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Structure Prediction of a Novel Exo-β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12

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Abstract

We report a detailed structural analysis of the psychrophilic exo-β-1,3-glucanase (GaExg55) from Glaciozyma antarctica PI12. This study elucidates the structural basis of exo-1,3-β-1,3-glucanase from this psychrophilic yeast. The structural prediction of GaExg55 remains a challenge because of its low sequence identity (37 %). A 3D model was constructed for GaExg55. Threading approach was employed to determine a suitable template and generate optimal target–template alignment for establishing the model using MODELLER9v15. The primary sequence analysis of GaExg55 with other mesophilic exo-1,3-β-glucanases indicated that an increased flexibility conferred to the enzyme by a set of amino acids substitutions in the surface and loop regions of GaExg55, thereby facilitating its structure to cold adaptation. A comparison of GaExg55 with other mesophilic exo-β-1,3-glucanases proposed that the catalytic activity and structural flexibility at cold environment were attained through a reduced amount of hydrogen bonds and salt bridges, as well as an increased exposure of the hydrophobic side chains to the solvent. A molecular dynamics simulation was also performed using GROMACS software to evaluate the stability of the GaExg55 structure at varying low temperatures. The simulation result confirmed the above findings for cold adaptation of the psychrophilic GaExg55. Furthermore, the structural analysis of GaExg55 with large catalytic cleft and wide active site pocket confirmed the high activity of GaExg55 to hydrolyze polysaccharide substrates.

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Acknowledgments

We acknowledge support given by the Australian Antarctic Division and the Malaysian Antarctic Research Programme (MARP) of the Academy of Science, Malaysia.

Funding

This research was supported by a research grant from the Ministry of Science Technology and Innovation (MOSTI), Malaysia under the research Grants 10-05-16-MB002 and 02-05-20-SF0007.

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Authors and Affiliations

  1. School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia

    Salimeh Mohammadi, Farah Diba Abu Bakar & Abdul MunirAbdul Murad

  2. Department of Bioprocess Engineering, Faculty of Chemical and Natural Resources Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia

    Rosli Md Illias

  3. Malaysia Genome Institue, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia

    Nor Muhammad Mahadi

  4. Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran

    Sepideh Parvizpour

  5. Department of Computer Sciences, University of Tabriz, Tabriz, Iran

    Jafar Razmara

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  1. Salimeh Mohammadi
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Correspondence to Salimeh Mohammadi.

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Mohammadi, S., Parvizpour, S., Razmara, J. et al. Structure Prediction of a Novel Exo-β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12. Interdiscip Sci Comput Life Sci 10, 157–168 (2018). https://doi.org/10.1007/s12539-016-0180-9

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