Determining OMP topology by computation, surface plasmon resonance and cysteine labelling: the test case of OMPG.
Bacterial outer-membrane proteins (OMP) are important in pathogenicity and the recently solved structure of OmpG provides an excellent test case for topological predictions since it is monomeric. Here we compare the results of applying several computerised structure prediction algorithms to the sequence of OmpG. Furthermore, we probe the OmpG topology by both an established chemical labelling approach and a new method which combines epitope insertion and surface plasmon resonance. The computational approaches are broadly accurate but the exact choice of the number of beta strands remains difficult. The algorithms also tend to predict the entire beta strand rather than just the transmembrane region. Epitope insertion clearly pinpoints exposed loops but its utility in defining buried or periplasmic sites is less clear cut. Cysteine-mutant labelling is largely confined to exposed residues but one periplasmic cysteine may be labelled by reagents entering via the OmpG pore.
Visudtiphole
Virak
V
Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle NE2 4HH, UK.
Chalton
David A
DA
Hong
Qi
Q
Lakey
Jeremy H
JH
D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D003545:Cysteine / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D018272:Porins / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D013194:Staining and Labeling; D020349:Surface Plasmon Resonance
D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; C114347:OmpG protein, E coli; D018272:Porins; D003545:Cysteine