NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex.
Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.
Pauptit
R A
RA
AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, England. richard.pauptit@astrazeneca.com
Dennis
C A
CA
Derbyshire
D J
DJ
Breeze
A L
AL
Weston
S A
SA
Rowsell
S
S
Murshudov
G N
GN
D001426:Bacterial Proteins / Q000737:chemistry*; D003087:Colicins; D018360:Crystallography, X-Ray; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017479:Receptors, Platelet-Derived Growth Factor / Q000737:chemistry; D018909:src Homology Domains
D001426:Bacterial Proteins; D003087:Colicins; D010446:Peptide Fragments; C007104:colicin immunity proteins; D019869:Phosphatidylinositol 3-Kinases; D017479:Receptors, Platelet-Derived Growth Factor