title: Relationship between thermal stability and 3-D structure in a homology model of 3-isopropylmalate dehydrogenase from Escherichia coli.
abstract: 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.
authors.affiliation: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
authors.forename: C
authors.initials: C
authors.lastname: Magyar
authors.forename: A
authors.initials: A
authors.lastname: Szilágyi
authors.forename: P
authors.initials: P
authors.lastname: Závodszky
mesh_terms: D050539:3-Isopropylmalate Dehydrogenase; D000429:Alcohol Oxidoreductases / Q000737:chemistry*; D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004795:Enzyme Stability; D004926:Escherichia coli; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment
chemical_list: D000429:Alcohol Oxidoreductases; D050539:3-Isopropylmalate Dehydrogenase