RELATIONSHIP BETWEEN THERMAL-STABILITY AND 3-D STRUCTURE IN A HOMOLOGY MODEL OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA-COLI

To reveal the structural basis of the increased thermal stability of 3 -isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus, an e xtreme thermophile, the homology-based structural model of one mesophi lic (Escherichia coli) counterpart, was constructed, Both IPMDHs are h omodimeric proteins. We built a model of one subunit using the 3-D str uctures of the Th.thermophilus IPMDH and the homologous E.,coli isocit rate dehydrogenase, Energy minimization and molecular dynamics simulat ed annealing were performed on the dimer, including a surrounding solv ation shell, No serious errors were detected in the refined model usin g 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 Thermophilus than in the E.coli enzyme, An increase was observed in the stabilities of alpha-helical regions in the thermophilic protei n. The preliminary X-ray coordinates of the E.coli IPMDH were received after the completion of this work, allowing an assessment of the mode l in terms of the X-ray structure, The comparison proved that most of the structural features underlying the stability differences between t he two enzymes were predicted correctly.