A novel modeling protocol for protein receptors guided by bound-ligand conformation.
A novel protocol for protein homology modeling is described, in which uncertainty in protein structure is resolved by applying the criterion that the protein must bind to a complementary ligand. A diverse library of protein models is created and then screened by docking with ligands of known conformation. The more accurate protein models form higher-quality docked complexes, and the quality of the fit is used to select the best models. The effectiveness of this technique with both natural and unnatural ligands is demonstrated by modeling the Fv fragment of an antibody and comparing the results to known crystal structures.
Johnson
Margaret A
MA
Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6. johnsont@sfu.ca
Höög
Christer
C
Pinto
B Mario
BM
D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry; D001666:Binding Sites, Antibody; D019295:Computational Biology / Q000379:methods; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D008024:Ligands; D051379:Mice; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry; D019151:Peptide Library; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D018000:Receptors, Peptide / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012763:Shigella flexneri / Q000276:immunology; D013816:Thermodynamics
D000911:Antibodies, Monoclonal; D007140:Immunoglobulin Fab Fragments; D008024:Ligands; D009842:Oligopeptides; D019151:Peptide Library; D018000:Receptors, Peptide