Computational analysis of phylogenetic, functional and structural features of Bacillus hyaluronate lyases
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ORIGINAL ARTICLE
Computational analysis of phylogenetic, functional and structural features of Bacillus hyaluronate lyases Zeinab Karimi 1 & Leili Abed 2 & Ahmad Abdollahi 1,3 & Navid Nezafat 2,4
&
Younes Ghasemi 2,4
Received: 10 April 2020 / Accepted: 13 August 2020 # Institute of Molecular Biology, Slovak Academy of Sciences 2020
Abstract Hyaluronidases are a group of glycosidases enzymes, which are widely produced by different organisms. To find a bacterial source of hyaluronidases with promising industrial characteristics, different species of Bacillus were analyzed according to their various physiochemical properties, multiple sequence alignment, phylogenetic tree construction, homology search for motifs, and structural and functional properties via various computational approaches. The evaluation showed that the hyaluronidase of B. selenitireducens with the highest molecular mass, a high level of thermostability and solubility, and the phylogenetic relationship to hyaluronidas derivative from S. aureus can be considered as a potential candidate for biotechnological applications. Generally, the present study provides a detailed overview of functional, and structural characteristics as well as phylogenetic relation of Bacillus hyaluronidases, which could be helpful for future investigations in order to find the best bacterial hyaluronidase. Keywords Hyaluronate lyase . Bacillus sp. . Bioinformatic strategy . 3D modeling . Phylogenetic
Abbreviations CDD HAase MD BTH pI
PSIPRED Conserved Domain Database Hyaluronate lyase Molecular Dynamics Bovine testicular hyaluronidase Isoelectric point
Electronic supplementary material The online version of this article (https://doi.org/10.2478/s11756-020-00580-1) contains supplementary material, which is available to authorized users.
CFSSP PSI-BLAST 3D Mw EC GRAVY MSA
PSIblast based secondary structure prediction Chou and Fasman secondary structure prediction Position Specific Iterated - BLAST Three-dimensional Molecular weight Extinction coefficient Grand average of hydropathicity Multiple sequence alignment
* Navid Nezafat [email protected]
Introduction
* Younes Ghasemi [email protected]
Hyaluronidases (HAases) are a group of enzymes that are able to break down hyaluronan (hyaluronate, hyaluronic acid) to various lengths of oligosaccharide units. They are classified into mammalian, hookworm and bacterial hyaloroidase based on substrate specificity, biochemical analysis, and their final products (Kreil 1995; Meyer 1971). The broad existence of hyaluronic acid in the body and its involvement in physiological and pathological processes ranging from fertilization to aging have been led to finding various applications for hyaluronidases, mainly in pharmaceutical biotechnological industry. Hyaluronidase has been successfully utilized in
1
Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
2
Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
3
Cancer Research Center, Geras
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