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Epitope mapping

Muhammad Ramzan Manwar Hussain, Zeeshan Iqbal, Wajahat M Qazi, Daniel C Hoessli
The structural and functional diversity of the human proteome is mediated by N - and O- linked glycosylations that define the individual properties of extracellular and membrane-associated proteins. In this study, we utilized different computational tools to perform in silico based genome-wide mapping of 1,117 human proteins and unravel the contribution of both penultimate and vicinal amino acids for the asparagine-based, site-specific N -glycosylation. Our results correlate the non-canonical involvement of charge and polarity environment of classified amino acids (designated as L, O, A, P, and N groups) in the N -glycosylation process, as validated by NetNGlyc predictions, and 130 literature-reported human proteins...
2018: Frontiers in Oncology
Kelvin J Yong, Tasneem M Vaid, Patrick J Shilling, Feng-Jie Wu, Lisa M Williams, Mattia Deluigi, Andreas Plückthun, Ross Ad Bathgate, Paul R Gooley, Daniel J Scott
α1A- and α1B-adrenoceptors (α1A-AR and α1B-AR) are closely related G protein-coupled receptors (GPCRs) that modulate the cardiovascular and nervous systems in response to binding epinephrine and norepinephrine. The GPCR gene super-family is made up of numerous sub-families that, like α1A-AR and α1B-AR, are activated by the same endogenous agonists but may modulate different physiological processes. A major challenge in GPCR research and drug discovery is determining how compounds interact with receptors at the molecular level, especially to assist in the optimization of drug leads...
March 14, 2018: ACS Chemical Biology
Cecilia Augustsson, Anders Svensson, Birgitte Kjaer, Tzu-Yuan Chao, Xia Wenjuan, Berit Olsen Krogh, Jens Breinholt, Jes Thorn Clausen, Ida Hilden, Helle Heibroch Petersen, Lars Christian Petersen
BACKGROUND: Initiation of coagulation is induced by binding of activated factor VII (FVIIa) to tissue factor (TF) and activation of factor X (FX) in a process regulated by tissue factor pathway inhibitor (TFPI). TFPI contains three Kunitz-type protease inhibitor domains (K1-K3) of which K1 and K2 block the active sites of FVIIa and FXa respectively. OBJECTIVE: To produce a monoclonal antibody (mAb) directed towards K1, to characterize the binding epitope, and to study its effect on TFPI inhibition...
March 12, 2018: Journal of Thrombosis and Haemostasis: JTH
Maryam Golshani, Melina Ghasemian, Nematollah Gheibi, Saeid Bouzari
Background: L7/L12 is a protective antigen conserved in main Brucella pathogens and is considered as potential vaccine candidate. Outer membrane protein 2b is an immunogen conserved in all Brucella pathogens. Materials and Methods: The purpose of the current study was to in silico design a L7/L12-SOmp2b fusion protein and in vitro production of the chimera. Two possible fusion forms, L7/L12-SOmp2b and SOmp2b-L7/L12, were subjected to in silico modeling and analysis...
2018: Advanced Biomedical Research
Andrew J Guy, Vashti Irani, James G Beeson, Benjamin Webb, Andrej Sali, Jack S Richards, Paul A Ramsland
Humoral immune responses against the malaria parasite are an important component of a protective immune response. Antibodies are often directed towards conformational epitopes, and the native structure of the antigenic region is usually critical for antibody recognition. We examined the structural features of various Plasmodium antigens that may impact on epitope location, by performing a comprehensive analysis of known and modelled structures from P. falciparum. Examining the location of known polymorphisms over all available structures, we observed a strong propensity for polymorphic residues to be exposed on the surface and to occur in particular secondary structure segments such as hydrogen-bonded turns...
March 12, 2018: Scientific Reports
Maite Ramírez, Saritza Santos, Osmarie Martínez, Ricardo Rodríguez, Eric Miranda, Willy D Ramos-Perez, Miguel Otero
Poxviruses are complex dsDNA viruses with over 200 genes, many of them with unknown role in the stimulation of immune responses. Among these, the vaccinia virus (VACV) L3L ORF encodes an essential protein for the transcription of the VACV early genes. To the best of our knowledge, the immune response elicited by L3 has not been characterized. In this regard, our data describes a DNA L3-coding plasmid (pL3L) that stimulates both, humoral- and cell-mediated immune responses in a mouse model. Cell-mediated immune responses were measured by IFN-γ and IL-4 ELISPOT assays...
March 7, 2018: Vaccine
Alireza Salimi Chirani, Robabeh Majidzadeh, Ramin Pouriran, Mohsen Heidary, Mohammad Javad Nasiri, Mehrdad Gholami, Mehdi Goudarzi, Vahid Fallah Omrani
The vaccine candidates that have been introduced for immunization against Pseudomonas aeruginosa (P. aeruginosa) strains are quite diverse. In fact, there has been no proper antigen to act as an effective immunogenic substance against this ubiquitous pathogen in the market as yet. The complications caused by this bacterium due to the rapid development of multiple drug resistant strains have led to clinical problems worldwide. P. aeruginosa encodes many specific virulence elements that could be used as appropriate vaccine candidates...
February 5, 2018: Computational Biology and Chemistry
Sajad Abdollahi, Iraj Rasooli, Seyed Latif Mousavi Gargari
Acinetobacter baumannii is an opportunistic multidrug resistant pathogen. TonB-dependent copper receptor is an outer membrane protein and has a role in binding of A. baumannii to host cell via attachment to fibronectin. Moreover, it is highly expressed in biofilm community. In this study the properties of copper receptor were analyzed in silico and its vaccine potential was investigated. TonB-dependent copper and iron receptor domains plus one plug domain at N-terminal were determined by domain analysis. Topology modeling showed 22 β-strands, 11 loops and 10 periplasmic turns...
March 7, 2018: Microbial Pathogenesis
Marco Bo, Magdalena Niegowska, Giannina Arru, Elia Sechi, Sara Mariotto, Chiara Mancinelli, Alessia Farinazzo, Daniela Alberti, Alberto Gajofatto, Sergio Ferrari, Ruggero Capra, Salvatore Monaco, GianPietro Sechi, Leonardo A Sechi
Epstein-Barr virus (EBV) is the main environmental agent associated to neuromyelitis optica spectrum disorder (NMOSD). Following to studies reporting an increased prevalence of antibodies against peptides derived from Mycobacterium avium subsp. paratuberculosis (MAP) homologous to EBV and human epitopes (MBP85-98 , IRF5424-434 ) in multiple sclerosis (MS), we investigated whether seroreactivity to these antigens display a NMOSD-specific pattern. The sera of 34 NMOSD patients showed elevated levels of antibodies against MAP and MBP compared to healthy controls (44% vs...
February 28, 2018: Journal of Neuroimmunology
Hao D Cheng, Sebastian K Grimm, Morgan Sa Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, Gina Donofrio, Gunilla B Karlsson Hedestam, Mattia Bonsignori, Barton F Haynes, Timothy P Lahey, Isaac Maro, C Fordham von Reyn, Miroslaw K Gorny, Susan Zolla-Pazner, Bruce D Walker, Galit Alter, Dennis R Burton, Merlin L Robb, Shelly J Krebs, Michael S Seaman, Chris Bailey-Kellogg, Margaret E Ackerman
Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth...
March 8, 2018: JCI Insight
Lingshu Wang, Wei Shi, James D Chappell, M Gordon Joyce, Yi Zhang, Masaru Kanekiyo, Michelle M Becker, Neeltje van Doremalen, Robert Fischer, Nianshuang Wang, Kizzmekia S Corbett, Misook Choe, Rosemarie D Mason, Joseph G Van Galen, Tongqing Zhou, Kevin O Saunders, Kathleen M Tatti, Lia M Haynes, Peter D Kwong, Kayvon Modjarrad, Wing-Pui Kong, Jason S McLellan, Mark R Denison, Vincent J Munster, John R Mascola, Barney S Graham
Middle East Respiratory Syndrome coronavirus (MERS-CoV) causes a highly lethal pulmonary infection with ∼35% mortality. The potential for a future pandemic originating from animal reservoirs or healthcare-associated events is a major public health concern. There are no vaccines or therapeutic agents currently available for MERS-CoV. Using a probe-based single B cell-cloning strategy, we have identified and characterized multiple neutralizing mAbs specifically binding to the receptor binding domain (RBD) or S1 (non-RBD) regions from a convalescent MERS-CoV-infected patient and from immunized rhesus macaques...
March 7, 2018: Journal of Virology
Margaret Lin, Denise Krawitz, Matthew D Callahan, Galahad Deperalta, Aaron T Wecksler
We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA...
March 6, 2018: Journal of the American Society for Mass Spectrometry
Ida K Myhrvold, Andrea Cremaschi, Johanne U Hermansen, Geir E Tjønnfjord, Ludvig A Munthe, Kjetil Taskén, Sigrid S Skånland
Chronic lymphocytic leukemia (CLL) has a high incidence and a steeply growing prevalence in the Western world. The heterogeneity of the disease necessitates individual mapping of biology and predicted drug response in each patient as basis for administration of tailored treatments. Cell signaling aberrations may serve as biological indicators for suitable therapy. By applying phospho-specific flow cytometry, we mapped basal and induced phosphorylation levels of 20 phospho-epitopes on proteins relevant to B-cell signaling in B cells from 22 CLL patients and 25 normal controls...
February 6, 2018: Oncotarget
Toolika Singh, Michaela Fakiola, Joyce Oommen, Akhil Pratap Singh, Abhishek K Singh, Noel Smith, Jaya Chakravarty, Shyam Sundar, Jenefer M Blackwell
HLA-DRB1 is the major genetic risk factor for visceral leishmaniasis (VL). We used SNP2HLA to impute HLA-DRB1 alleles and SNPTEST to carry out association analyses in 889 human cases and 977 controls from India. NetMHCIIpan 2.1 was used to map epitopes and binding affinities across 49 Leishmania vaccine candidates, as well as across peptide epitopes captured from dendritic cells treated with crude Leishmania Ag and identified using mass spectrometry and alignment to amino acid sequences of a reference Leishmania genome...
March 5, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Kritika Gupta, Raghavan Varadarajan
Where convenient phenotypic readouts are available, saturation mutagenesis coupled to deep sequencing provides a rapid and facile method to infer sequence determinants of protein structure, stability and function. We provide brief descriptions and currently available options for the various steps involved, and mention limitations of current implementations. We also highlight recent applications such as estimating relative stabilities and affinities of protein variants, mapping epitopes, protein model discrimination and prediction of mutant phenotypes...
March 2, 2018: Current Opinion in Structural Biology
Tippawan Pissawong, Santi Maneewatchararangsri, Nonglucksanawan Ritthisunthorn, Ngamphol Soonthornworasiri, Onrapak Reamtong, Poom Adisakwattana, Thareerat Kalambaheti, Urai Chaisri, Galayanee Doungchawee
BACKGROUND/PURPOSE: Leptospirosis is a neglected zoonosis, imposing significant human and veterinary public health burdens. In this study, recombinant LipL3293-147 and LipL32148-184 middle domain of LipL3293-184 , and LipL32171-214 , and LipL32215-272 of c-terminal LipL32171-272 truncations were defined for immunodominance of the molecule during Leptospira infections revealed by leptospirosis sera. RESULTS: IgM-dominant was directed to highly surface accessible LipL32148-184 and Lipl32171-214 ...
February 14, 2018: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
Toshiaki Ono, Yuriko Fujita, Tetsuro Matano, Satoshi Takahashi, Tomohiro Morio, Ai Kawana-Tachikawa
Adoptive transfer of virus-specific T cells has emerged as a promising therapeutic approach for treatment of virus infections in immunocompromised hosts. Characterization of virus-specific T cells provides essential information for the curative mechanism of the treatment. In this study, we developed a T cell epitope mapping system for 718 overlapping peptides spanning 6 viral proteins from three viruses (pp65 and IE1 from CMV; LMP1, EBNA1 and BZLF1 from EBV; Penton from AdV). PBMCs from 33 healthy Japanese donors were stimulated with these peptides and virus-specific CD4+ and CD8+ T cell were expanded in vitro in the presence of IL4 and IL7...
February 28, 2018: Japanese Journal of Infectious Diseases
Estefania Fernandez, Nurgun Kose, Melissa A Edeling, Jagat Adhikari, Gopal Sapparapu, Susana M Lazarte, Christopher A Nelson, Jennifer Govero, Michael L Gross, Daved H Fremont, James E Crowe, Michael S Diamond
Japanese encephalitis virus (JEV) remains a leading cause of viral encephalitis worldwide. Although JEV-specific antibodies have been described, an assessment of their ability to neutralize multiple genotypes of JEV has been limited. Here, we describe the development of a panel of mouse and human neutralizing monoclonal antibodies (MAbs) that inhibit infection in cell culture of four different JEV genotypes tested. Mechanism-of-action studies showed that many of these MAbs inhibited infection at a postattachment step, including blockade of virus fusion...
February 27, 2018: MBio
Pengpeng Xia, Guomei Quan, Yi Yang, Jing Zhao, Yiting Wang, Mingxu Zhou, Philip R Hardwidge, Jianzhong Zhu, Siguo Liu, Guoqiang Zhu
The binding of F4+ enterotoxigenic Escherichia coli (ETEC) and the specific receptor on porcine intestinal epithelial cells is the initial step in F4+ ETEC infection. Porcine aminopeptidase N (APN) is a newly discovered receptor for F4 fimbriae that binds directly to FaeG adhesin, which is the major subunit of the F4 fimbriae variants F4ab, F4ac, and F4ad. We used overlapping peptide assays to map the APN-FaeG binding sites, which has facilitated in the identifying the APN-binding amino acids that are located in the same region of FaeG variants, thereby limiting the major binding regions of APN to 13 peptides...
February 26, 2018: Veterinary Research
Emily N Gallichotte, Thomas J Baric, Boyd L Yount, Douglas G Widman, Anna Durbin, Steve Whitehead, Ralph S Baric, Aravinda M de Silva
Dengue virus (DENV) infection causes dengue fever, dengue hemorrhagic fever and dengue shock syndrome. It is estimated that a third of the world's population is at risk for infection, with an estimated 390 million infections annually. Dengue virus serotype 2 (DENV2) causes severe epidemics, and the leading tetravalent dengue vaccine has lower efficacy against DENV2 compared to the other 3 serotypes. In natural DENV2 infections, strongly neutralizing type-specific antibodies provide protection against subsequent DENV2 infection...
February 26, 2018: PLoS Pathogens
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