Structural vaccinology for melioidosis vaccine design and immunodiagnostics

Purpose of Review Spurred by the successful application of structural vaccinology to other challenging bacterial and viral pathogens, we review the possibility of exploiting 3D structure computational-based recombinant antigen engineering strategies for the development of a protective melioidosis vaccine. Recent Findings Structure-based epitope design approaches in the melioidosis field are preliminary and applied essentially by one research network. By combining Burkholderia pseudomallei antigen 3D structures and in silico epitope discovery methods, a panel of synthetic epitope peptides were designed and tested for their B and T cell stimulatory activities. Several peptides were found to be serodiagnostic for B. pseudomallei infection and two elicited bactericidal antibodies. Summary A significant amount of B. pseudomallei antigen structures, epitopes, and immunological data is available. Future challenges will be to test all available B. pseudomallei epitopes, focusing on combing multiple B/T cell epitopes onto a single scaffold to generate components, stimulating both arms of the immune system

A structure-based approach for novel immunodiagnostics targeting Trypanosoma cruzi and Schistosoma spp.

The tropical diseases Chagas Disease and Schistosomiasis, caused by the parasites Trypanosoma cruzi and Schistosoma spp, respectively, are often misdiagnosed and if untreated can be fatal. Indeed, their diagnosis presents a current challenge, due to difficulties in recognizing clinical symptoms and the lack of specific and reliable diagnostic tools. Highest prevalence is respectively in Latin America and Central Africa. However, massive human migration from endemic areas and travelling to tropical regions, contribute to the diffusion of these diseases in non-endemic areas, increasing the need of rapid diagnostic tools and prevention strategies. The aim of this project is to develop rapid, peptide-based microarrays that present multiple immunoreactive epitopes predicted from 3D protein structures of antigens from several pathogens, to be applied in point-of-care diagnostic kits for use in the Lombardy area of Italy. This approach showed promising results when applied to antigens from bacterial pathogens, in particular Burkholderia pseudomallei that led to the identification of epitopes with both diagnostic and therapeutic potential. Putative antigens selected from both parasites will be overexpressed, purified and crystallized for 3D structure studies. Based on the determined 3D protein structures, Molecular Dynamics (MD) analyses will be carried out and epitope predictions will be made on output MD structures using the Matrix of Local Coupling Energies method that detects residues located in conformationally dynamic regions of the protein surface. Predicted reactive epitopes will be synthetized as peptides, tested for immunoreactivity against immune sera from infected patients and used for antibody production. Selected immunoreactive synthetic peptides will be immobilised in specific orientations, using click chemistry, on a polymeric coated microarray chip. Sensitivity and specificity of the chip will be evaluated with sera of infected patients

The Escherichia coli Lpt transenvelope protein complex for lipopolysaccharide export is assembled via conserved structurally homologous domains

Lipopolysaccharide is a major glycolipid component in the outer leaflet of the outer membrane (OM), a peculiar permeability barrier of Gram-negative bacteria that prevents many toxic compounds from entering the cell. Lipopolysaccharide transport (Lpt) across the periplasmic space and its assembly at the Escherichia coli cell surface are carried out by a transenvelope complex of seven essential Lpt proteins spanning the inner membrane (LptBCFG), the periplasm (LptA), and the OM (LptDE), which appears to operate as a unique machinery. LptC is an essential inner membrane-anchored protein with a large periplasm-protruding domain. LptC binds the inner membrane LptBFG ABC transporter and interacts with the periplasmic protein LptA. However, its role in lipopolysaccharide transport is unclear. Here we show that LptC lacking the transmembrane region is viable and can bind the LptBFG inner membrane complex; thus, the essential LptC functions are located in the periplasmic domain. In addition, we characterize two previously described inactive single mutations at two conserved glycines (G56V and G153R, respectively) of the LptC periplasmic domain, showing that neither mutant is able to assemble the transenvelope machinery. However, while LptCG56V failed to copurify any Lpt component, LptCG153R was able to interact with the inner membrane protein complex LptBFG. Overall, our data further support the model whereby the bridge connecting the inner and outer membranes would be based on the conserved structurally homologous jellyroll domain shared by five out of the seven Lpt components

BPSL1626 : Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design Against Burkholderia pseudomallei

Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 angstrom resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules

Channel Assignment with Separation for Interference Avoidance in Wireless Networks

Given an integer $\sigma > 1$, a vector $(\delta_1, \delta_2, \ldots, \delta_{\sigma-1})$ of nonnegative integers, and an undirected graph $G=(V,E)$, an $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring of $G$ is a function $f$ from the vertex set $V$ to a set of nonnegative integers such that $| f(u) -f(v) | \ge \delta_i$, if $d(u,v) = i, \ 1 \le i \le \sigma-1, \$ where $d(u,v)$ is the distance (i.e. the minimum number of edges) between the vertices $u$ and $v$. An optimal $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring for $G$ is one using the smallest range $\lambda$ of integers over all such colorings. This problem has relevant application in channel assignment for interference avoidance in wireless networks, where channels (i.e. colors) assigned to interfering stations (i.e. vertices) at distance $i$ must be at least $\delta_i$ apart, while the same channel can be reused in vertices whose distance is at least $\sigma$. In particular, two versions of the coloring problem -- $L(2,1,1)$, and $L(\delta_1, 1, \ldots,1)$ -- are considered. Since these versions of the problem are $NP$-hard for general graphs, efficient algorithms for finding optimal colorings are provided for specific graphs modeling realistic wireless networks including rings, bidimensional grids, and cellular grids

Guillain-Barré syndrome during the Zika virus outbreak in Northeast Brazil: An observational cohort study

Objective: To determine the clinical phenotype of Guillain-Barré syndrome (GBS) after Zika virus (ZIKV) infection, the anti-glycolipid antibody signature, and the role of other circulating arthropod-borne viruses, we describe a cohort of GBS patients identified during ZIKV and chikungunya virus (CHIKV) outbreaks in Northeast Brazil. Methods: We prospectively recruited GBS patients from a regional neurology center in Northeast Brazil between December 2014 and February 2017. Serum and CSF were tested for ZIKV, CHIKV, and dengue virus (DENV), by RT-PCR and antibodies, and serum was tested for GBS-associated antibodies to glycolipids. Results: Seventy-one patients were identified. Forty-eight (68%) had laboratory evidence of a recent arbovirus infection; 25 (52%) ZIKV, 8 (17%) CHIKV, 1 (2%) DENV, and 14 (29%) ZIKV and CHIKV. Most patients with a recent arbovirus infection had motor and sensory symptoms (72%), a demyelinating electrophysiological subtype (67%) and a facial palsy (58%). Patients with a recent infection with ZIKV and CHIKV had a longer hospital admission and more frequent mechanical ventilation compared to the other patients. No specific anti-glycolipid antibody signature was identified in association with arbovirus infection, although significant antibody titres to GM1, GalC, LM1, and GalNAc-GD1a were found infrequently. Conclusion: A large proportion of cases had laboratory evidence of a recent infection with ZIKV or CHIKV, and recent infection with both viruses was found in almost one third of patients. Most patients with a recent arbovirus infection had a sensorimotor, demyelinating GBS. We did not find a specific anti-glycolipid antibody signature in association with arbovirus-related GBS

Crystal structure of an R-selective transaminase from Thermomyces stellatus

https://www.wwpdb.org/pdb?id=pdb_00006xw

Bovine mitochondrial peroxiredoxin III forms a two-ring catenane

SummaryA crystal structure is reported for the C168S mutant of a typical 2-Cys peroxiredoxin III (Prx III) from bovine mitochondria at a resolution of 3.3 Å. Prx III is present as a two-ring catenane comprising two interlocking dodecameric toroids that are assembled from basic dimeric units. Each ring has an external diameter of 150 Å and encompasses a central cavity that is 70 Å in width. The concatenated dodecamers are inclined at an angle of 55°, which provides a large contact surface between the rings. Dimer-dimer contacts involved in toroid formation are hydrophobic in nature, whereas the 12 areas of contact between interlocked rings arise from polar interactions. These two major modes of subunit interaction provide important insights into possible mechanisms of catenane formation

Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen

The unintentional crystallization of contaminant proteins in the place of target recombinant proteins is sporadically reported, despite the availability of stringent expression/purification protocols and of software for the detection of contaminants. Typically, the contaminant protein originates from the expression organism (for example Escherichia coli), but in rare circumstances contaminants from different sources have been reported. Here, a case of contamination from a Serratia bacterial strain that occurred while attempting to crystallize an unrelated protein from Burkholderia pseudomallei (overexpressed in E. coli) is presented. The contamination led to the unintended crystallization and structure analysis of a cyanase hydratase from a bacterial strain of the Serratia genus, an opportunistic enterobacterium that grows under conditions similar to those of E. coli and that is found in a variety of habitats, including the laboratory environment. In this context, the procedures that were adopted to identify the contaminant based on crystallographic data only are presented and the crystal structure of Serrata spp. cyanase hydratase is briefly discussed