Homology Model of Surface Antigen OmpC FromSalmonella typhiand its Functional Implications

Abstract

Homology based 3D structural model of the immunodominant major surface antigen OmpC from Salmonella typhi, an obligatory human pathogen, was built to understand the possible unique conformational features of its antigenic loops with respect to other immunologically cross reacting porins. The homology model was built based on the known crystal structures of the E. coli porins OmpF and PhoE. Structure based sequence alignment helped to define the structurally conserved regions (SCRs). The SCR regions of OmpC were modelled using the coordinates of corresponding regions from reference proteins. Surface exposed variable regions were modelled based on the sequence similarity and loop search in PDB. Structural refinement based on symmetry restrained energy minimization resulted in an agreeable model for the trimer of OmpC. The resulting model was compared with other porin structures, having b-barrel fold with 16 transmembrane beta-strands, and found that the variable regions are unique in terms of sequence and structure. A ranking of the loops taking into account the antigenic index, the sequence variability, the surface accessibility in the context of the trimer, and the structural variability suggests that loop 4 (151-172), loop 5 (194-218) and loop 6 (237-264) are the best ranked B-cell epitopes. The model provides possible explanations for the functional and unique immunological properties associated with the surface exposed regions and outlines the implications for structure based experimental design.

Identification of an I-Ed-Restricted T-Cell Epitope ofEscherichia coliOuter Membrane Protein F

“…In examining the threedimensional structure of OmpF (15), it was observed that the amino acid 295 to 314 T-cell epitope comprises a portion of the transmembrane region of the protein. The transmembrane regions of E. coli OmpF show limited sequence heterogeneity compared to OmpF sequences from other members of the family Enterobacteriaceae and compared to other E. coli porin molecules (OmpC, PhoE) (3,56). The comparison of known porin sequences from E. coli (11), Salmonella enterica serovar Typhimurium (39), S. enterica serovar Typhi (45), and Shigella flexneri 2a (67) 5.…”

Conformational epitope mapping of OmpC, a major cell surface antigen from Salmonella typhi

“…Though the S. typhi OmpC structure is from homology modelling, the residues His 21 and Asp 30 in the S. typhi OmpC model are in a similar conformation as the corresponding conserved residues in E. coli OmpF and PhoE structures. This hydrogen bond could stabilise the Loop-1 (Arockiasamy and Krishnaswamy, 2000b). Modification of His 21 would break this bond and destabilise Loop-1 that is located at the subunit interface region.…”

“…As indicated by the two Asp residues identified here, MPN5 binding seems to be mediated more by negative charge. Interestingly, from the structure based sequence alignment (Arockiasamy and Krishnaswamy, 2000b) Lys 334 and Asp 340, the residues implicated here as being part of the MPN5 (Salmonella specific) epitope are not present in E. coli. Protein was transferred to PVDF membrane from SDS-PAGE 10% gel.…”

“…Studies using Salmonella porin specific monoclonal antibodies (Muthukkaruppan et al, 1992) showed that S. typhi OmpC is the major surface antigen with unique exposed epitopes. Earlier, we have predicted possible continuous epitopes of S. typhi based on sequence (Arockiasamy and Krishnaswamy, 1995) and structural analysis (Arockiasamy and Krishnaswamy, 2000b;Sujatha et al, 2001). We here report, a study carried out on the conformational epitope mapping, a major cell surface antigen from the human pathogen S. typhi.…”

“…or 18 membrane spanning b-strands (specific porins: LamB and ScrY). The porin OmpC from Salmonella typhi is a 16-stranded porin (Arockiasamy and Krishnaswamy, 2000b). The possible expression of OmpC throughout the infection period (Puente et al, 1989) and its capacity to display heterologous epitopes on the cell surface (Puente et al, 1995) make it an important candidate antigen with potential applications in immunology and vaccine design.…”