Protein Engineering vol. 8 no. 8 pp. 779-789, 1995
© 1995 Oxford University Press
RESEARCH-ARTICLE |
Structural basis for the extreme thermostability of D-glyceraldehyde-3-phosphate dehydrogenase from Thermotoga maritima: analysis based on homology modelling
Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences Pf. 7, H–1518 Budapest, Hungary
1To whom correspondence should be addressed
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.
Keywords: glyceraldehyde-3-phosphate dehydrogenase/homology/modelling/protein structure prediction/thermophiles/thermostability
Received November 21, 1994; revised May 2, 1995; accepted May 29, 1995.
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