Relationship between thermal stability and 3-D structure in a homology model of 3-isopropylmalate dehydrogenase from Escherichia coli

Protein Eng. 1996 Aug;9(8):663-70. doi: 10.1093/protein/9.8.663.


To reveal the structural basis of the increased thermal stability of 3-isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus, an extreme thermophile, the homology-based structural model of one mesophilic (Escherichia coli) counterpart, was constructed. Both IPMDHs are homodimeric proteins. We built a model of one subunit using the 3-D structures of the Th. thermophilus IPMDH and the homologous E.coli isocitrate dehydrogenase. Energy minimization and molecular dynamics simulated annealing were performed on the dimer, including a surrounding solvation shell. No serious errors were detected in the refined model using the 3-D profile method. The resulting structure was scrutinized and compared with the structure of the Th.thermophilus IPMDH. Significant differences were found in the non-specific interactions including the hydrophobic effect. The model predicts a higher number of ion pairs in the Th.thermophilus than in the E.coli enzyme. An increase was observed in the stabilities of alpha-helical regions in the thermophilic protein. The preliminary X-ray coordinates of the E.coli IPMDH were received after the completion of this work, allowing an assessment of the model in terms of the X-ray structure. The comparison proved that most of the structural features underlying the stability differences between the two enzymes were predicted correctly.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3-Isopropylmalate Dehydrogenase
  • Alcohol Oxidoreductases / chemistry*
  • Amino Acid Sequence
  • Crystallography, X-Ray
  • Enzyme Stability
  • Escherichia coli
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Sequence Alignment


  • Alcohol Oxidoreductases
  • 3-Isopropylmalate Dehydrogenase