Bioinformatics Centre, School of Biotechnology Madurai Kamaraj University, Maduari-625 021. India.
sa@caticsuf.CATI.CSUFresno.EDU
Porins are pore forming proteins present as trimers on the outermembrane of Gram negative bacteria and shown to be B-cell polyclonal activators. Presence of antiporin antibodies in typhoid patients sera shows the potential applications of S.typhi porins as diagnostic reagents and a tool for vaccine design. S.typhi OmpC, which is of 357 aa and 39 KDa mol Wt, is shown to be present in larger amounts during infection. The study of antigenic epitopes of S. typhi OmpC is important in order to understand its conformational features and uniqueness in comparision with other porins of Gram negative bacteria as they are highly cross reactive. A homology model of S.typhi OmpC monomer was built based on the crystal structures of E.coli porins OmpF and PhoE. The antigenic loops of S.typhi OmpC were compared in terms of sequence, conformational features and surface accessibility and compared with E.coli porins. S.typhi OmpC loops are unique in terms of length, sequence and structure. This model will be used for the structure determination of S.typhi OmpC which are being carried out. S.typhi OmpC trimer is generated using the symmetry information of E.coli OmpF. Antigenic loops are analysed in context of trimer and compared with E.coli porins. Electrostatic calculations of S.typhi OmpC is being carried out. These results will be discussed.