A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins

Abstract

Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted diseases and the leading cause of preventable blindness worldwide. Global control of Chlamydia will best be achieved with a vaccine, a primary target for which is the major outer membrane protein, MOMP, which comprises ~60% of the outer membrane protein mass of this bacterium. In the absence of experimental structural information on MOMP, three previously published topology models presumed a16-stranded barrel architecture. Here, we use the latest β-barrel prediction algorithms, previous 2D topology modeling results, and comparative modeling methodology to build a 3D model based on the 16-stranded, trimeric assumption. We find that while a 3D MOMP model captures many structural hallmarks of a trimeric 16-stranded β-barrel porin, and is consistent with most of the experimental evidence for MOMP, MOMP residues 320-334 cannot be modeled as β-strands that span the entire membrane, as is consistently observed in published 16-stranded β-barrel crystal structures. Given the ambiguous results for β-strand delineation found in this study, recent publications of membrane β-barrel structures breaking with the canonical rule for an even number of β-strands, findings of β-barrels with strand-exchanged oligomeric conformations, and alternate folds dependent upon the lifecycle of the bacterium, we suggest that although the MOMP porin structure incorporates canonical 16-stranded conformations, it may have novel oligomeric or dynamic structural changes accounting for the discrepancies observed.

Figure 1. TMBpro β-barrel topology predictions.

Normalized predicted probabilities for various strand models of (A) full length C. trachomatis serovar C sequence; (B) example output for C. trachomatis serovar C excluding a subset of residues that contains the leader sequence and all or parts of the four VDs: M1 – A23, A64 – P85, K152 – A158, T216 – I247, T282 – V310; (C) Neissera meningitidis PorB (3A2T.pdb protein sequence) ; and (D) Klebsiella pneumonia OmpK36 (1OSM.pdb protein sequence) .

Figure 2. β-strand predictions mapped onto MOMP sequences.

The output from β-strand prediction algorithms TMBpro, TMPRED and TMBBETA-NET (labeled pred1, pred2, and pred3, respectively) are delineated as blue boxes on the MOMP sequences from C. trachomatis serovar C. Previously reported β-strand predictions from 2D topology mapping for MOMP are shown for comparison on the sequences used in each publication, namely MOMP C. trachomatis serovar F and serovar D and C. muridarum . Red and black boxes delineate the N-terminal leader sequence and 4 variable domains, respectively. Sequence alignments and illustration made with UCSF-Chimera visualization tools (http://www.cgl.ucsf.edu/chimera) .

Figure 3. MOMP monomer model.

(A, B) Backbone superpositions of the 10 lowest energy monomer structures. The ribbons illustrate the relative RMS deviations for the backbone heavy atoms to the average structure by color from low to high (red). (C) The average backbone representation for the MOMP monomer superposed onto backbone coordinates for crystal structures OmpF, OmpC , Omp36K , PhoE , PorB and OprP (gray ribbon). Superpositions were made using MOE, optimizing for structural and sequence alignments. (D, E) The MOMP monomer 16-stranded β-barrel with backbone in ribbon representation, aromatic girdle residues and position of basic residue girdle (blue spheres), trimer interface and membrane interfaces, respectively. (F) The MOMP model, looking down the pore channel from the membrane exterior side (cyan ribbon) with putative anion pathway residues shown (cyan stick representation for R39, H92, R112) superposed on E. coli OmpF structure illustrating anion pathway residues (gray, 1HXX [73]).

Figure 4. Predicted topology of the C. trachomatis MOMP serovar C monomer.

Figure 5. MOMP trimer structural features.

(A) MOMP model surface, mapping of VD. Positions attaching the VDs to the barrel mapped (orange) onto the molecular surface of the MOMP trimer model. (B) MOMP loops 1 and 4 potential inter-monomer stabilizing contacts. Two of the three monomer β-barrels (green and magenta ribbon representation) illustrate the proximity of Loops 1 and 4. Their tryptophan and cysteine residues (space-filling atom representation) on neighboring trimer subunits are shown (C29 not modeled). Residues W252 and W273 are at the exterior membrane interface in the putative aromatic girdle.

Figure 6. MOMP model construction flowchart.