Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development.
Sleeping sickness and Chagas disease are among the most severe diseases in Africa as well as Latin America. These two diseases are caused by Trypanosoma spp. Recently, an enzyme of a glycolytic pathway, NAD-dependent glycerol-3-phosphate dehydrogenase, of Leishmania mexicana was crystallized and its structure determined by x-ray crystallography. This structure has offered an excellent template for modeling of the homologous enzymes from another Trypanosoma species. Here, a homology model of the T. brucei enzyme based on the x-ray structure of LmGPDH has been generated. This model was used as the starting point for molecular dynamics simulation in a water box. The analysis of the molecular dynamics trajectory indicates that the functionally important motifs have both a very stable secondary structure and tertiary arrangement.
Zubrzycki
Igor Z
IZ
Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa. i.zubrzycki@ru.ac.za
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D015195:Drug Design; D004795:Enzyme Stability; D005993:Glycerolphosphate Dehydrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007894:Leishmania mexicana / Q000201:enzymology / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009243:NAD / Q000378:metabolism; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013816:Thermodynamics; D016833:Trypanosoma brucei rhodesiense / Q000201:enzymology* / Q000235:genetics; D014353:Trypanosomiasis, African / Q000188:drug therapy / Q000469:parasitology
D009243:NAD; D005993:Glycerolphosphate Dehydrogenase