated in incidence of mammary tumors in bitches. Therefore, it becomes significant to study the structural and functional features of this enzyme for a better understanding of its molecular mechanisms. RESULTS:The detailed computational investigation of the canine lysyl oxidase protein was analyzed in silico with respect to its physicochemical properties, secondary and tertiary structure predictions and functional analysis using standard bioinformatic tools. Lysyl oxidase is a flexible protein with an average molecular weight of around 46?kDa, unstable, hydrophilic, and extracellular (secretory) in nature. Twelve cysteine residues and a disulfide bridge were also found. Secondary structure analysis shows that most of the protein has predominant coiled configuration. A putative copper-binding region signature was predicted. The phylogenetic relationship of canine lysyl oxidase with a vast range of mammalian species indicates that the protein was very well conserved throughout the course of evolution. Top 10 interacting proteins were identified using STRING v10.0 analysis, elastin being the closest interacting protein. Functional analysis by InterproScan predicted protein's biological role in oxidation-reduction process. CONCLUSION:Understanding the structural and functional properties of the protein will facilitate a better understanding of its mechanism of enzyme action. Further, the predicted 3D model will serve as a cornerstone for further understanding towards the tumorigenesis potential of the protein.

SUBMITTER: Saleem A

PROVIDER: S-EPMC7295881 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Insights from the in silico structural, functional and phylogenetic characterization of canine lysyl oxidase protein.

Saleem Afnan A Rajput Shiveeli S

Journal, genetic engineering & biotechnology 20200616 1

<h4>Background</h4>Lysyl oxidase is an extracellular regulatory enzyme with an imperative role in interlinking of collagen and elastin by oxidizing lysine residues. Lysyl oxidase has been implicated in incidence of mammary tumors in bitches. Therefore, it becomes significant to study the structural and functional features of this enzyme for a better understanding of its molecular mechanisms.<h4>Results</h4>The detailed computational investigation of the canine lysyl oxidase protein was analyzed ...[more]

PMID: 32542505

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Project description:BackgroundCellulose is the primary component of the plant cell wall and an important source of energy for the ruminant and microbial protein synthesis in the rumen. Cell wall content is digested by anaerobic fermentation activity mainly of bacteria belonging to species Fibrobacter succinogenes, Ruminicoccus albus, Ruminococcus flavefaciens, and Butyrivibrio fibrisolvens. Bacteria belonging to the species Ruminococcus albus contain cellulosomes that enable it to adhere to and digest cellulose, and its genome encodes cellulases and hemicellulases. This study aimed to perform an in silico comparative characterization and functional analysis of cellulase from Ruminococcus albus to explore physicochemical properties and to estimate primary, secondary, and tertiary structure using various bio-computational tools. The protein sequences of cellulases belonging to 6 different Ruminococcus albus strains were retrieved using UniProt. In in silico composition of amino acids, basic physicochemical characteristics were analyzed using ProtParam and Protscale. Multiple sequence alignment of retrieved sequences was performed using Clustal Omega and the phylogenetic tree was constructed using Mega X software. Bioinformatics tools are used to better understand and determine the 3D structure of cellulase. The predicted model was refined by ModRefiner. Structure alignment between the best-predicted model and the template is applied to evaluate the similarity between structures.ResultsIn this study are demonstrated several physicochemical characteristics of the cellulase enzyme. The instability index values indicate that the proteins are highly stable. Proteins are dominated by random coils and alpha helixes. The aliphatic index was higher than 71 providing information that the proteins are highly thermostable. No transmembrane domain was found in the protein, and the enzyme is extracellular and moderately acidic. The best tertiary structure model of the enzyme was obtained by the use of Raptor X, which was refined by ModRefiner. Raptor X suggested the 6Q1I_A as one of the best homologous templates for the predicted 3D protein structure. Ramachandran plot analysis showed that 90.1% of amino acid residues are within the most favored regions.ConclusionsThis study provides for the first time insights about the physicochemical properties, structure, and function of cellulase, from Ruminococcus albus, that will help for detection and identification of such enzyme in vivo or in silico.

Project description:BackgroundCocoonase is a serine protease present in sericigenous insects and majorly involved in dissolving of sericin protein allowing moth to escape. Cocoon structure is made up of sericin protein which holds fibroin filaments together. Cocoonase enzyme hydrolyzes sericin protein without harming the fibroin. However, until date, no detailed characterization of cocoonase enzyme and its presence in wild silk moth Antheraea mylitta has been carried out. Therefore, current study aimed for detailed characterization of amplified cocoonase enzyme, secondary and tertiary structure prediction, sequence and structural alignment, phylogenetic analysis, and computational validation. Several computational tools such as ProtParam, Iterative Threading Assembly Refinement (I-TASSER), PROCHECK, SAVES v6.0, TM-align, Molecular Evolutionary Genetics Analysis (MEGA) X, and Figtree were employed for characterization of cocoonase protein.ResultsThe present study elucidates about the isolation of RNA, cDNA preparation, PCR amplification, and in silico characterization of cocoonase from Antheraea mylitta. Here, total RNA was isolated from head region of A. mylitta, and gene-specific primers were designed using Primer3 followed by PCR-based amplification and sequencing. The newly constructed 377-bp length sequence of cocoonase was subjected to in silico characterization. In silico study of A. mylitta cocoonase showed 26% similarity to A. pernyi strain Qing-6 cocoonase using Blastp and belongs to member of chymotrypsin-like serine protease superfamily. From phylogenetic study, it was found that A. mylitta cocoonase sequence is closely related to A. pernyi cocoonase sequence.ConclusionsThe present study revealed about the detailed in silico characterization of cocoonase gene and encoded protein obtained from A. mylitta head region. The results obtained infer the presence of cocoonase enzyme in the wild silkworm A. mylitta and can be used for cocoon degumming which will be a valuable and cost-effective strategy in silk industry.

Dataset Information

Insights from the in silico structural, functional and phylogenetic characterization of canine lysyl oxidase protein.

Publications

Insights from the in silico structural, functional and phylogenetic characterization of canine lysyl oxidase protein.

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