Analysis of Important H.pylori Outer Membrane Proteins by Detection of Common Sequences in Exposed Areas; in Silico Study

Fatemeh Tohidi¹, Omid Teymournejad^2*, Ali Taravati³, Khadijeh Jami al Ahmadi⁴ and Ramazan Rajabnia²

¹Department of Medical Biotechnology, School of Medicine, MashhadUniversity of Medical Sciences, Mashhad, Iran.

²Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran.

³Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran.

⁴Biotechnology Research Centre, Mashad University of Medical Sciences, Mashad, Iran.

DOI : http://dx.doi.org/10.13005/bbra/2184

ABSTRACT: H. pylori Outer membrane proteins (OMPs) play a main role in the pathogenesis.Our study aimed to study on computational investigation for determination of H. pylori OMPsstructures, accessible surface area and common amino acid sequences in exposed regions. BabA/BabB,AlpA/AlpB andSabA/SabB were analyzed. NCBI and PDB were used as databases. PHD, GOR4, SignalP3.0, CPH Models, PHYRE and VADAR servers and two software including Swiss PDB viewer and Discovery studio were used for all analysis. Seven, six, five, five, four and two sequences of exposed amino acid were identified for SabB, SabA, Alpa, AlpB, BabA and BabB, respectively. Sequence similarities between BabA,BabB,AlpA,AlpB,SabA and SabB were 7.6%. Similarity between BabA / BabB and AlpA/AlpB were approximately 41%. Similarity betweenSabA and SabB were 71.19%. The common areas in expose amino acid region were 86-89/56-58 in SabA/ SabB and 170-171, 34-37/186-187, 54-57 in AlpA /AlpB, respectively. Detection of exposed amino acid sequences of OMPs is very helpful for characterization of their corresponding receptor. A number of common regions, between SabA/ SabB and AlpA /AlpB, located on the exposed amino acid areas but none of the similar areas in BabA/B is located on the exposed amino acid regions. Exposed amino acid of OMPs isthe main sequences which are related to interaction with stomach epithelial cells.

KEYWORDS: AlpA; AlpB; BabA; SabA; Exposed amino acid sequences

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