Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: construction of models and comparison with experiment.
Homology modeling methods have been used to construct models of two proteins--the histidine-containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil-derived neurotoxin (EDN). Comparison of the models with the subsequently determined X-ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X-ray structures in these regions--possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X-ray structure. The loop regions of EDN were incorrectly modeled--reasons for this and possible enhancements are discussed.
Church
W B
WB
Biosym Technologies, Inc., San Jose, California 95129, USA.
Palmer
A
A
Wathey
J C
JC
Kitson
D H
DH
D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D003196:Computer Graphics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D047208:Eosinophil-Derived Neurotoxin; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009174:Mycoplasma / Q000737:chemistry; D009498:Neurotoxins / Q000737:chemistry*; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012260:Ribonucleases; D016415:Sequence Alignment; D012984:Software
D001426:Bacterial Proteins; D009498:Neurotoxins; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; D047208:Eosinophil-Derived Neurotoxin; D012260:Ribonucleases