title: Protein flexibility and conformational states of Leishmania antigen eIF-4A: identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling.
abstract: Recent homology modeling studies have identified specific residues (epitope) of the Leishmania RNA helicase protein (LmeIF) that stimulates production of IL-12 cytokine. However, question remains concerning how LmeIF's N-terminal moiety initiates adjuvant effects. Extensive molecular modeling combining the normal mode analysis (NMA) and molecular dynamics simulations, in the present study, has demonstrated that the LmeIF structure may exist in two different forms corresponding to the extended and collapsed (closed) states of the entire structure. The computational results showed that the two domains of the LmeIF structure tend to undergo large fluctuations in a concerted fashion and have strong effect on the solvent accessible surface of the epitope situated on the N-terminal structure. The conformational freedom of the C-terminal domains may explain why the entire LmeIF protein is not as active as the N-terminal moiety. Thereafter, a comparative genome analysis with subsequent homology modeling and molecular electrostatic potential (MEP) techniques allowed us to predict a novel and plausible RNA helicase (LI-helicase) from the Listeria source with adjuvant property as observed for the Leishmania eIF-4A protein. The structural folding and MEP maps revealed similar topologies of the epitope of both LmeIF and LI-helicase proteins and striking identity in the local disposition of the charged groups. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:7.
authors.affiliation: Department of Pharmaceutical Sciences , College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA.
authors.forename: Ning-Ning
authors.initials: NN
authors.lastname: Wei
authors.forename: Adel
authors.initials: A
authors.lastname: Hamza
authors.forename: Ce
authors.initials: C
authors.lastname: Hao
authors.forename: Trudy
authors.initials: T
authors.lastname: Johnson-Scalise
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Xiu
authors.forename: Frederick
authors.initials: F
authors.lastname: Naftolin
authors.forename: Chang-Guo
authors.initials: CG
authors.lastname: Zhan
mesh_terms: D000595:Amino Acid Sequence; D000953:Antigens, Protozoan / Q000737:chemistry* / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D039601:Eukaryotic Initiation Factor-4A / Q000737:chemistry* / Q000235:genetics; D023281:Genomics; D007891:Leishmania / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment
chemical_list: D000953:Antigens, Protozoan; D039601:Eukaryotic Initiation Factor-4A