Structure Prediction of a Novel Exo-β-1,3-Glucanase

Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12

Salimeh Mohammadi, Sepideh Parvizpour, Jafar Razmara, Farah Diba Abu Bakar, Rosli Md Illias, Nor Muhammad Mahadi, Abdul Munir Abd. Murad

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)157-168
Number of pages12
JournalInterdisciplinary Sciences: Computational Life Sciences
Volume10
Issue number1
DOIs
Publication statusPublished - 1 Mar 2018

Fingerprint

Structural analysis
Yeast
Yeasts
Polysaccharides
Molecular dynamics
Amino acids
Catalyst activity
Hydrogen bonds
Substitution reactions
Enzymes
Salts
Amino Acid Substitution
Molecular Dynamics Simulation
Amino Acids
Sequence Analysis
Hydrogen
Catalytic Domain
Computer simulation
Substrates
Software

Keywords

  • Cold-adapted exo-β-1,3-glucanase
  • Flexibility
  • Homology modeling
  • Psychrophilic

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science Applications
  • Health Informatics

Cite this

Structure Prediction of a Novel Exo-β-1,3-Glucanase : Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12. / Mohammadi, Salimeh; Parvizpour, Sepideh; Razmara, Jafar; Abu Bakar, Farah Diba; Illias, Rosli Md; Mahadi, Nor Muhammad; Abd. Murad, Abdul Munir.

In: Interdisciplinary Sciences: Computational Life Sciences, Vol. 10, No. 1, 01.03.2018, p. 157-168.

Research output: Contribution to journalArticle

@article{5ba475073809430f95d6bfc853cf62c4,
title = "Structure Prediction of a Novel Exo-β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12",
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.",
keywords = "Cold-adapted exo-β-1,3-glucanase, Flexibility, Homology modeling, Psychrophilic",
author = "Salimeh Mohammadi and Sepideh Parvizpour and Jafar Razmara and {Abu Bakar}, {Farah Diba} and Illias, {Rosli Md} and Mahadi, {Nor Muhammad} and {Abd. Murad}, {Abdul Munir}",
year = "2018",
month = "3",
day = "1",
doi = "10.1007/s12539-016-0180-9",
language = "English",
volume = "10",
pages = "157--168",
journal = "Interdisciplinary sciences, computational life sciences",
issn = "1913-2751",
publisher = "Springer Verlag",
number = "1",

}

TY - JOUR

T1 - Structure Prediction of a Novel Exo-β-1,3-Glucanase

T2 - Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12

AU - Mohammadi, Salimeh

AU - Parvizpour, Sepideh

AU - Razmara, Jafar

AU - Abu Bakar, Farah Diba

AU - Illias, Rosli Md

AU - Mahadi, Nor Muhammad

AU - Abd. Murad, Abdul Munir

PY - 2018/3/1

Y1 - 2018/3/1

N2 - 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.

AB - 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.

KW - Cold-adapted exo-β-1,3-glucanase

KW - Flexibility

KW - Homology modeling

KW - Psychrophilic

UR - http://www.scopus.com/inward/record.url?scp=85034011842&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85034011842&partnerID=8YFLogxK

U2 - 10.1007/s12539-016-0180-9

DO - 10.1007/s12539-016-0180-9

M3 - Article

VL - 10

SP - 157

EP - 168

JO - Interdisciplinary sciences, computational life sciences

JF - Interdisciplinary sciences, computational life sciences

SN - 1913-2751

IS - 1

ER -