title: Homology-Based Modeling of Universal Stress Protein fromListeria innocuaUp-Regulated under Acid Stress Conditions.
abstract: An Universal Stress Protein (USP) expressed under acid stress condition byListeria innocuaATCC 33090 was investigated. The USP was up-regulated not only in the stationary phase but also during the exponential growth phase. The three dimensional (3D) structure of USP was predicted using a combined proteomic and bioinformatics approach. Phylogenetic analysis showed that the USP fromListeriadetected in our study was distant from the USPs of other bacteria (such asPseudomonasspp.,Escherichia coli, Salmonellaspp.) and clustered in a separate and heterogeneous class including several USPs fromListeriaspp. andLactobacillusspp. An important information on the studied USP was obtained from the 3D-structure established through the homology modeling procedure. In detail, the Model_USP-691 suggested that the investigated USP had a homo-tetrameric quaternary structure. Each monomer presented an architecture analogous to the Rossmann-like α/β-fold with five parallel β-strands, and four α-helices. The analysis of monomer-monomer interfaces and quality of the structure alignments confirmed the model reliability. In fact, the structurally and sequentially conserved hydrophobic residues of the β-strand 5 (in particular the residues V146and V148) were involved in the inter-chains contact. Moreover, the highly conserved residues I139and H141in the region α4 were involved in the dimer association and functioned as hot spots into monomer-monomer interface assembly. The hypothetical assembly of dimers was also supported by the large interface area and by the negative value of solvation free energy gain upon interface interaction. Finally, the structurally conserved ATP-binding motif G-2X-G-9X-G(S/T-N) suggested for a putative role of ATP in stabilizing the tetrameric assembly of the USP. Therefore, the results obtained from a multiple approach, consisting in the application of kinetic, proteomic, phylogenetic and modeling analyses, suggest thatListeriaUSP could be considered a new type of ATP-binding USP involved in the response to acid stress condition during the exponential growth phase.
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Patrizio
authors.initials: P
authors.lastname: Tremonte
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Mariantonietta
authors.initials: M
authors.lastname: Succi
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Coppola
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Sorrentino
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Tipaldi
authors.affiliation: Institute of Food Science, National Research Council (ISA-CNR) Avellino, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Picariello
authors.affiliation: Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy.
authors.forename: Gianfranco
authors.initials: G
authors.lastname: Pannella
authors.affiliation: Randall Division of Cellular and Molecular Biophysics, New Hunt's House King's College London, UK.
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali
keywords: 2-D Electrophoresis; ATP-binding motif; Listeria; acid stress; exponential growth phase; homology modeling; universal stress protein