In Silico Pocket and Binding Sites Detection of Acinetobacter Baumannii Outer Membrane Protein, FilF, As a Potential Vaccine Candidate

Introduction: Acinetobacter baumannii has emerged as an important pathogen causing a variety of infections. Due to the prevalence of infections and outbreaks caused by multi-drug resistant A. baumannii, few antibiotics are effective for treating infections caused by this pathogen. Therefore treatment of A. baumannii infections has become a considerable health care challenge and new strategies against its infections are needed. Because of outer membrane proteins importance as vaccine candidate, we exploited bioinformatic tools to detection of pocket and binding sites of baumannii fimbrial protein, FilF, that recently was predicted as a potential vaccine candidate.Methods: multi-scale pockets on protein surfaces were finding by GHECOM server that used mathematical morphology. castP is another server we used to identification and measurements of surface accessible pockets as well as interior inaccessible cavities for query protein. MetaPocket 2.0 (MPK2) server employs eight element predictors: LIGSITEcs, PASS, Q-SiteFinder, SURFNET, Fpocket, GHECOM, ConCavity and POCASA to predict protein pockets and potential binding sites. Furthermore we used SiteHound-web, PLB_SAVE web system, eF-seek and Depth servers for potential binding sites prediction.Results: Ligand binding sites determined using these softwares, indicate involvement of conserved residues from 477 to 590. Pockets and graph of residue-based pocketness are presented in the article.

کلیدواژه ها:

Acinetobacter baumannii ، Vaccine candidate ، FilF ، Pocket and Binding sites ، Bioinformatic