keyword
MENU ▼
Read by QxMD icon Read
search

Epitope mapping

keyword
https://www.readbyqxmd.com/read/28208616/immunoinformatics-features-linked-to-leishmania-vaccine-development-data-integration-of-experimental-and-in-silico-studies
#1
Rory C F Brito, Frederico G Guimarães, João P L Velloso, Rodrigo Corrêa-Oliveira, Jeronimo C Ruiz, Alexandre B Reis, Daniela M Resende
Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28202756/a-glycosylation-benchmark-profile-for-hiv-1-envelope-glycoprotein-production-based-on-eleven-env-trimers
#2
Eden P Go, Haitao Ding, Shijian Zhang, Rajesh P Ringe, Nathan Nicely, David Hua, Robert T Steinbock, Michael Golabek, James Alin, S Munir Alam, Albert Cupo, Barton F Haynes, John C Kappes, John P Moore, Joseph G Sodroski, Heather Desaire
HIV-1 envelope glycoprotein (Env) glycosylation is important because individual glycans are components of multiple broadly neutralizing antibody epitopes, while shielding other sites that might otherwise be immunogenic. The glycosylation on Env is influenced by a variety of factors, including the genotype of the protein, the cell line used for its expression, and the details of the construct design. Here, we used a mass spectrometry-based approach to map the complete glycosylation profile at every site in multiple HIV-1 Env trimers, accomplishing two goals: 1) We determined which glycosylation sites contain conserved glycan profiles across many trimeric Envs...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28197388/inhibition-of-tumor-growth-and-metastasis-by-emmprin-multiple-antigenic-peptide-map-vaccination-is-mediated-by-immune-modulation
#3
Elina Simanovich, Vera Brod, Maya M Rahat, Ella Drazdov, Miriam Walter, Jivan Shakya, Michal A Rahat
Previously, we have identified a new epitope in EMMPRIN, a multifunctional protein that mediates tumor cell-macrophage interactions and induces both MMP-9 and VEGF. Here, we synthesized this epitope as an octa-branched multiple antigenic peptide (MAP) to vaccinate mice implanted with subcutaneous syngeneic colon (CT26), prostate (TRAMP-C2) or renal (RENCA) cell line carcinomas. Vaccination inhibited, and sometimes regressed, tumor growth in a dose-dependent manner, reaching 94%, 71% and 72% inhibition, respectively, at a 50 μg dose (p < 0...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28196145/correction-mapping-of-a-mycoplasma-neutralizing-epitope-on-the-mycoplasmal-p37-protein
#4
Min Kyu Kim, Won-Tae Kim, Hyun Min Lee, Hong Seo Choi, Yu Ra Jo, Yangsoon Lee, Jaemin Jeong, Dongho Choi, Hee Jin Chang, Dae Shick Kim, Young-Joo Jang, Chun Jeih Ryu
[This corrects the article DOI: 10.1371/journal.pone.0169091.].
2017: PloS One
https://www.readbyqxmd.com/read/28193005/mapping-the-energetic-epitope-of-an-antibody-interleukin-23-interaction-with-hydrogen-deuterium-exchange-fast-photochemical-oxidation-of-proteins-mass-spectrometry-and-alanine-shave-mutagenesis
#5
Jing Li, Hui Wei, Stanley R Krystek, Derek Bond, Ty M Brender, Daniel Cohen, Jena Feiner, Nels Hamacher, Johanna Harshman, Richard Y-C Huang, Susan H Julien, Zheng Lin, Kristina Moore, Luciano Mueller, Claire Noriega, Preeti Sejwal, Paul Sheppard, Brenda Stevens, Guodong Chen, Adrienne A Tymiak, Michael L Gross, Lumelle A Schneeweis
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28186093/conformational-changes-in-intact-dengue-virus-reveal-serotype-specific-expansion
#6
Xin-Xiang Lim, Arun Chandramohan, Xin Ying Elisa Lim, Nirmalya Bag, Kamal Kant Sharma, Melissa Wirawan, Thorsten Wohland, Shee-Mei Lok, Ganesh S Anand
Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28177609/fine-epitope-mapping-of-two-antibodies-neutralizing-the-bordetella-adenylate-cyclase-toxin
#7
Xianzhe Wang, James A Stapleton, Justin R Klesmith, Erik L Hewlett, Tim A Whitehead, Jennifer A Maynard
Adenylate cyclase toxin (ACT) is an important B. pertussis virulence factor that is not included in current acellular pertussis vaccines. We previously demonstrated that immunization with the repeat-in-toxin (RTX) domain of ACT elicits neutralizing antibodies in mice and discovered the first two antibodies to neutralize ACT activities by occluding the receptor-binding site. Here, we fully characterized these antibodies and their epitopes. Both antibodies bind ACT with low nanomolar affinity and cross-react with ACT homologs produced by B...
February 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/28170421/comprehensive-mapping-of-antigen-specific-t-cell-responses-in-hepatitis-c-virus-infected-patients-with-or-without-spontaneous-viral-clearance
#8
Chao Zhang, Rui Hua, Yuanyuan Cui, Shasha Wang, Hongqing Yan, Dongmei Li, Yonghong Zhang, Zhengkun Tu, Pei Hao, Xinyue Chen, Jin Zhong, Junqi Niu, Xia Jin
Elucidating protective immunity against HCV is important for the development of a preventative vaccine. We hypothesize that spontaneous resolution of acute HCV infection offers clue to protective immune responses, and that DAA therapy affects the quality and quantity of HCV-specific T cell responses. To test these hypotheses, we performed T cell epitope mapping in 111 HCV-infected individuals including 61 chronically HCV-1b (CHC-1b) infected, 24 chronically HCV-2a (CHC-2a) infected and 26 spontaneously recovered (SPR) patients with 376 overlapping peptides covering the entire HCV polyprotein...
2017: PloS One
https://www.readbyqxmd.com/read/28155721/computer-prediction-of-paratope-on-antithrombotic-antibody-10b12-and-epitope-on-platelet-glycoprotein-vi-via-molecular-dynamics-simulation
#9
Wenping Liu, Guangjian Liu, Huiyun Zhou, Xiang Fang, Ying Fang, Jianhua Wu
BACKGROUND: Interaction between immunoglobulin-like receptor glycoprotein VI (GPVI) and collagen plays a central role in platelet activation and sequent firm adhesion. Of various antithrombotic agents targeting GPVI, antibody 10B12 is of great potential to block the GPVI-collagen interaction, but less is known about 10B12 paratope and GPVI epitope. METHODS: Along the pathway in the computer strategy presented in our previous work, the 10B12/GPVI complex model was constructed through homology modeling and rigid-body docking, and the molecular dynamics (MD) simulation was used to detect the paratope residues on 10B12 and their partners on GPVI...
December 28, 2016: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28154562/indian-long-term-non-progressors-show-broad-adcc-responses-with-preferential-recognition-of-v3-region-of-envelope-and-a-region-from-tat-protein
#10
Archana Kulkarni, Swarali Kurle, Ashwini Shete, Manisha Ghate, Sheela Godbole, Vijaya Madhavi, Stephen J Kent, Ramesh Paranjape, Madhuri Thakar
HIV-specific antibody-dependent cell cytotoxicity (ADCC) is likely to be important in governing protection from human immunodeficiency virus (HIV) and slowing disease progression. Little is known about the ADCC responses to HIV-1 subtype C. We characterized ADCC responses in HIV-1 subtype C-infected Indian subjects with slow disease progression and identified the dominant antigenic regions recognized by these antibodies. ADCC responses were measured in plasma from 34 long-term non-progressors (LTNPs), who were asymptomatic and maintained CD4 count above 500 cells/mm(3) for the last 7 years in the absence of antiretroviral therapy (ART), and 58 ART naïve progressors with CD4 count <500 cells/mm(3) against overlapping HIV-1 peptides using a flow cytometry-based antibody-dependent natural killer (NK) cell activation assay...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28148736/gliadin-specific-cd8-t-cell-responses-restricted-by-hla-class-i-a-0101-and-b-0801-molecules-in-celiac-disease-patients
#11
Stefania Picascia, John Sidney, Alessandra Camarca, Giuseppe Mazzarella, Nicola Giardullo, Luigi Greco, Renata Auricchio, Salvatore Auricchio, Riccardo Troncone, Alessandro Sette, Carmen Gianfrani
Initial studies associated the HLA class I A*01 and B*08 alleles with celiac disease (CD) susceptibility. Subsequent analyses showed a primary association with HLA class II alleles encoding for the HLA DQ2.5 molecule. Because of the strong linkage disequilibrium of A*01 and B*08 alleles with the DR3-DQ2.5 haplotype and a recent genome-wide association study indicating that B*08 and B*39 are predisposing genes, the etiologic role of HLA class I in CD pathogenesis needs to be addressed. We screened gliadin proteins (2α-, 2ω-, and 2γ-gliadin) using bioinformatic algorithms for the presence of peptides predicted to bind A*0101 and B*0801 molecules...
February 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28142214/epitope-mapping-of-borrelia-burgdorferi-ospc-protein-in-homodimeric-fold
#12
Adam Norek, Lubomír Janda
In current work, we used recombinant OspC protein derived from B. afzelii strain BRZ31 in the native homodimeric fold for mice immunisation and following selection process to produce three mouse monoclonal antibodies able to bind to variable parts of up to five different OspC proteins. Applying the combination of mass spectrometry assisted epitope mapping and affinity based theoretical prediction we have localised regions responsible for antigen-antibody interactions and approximate epitopes' amino acid composition...
January 31, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28135273/cellular-immune-responses-to-live-attenuated-japanese-encephalitis-je-vaccine-sa14-14-2-in-adults-in-a-je-dengue-co-endemic-area
#13
Lance Turtle, Filippo Tatullo, Tanushka Bali, Vasanthapuram Ravi, Mohammed Soni, Sajesh Chan, Savita Chib, Manjunatha M Venkataswamy, Prachi Fadnis, Mansour Yaïch, Stefan Fernandez, Paul Klenerman, Vijaya Satchidanandam, Tom Solomon
BACKGROUND: Japanese encephalitis (JE) virus (JEV) causes severe epidemic encephalitis across Asia, for which the live attenuated vaccine SA14-14-2 is being used increasingly. JEV is a flavivirus, and is closely related to dengue virus (DENV), which is co-endemic in many parts of Asia, with clinically relevant interactions. There is no information on the human T cell response to SA14-14-2, or whether responses to SA14-14-2 cross-react with DENV. We used live attenuated JE vaccine SA14-14-2 as a model for studying T cell responses to JEV infection in adults, and to determine whether these T cell responses are cross-reactive with DENV, and other flaviviruses...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28132782/mapping-protein-binding-sites-and-conformational-epitopes-using-cysteine-labeling-and-yeast-surface-display
#14
Tariq Ahmad Najar, Shruti Khare, Rajesh Pandey, Satish K Gupta, Raghavan Varadarajan
We describe a facile method for mapping protein:ligand binding sites and conformational epitopes. The method uses a combination of Cys scanning mutagenesis, chemical labeling, and yeast surface display. While Ala scanning is widely used for similar purposes, often mutation to Ala (or other amino acids) has little effect on binding, except at hotspot residues. Many residues in physical contact with a binding partner are insensitive to substitution with Ala. In contrast, we show that labeling of Cys residues in a binding site consistently abrogates binding...
January 18, 2017: Structure
https://www.readbyqxmd.com/read/28119396/differential-expression-of-human-%C3%AE-tubulin-isotypes-during-neuronal-development-and-oxidative-stress-points-to-a-%C3%AE-tubulin-2-prosurvival-function
#15
Eduarda Dráberová, Vadym Sulimenko, Stanislav Vinopal, Tetyana Sulimenko, Vladimíra Sládková, Luca D'Agostino, Margaryta Sobol, Pavel Hozák, Leoš Křen, Christos D Katsetos, Pavel Dráber
γ-Tubulins are highly conserved members of the tubulin superfamily essential for microtubule nucleation. Humans possess 2 γ-tubulin genes. It is thought that γ-tubulin-1 represents a ubiquitous isotype, whereas γ-tubulin-2 is found predominantly in the brain, where it may be endowed with divergent functions beyond microtubule nucleation. The molecular basis of the purported functional differences between γ-tubulins is unknown. We report discrimination of human γ-tubulins according to their electrophoretic and immunochemical properties...
January 24, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28119056/prp-c1-fragment-in-cattle-brains-reveals-features-of-the-transmissible-spongiform-encephalopathy-associated-prp-sc
#16
Fabienne Serra, Joachim Müller, John Gray, Ramona Lüthi, Sandor Dudas, Stefanie Czub, Torsten Seuberlich
Three different types of Bovine spongiform encephalopathy (BSE) are known and supposedly caused by distinct prion strains: the classical (C-) BSE type that was typically found during the BSE epidemic, and two relatively rare atypical BSE types, termed H-BSE and L-BSE. The three BSE types differ in the molecular phenotype of the disease associated prion protein, namely the N-terminally truncated Proteinase K (PK) resistant prion protein fragment (PrP(res)). In this study, we report and analyze yet another PrP(res) type (PrP(res-2011)), which was found in severely autolytic brain samples of two cows in the framework of disease surveillance in Switzerland in 2011...
January 21, 2017: Brain Research
https://www.readbyqxmd.com/read/28112950/identification-of-receptor-binding-to-the-biomolecular-corona-of-nanoparticles
#17
Sandra Lara, Fatima Alnasser, Ester Polo, David Garry, Maria Cristina Lo Giudice, Delyan R Hristov, Louise Rocks, Anna Salvati, Yan Yan, Kenneth A Dawson
Biomolecules adsorbed on nanoparticles are known to confer a biological identity to nanoparticles, mediating the interactions with cells and biological barriers. However, how these molecules are presented on the particle surface in biological milieu remains unclear. The central aim of this study is to identify key protein recognition motifs and link them to specific cell-receptor interactions. Here, we employed an immuno-mapping technique to quantify epitope presentations of two major proteins in the serum corona, low-density lipoprotein and immunoglobulin G...
January 31, 2017: ACS Nano
https://www.readbyqxmd.com/read/28111636/antigenicity-of-peptides-comprising-the-immunosuppressive-domain-of-the-retroviral-envelope-glycoprotein
#18
Bryony Jenkins, Urszula Eksmond, George Young, George Kassiotis
To achieve persistent infection of the host, viruses often subvert or suppress host immunity through mechanisms that are not entirely understood. The envelope glycoprotein of several retroviruses is thought to possess potent immunosuppressive activity, mapped to a 17-amino acid residue conserved domain. Synthetic peptides corresponding to this immunosuppressive domain can inhibit lymphocyte activation, whereas mutation of key domain residues can increase the lymphocyte response to linked antigenic epitopes...
December 6, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/28109201/genetic-analyses-of-the-fusion-protein-genes-in-human-parainfluenza-virus-types-1-and-3-among-patients-with-acute-respiratory-infections-in-eastern-japan-from-2011-to-2015
#19
Rika Tsutsui, Hiroyuki Tsukagoshi, Koo Nagasawa, Masaki Takahashi, Yuki Matsushima, Akihide Ryo, Makoto Kuroda, Hideki Takami, Hirokazu Kimura
PURPOSE: To genetically explorer the fusion protein gene (F) in human parainfluenza virus type 1 (HPIV1) and type 3 (HPIV3) strains, we analyzed them in the patients with acute respiratory infections (ARI) in Eastern Japan from 2011 to 2015. METHODOLOGY: We constructed phylogenetic trees based on the HPIV and HPIV3 F gene using the maximum likelihood method and conducted p-distance, and selective pressure analyses. We also predicted the linear epitopes of the protein in the prototype strains...
January 20, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28100093/p19-targeted-abd-derived-protein-variants-inhibit-il-23-binding-and-exert-suppressive-control-over-il-23-stimulated-expansion-of-primary-human-il-17-t-cells
#20
Lucie Křížová, Milan Kuchař, Hana Petroková, Radim Osička, Marie Hlavničková, Ondřej Pelák, Jiří Černý, Tomáš Kalina, Petr Malý
Interleukin-23 (IL-23), a heterodimeric cytokine of covalently bound p19 and p40 proteins, has recently been closely associated with development of several chronic autoimmune diseases such as psoriasis, psoriatic arthritis or inflammatory bowel disease. Released by activated dendritic cells, IL-23 interacts with IL-23 receptor (IL-23R) on Th17 cells, thus promoting intracellular signaling, a pivotal step in Th17-driven pro-inflammatory axis. Here, we aimed to block the binding of IL-23 cytokine to its cell-surface receptor by novel inhibitory protein binders targeted to the p19 subunit of human IL-23...
January 19, 2017: Autoimmunity
keyword
keyword
8537
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"