Structural basis for the extreme thermostability of d-glyceraldehyde-3-phosphate dehydrogenase from Thermotoga maritima: Analysis based on homology modelling

András Szilágyi, P. Závodszky

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31 Citations (Scopus)

Abstract

D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from a hyperthermophilic eubacterium, Thermotoga maritima, is remarkably heat stable (Tm = 109°C). In this work, we have applied homology modelling to predict the 3-D structure of Th.maritima GAPDH to reveal the structural basis of thermostability. Three known GAPDH structures were used as reference proteins. First, the rough model of one subunit was constructed using the identified structurally conserved and variable regions of the reference proteins. The holoenzyme was assembled from four subunits and the NAD molecules. The structure was refined by energy minimization and molecular dynamics simulated annealing. No errors were detected in the refined model using the 3-D profile method. The model was compared with the structure of Bacillus stearothermophilus GAPDH to identify structural details underlying the increased thermostability. In all, 12 extra ion pairs per subunit were found at the protein surface. This seems to be the most important factor responsible for thermostability. Differences in the non-specific interactions, including hydration effects, were also found. Minor changes were detected in the secondary structure. The model predicts that a slight increase in a-helical propensities and helix-dipole interactions also contribute to increased stability, but to a lesser degree.

Original languageEnglish
Pages (from-to)779-789
Number of pages11
JournalProtein Engineering, Design and Selection
Volume8
Issue number8
DOIs
Publication statusPublished - Aug 1995

Fingerprint

Thermotoga maritima
Glyceraldehyde-3-Phosphate Dehydrogenases
Phosphates
Proteins
Eubacterium
Geobacillus stearothermophilus
Holoenzymes
Bacilli
Molecular Dynamics Simulation
Simulated annealing
Hydration
NAD
Molecular dynamics
Membrane Proteins
Hot Temperature
Ions
Molecules
Oxidoreductases

Keywords

  • Glyceraldehyde-3-phosphate dehydrogenase
  • Homology
  • Modelling
  • Protein structure prediction
  • Thermophiles
  • Thermostability

ASJC Scopus subject areas

  • Pharmacology
  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Molecular Biology
  • Bioengineering
  • Biotechnology
  • Biochemistry

Cite this

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abstract = "D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from a hyperthermophilic eubacterium, Thermotoga maritima, is remarkably heat stable (Tm = 109°C). In this work, we have applied homology modelling to predict the 3-D structure of Th.maritima GAPDH to reveal the structural basis of thermostability. Three known GAPDH structures were used as reference proteins. First, the rough model of one subunit was constructed using the identified structurally conserved and variable regions of the reference proteins. The holoenzyme was assembled from four subunits and the NAD molecules. The structure was refined by energy minimization and molecular dynamics simulated annealing. No errors were detected in the refined model using the 3-D profile method. The model was compared with the structure of Bacillus stearothermophilus GAPDH to identify structural details underlying the increased thermostability. In all, 12 extra ion pairs per subunit were found at the protein surface. This seems to be the most important factor responsible for thermostability. Differences in the non-specific interactions, including hydration effects, were also found. Minor changes were detected in the secondary structure. The model predicts that a slight increase in a-helical propensities and helix-dipole interactions also contribute to increased stability, but to a lesser degree.",
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author = "Andr{\'a}s Szil{\'a}gyi and P. Z{\'a}vodszky",
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