Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function

Aizi Nor Mazila Ramli, Nor Muhammad Mahadi, Mohd Shahir Shamsir, Amir Rabu, Kwee Hong Joyce-Tan, Abdul Munir Abd. Murad, Rosli Md. Illias

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

The structure of psychrophilic chitinase (CHI II) from Glaciozyma antarctica PI12 has yet to be studied in detail. Due to its low sequence identity (<30 %), the structural prediction of CHI II is a challenge. A 3D model of CHI II was built by first using a threading approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9v7. Analysis of the catalytic insertion domain structure in CHI II revealed an increase in the number of aromatic residues and longer loops compared to mesophilic and thermophilic chitinases. A molecular dynamics simulation was used to examine the stability of the CHI II structure at 273, 288 and 300 K. Structural analysis of the substrate-binding cleft revealed a few exposed aromatic residues. Substitutions of certain amino acids in the surface and loop regions of CHI II conferred an increased flexibility to the enzyme, allowing for an adaptation to cold temperatures. A substrate binding comparison of CHI II with the mesophilic chitinase from Coccidioides immitis, 1D2K, suggested that the psychrophilic adaptation and catalytic activity at low temperatures were achieved through a reduction in the number of salt bridges, fewer hydrogen bonds and an increase in the exposure of the hydrophobic side chains to the solvent.

Original languageEnglish
Pages (from-to)947-961
Number of pages15
JournalJournal of Computer-Aided Molecular Design
Volume26
Issue number8
DOIs
Publication statusPublished - Aug 2012

Fingerprint

Chitinases
Antarctic regions
Structural properties
templates
Substrates
predictions
structural analysis
Coccidioides
Structural analysis
amino acids
Molecular dynamics
catalytic activity
Amino acids
enzymes
insertion
Catalyst activity
Hydrogen bonds
flexibility
Substitution reactions
Enzymes

Keywords

  • 3D model
  • Chitinase
  • Cold adaptation
  • Flexibility
  • Psychrophilic

ASJC Scopus subject areas

  • Drug Discovery
  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. / Ramli, Aizi Nor Mazila; Mahadi, Nor Muhammad; Shamsir, Mohd Shahir; Rabu, Amir; Joyce-Tan, Kwee Hong; Abd. Murad, Abdul Munir; Md. Illias, Rosli.

In: Journal of Computer-Aided Molecular Design, Vol. 26, No. 8, 08.2012, p. 947-961.

Research output: Contribution to journalArticle

Ramli, Aizi Nor Mazila ; Mahadi, Nor Muhammad ; Shamsir, Mohd Shahir ; Rabu, Amir ; Joyce-Tan, Kwee Hong ; Abd. Murad, Abdul Munir ; Md. Illias, Rosli. / Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. In: Journal of Computer-Aided Molecular Design. 2012 ; Vol. 26, No. 8. pp. 947-961.
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