Structural analyses and engineering of the pmHAS enzyme to improve its functional performance: An in silico study

Abstract The Pasteurella multocida hyaluronic acid synthase (pmHAS) is reported to be able to solve the problem of hyaluronic acid (HA) polydispersity, while simplifying its purification process. In the present study, we tried to design a mutant pmHAS enzyme with improved functional properties. In this regard, several mutations were predicted and exerted within the active site of the enzyme. The obtained results showed that the mutant enzyme was more stable and was able to bind to its ligands with higher affinity. Given our results, the mutated enzyme could be used to produce HA more efficiently and prevent the breakdown of HA. Graphical Abstract

[1]  M. Rasaee,et al.  Design of an engineered ACE2 as a novel therapeutics against COVID-19 , 2020, Journal of Theoretical Biology.

[2]  S. Khalili,et al.  Suramin could block the activity of Arabinono-1, 4-lactone oxidase enzyme from Leishmania donovani: structure-based screening and molecular dynamics analyses. , 2020, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[3]  Zahra Payandeh,et al.  Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein , 2019, International reviews of immunology.

[4]  Y. Ghasemi,et al.  Trimeric autotransporter adhesins in Acinetobacter baumannii, coincidental evolution at work. , 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[5]  Yang Li,et al.  LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins , 2019, Nucleic Acids Res..

[6]  M. Ebrahimi,et al.  Bioinformatics analysis of single and multi-hybrid epitopes of GRA-1, GRA-4, GRA-6 and GRA-7 proteins to improve DNA vaccine design against Toxoplasma gondii , 2018, Journal of Parasitic Diseases.

[7]  J. Necas,et al.  Hyaluronic acid (hyaluronan): a review , 2018 .

[8]  M. Rasaee,et al.  In silico Prediction and in vitro Verification of a Novel Multi-Epitope Antigen for HBV Detection , 2017, Molecular Genetics, Microbiology and Virology.

[9]  S. Khalili,et al.  Structural analyses of the interactions between the thyme active ingredients and human serum albumin , 2017 .

[10]  Michael Feig,et al.  Computational protein structure refinement: almost there, yet still so far to go , 2017, Wiley interdisciplinary reviews. Computational molecular science.

[11]  K. Bebenek,et al.  Physiochemical properties and application of hyaluronic acid: a systematic review , 2016, Journal of cosmetic dermatology.

[12]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[13]  Oliviero Carugo,et al.  Half a century of Ramachandran plots. , 2013, Acta crystallographica. Section D, Biological crystallography.

[14]  Debswapna Bhattacharya,et al.  i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10 , 2013, PloS one.

[15]  C. Boeriu,et al.  Production methods for hyaluronan , 2013 .

[16]  Debswapna Bhattacharya,et al.  3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization , 2013, Proteins.

[17]  Marco Biasini,et al.  Toward the estimation of the absolute quality of individual protein structure models , 2010, Bioinform..

[18]  Ian R. Wickersham,et al.  Production of glycoprotein-deleted rabies viruses for monosynaptic tracing and high-level gene expression in neurons , 2010, Nature Protocols.

[19]  Yang Zhang.  Protein structure prediction: when is it useful? , 2009, Current opinion in structural biology.

[20]  Sitao Wu,et al.  MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information , 2008, Proteins.

[21]  Silvio C. E. Tosatto,et al.  QMEAN: A comprehensive scoring function for model quality assessment , 2008, Proteins.

[22]  Cheng-Kang Lee,et al.  Hyaluronic acid production by recombinant Lactococcus lactis , 2007, Applied Microbiology and Biotechnology.

[23]  Sitao Wu,et al.  LOMETS: A local meta-threading-server for protein structure prediction , 2007, Nucleic acids research.

[24]  Robert Stern,et al.  Hyaluronic acid: a natural biopolymer with a broad range of biomedical and industrial applications , 2006, Biotechnology Letters.

[25]  René Thomsen,et al.  MolDock: a new technique for high-accuracy molecular docking. , 2006, Journal of medicinal chemistry.

[26]  P. Weigel,et al.  Hyaluronic Acid Production in Bacillus subtilis , 2005, Applied and Environmental Microbiology.

[27]  W. Jing,et al.  Synchronized Chemoenzymatic Synthesis of Monodisperse Hyaluronan Polymers* , 2004, Journal of Biological Chemistry.

[28]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[29]  Daniel F Gay,et al.  Rapid Chemoenzymatic Synthesis of Monodisperse Hyaluronan Oligosaccharides with Immobilized Enzyme Reactors* , 2003, Journal of Biological Chemistry.

[30]  M. Tammi,et al.  Hyaluronan-Cell Interactions in Cancer and Vascular Disease* , 2002, The Journal of Biological Chemistry.

[31]  P. Weigel,et al.  Topological Organization of the Hyaluronan Synthase fromStreptococcus pyogenes * , 2001, The Journal of Biological Chemistry.

[32]  R. Cortivo,et al.  In vitro reconstructed dermis implanted in human wounds: degradation studies of the HA-based supporting scaffold. , 2000, Biomaterials.

[33]  W. Jing,et al.  Dissection of the two transferase activities of the Pasteurella multocida hyaluronan synthase: two active sites exist in one polypeptide. , 2000, Glycobiology.

[34]  P. DeAngelis.  Hyaluronan synthases: fascinating glycosyltransferases from vertebrates, bacterial pathogens, and algal viruses , 1999, Cellular and Molecular Life Sciences CMLS.

[35]  P. DeAngelis.  Molecular Directionality of Polysaccharide Polymerization by thePasteurella multocida Hyaluronan Synthase* , 1999, The Journal of Biological Chemistry.

[36]  I. Stamenkovic,et al.  Inhibition of tumor growth in vivo by hyaluronan oligomers , 1998, International journal of cancer.

[37]  R. Drake,et al.  Identification and Molecular Cloning of a Unique Hyaluronan Synthase from Pasteurella multocida * , 1998, The Journal of Biological Chemistry.

[38]  M. Tammi,et al.  Hyaluronan Synthases* , 1997, The Journal of Biological Chemistry.

[39]  P. Prehm.  Release of hyaluronate from eukaryotic cells. , 1990, The Biochemical journal.

[40]  P. Prehm.  Hyaluronate is synthesized at plasma membranes. , 1984, The Biochemical journal.

[41]  K. Meyer.  The biological significance of hyaluronic acid and hyaluronidase. , 1947, Physiological reviews.

[42]  G. Stephanopoulos,et al.  Metabolic engineering of Escherichia coli for biosynthesis of hyaluronic acid. , 2008, Metabolic engineering.

[43]  Rachel Chen,et al.  Recombinant Synthesis of Hyaluronan by Agrobacterium sp. , 2007, Biotechnology progress.

[44]  Cheng-Kang Lee,et al.  Enhanced Hyaluronic Acid Production in Bacillussubtilis by Coexpressing Bacterial Hemoglobin , 2007, Biotechnology progress.

[45]  R. Savani,et al.  Hyaluronan-mediated angiogenesis in vascular disease: uncovering RHAMM and CD44 receptor signaling pathways. , 2007, Matrix biology : journal of the International Society for Matrix Biology.

[46]  L. Blank,et al.  Microbial hyaluronic acid production , 2004, Applied Microbiology and Biotechnology.