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Epitope mapping

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https://www.readbyqxmd.com/read/28095436/arraypitope-automated-analysis-of-amino-acid-substitutions-for-peptide-microarray-based-antibody-epitope-mapping
#1
Christian Skjødt Hansen, Thomas Østerbye, Paolo Marcatili, Ole Lund, Søren Buus, Morten Nielsen
Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes...
2017: PloS One
https://www.readbyqxmd.com/read/28090632/identification-of-highly-selective-mmp-14-inhibitory-fabs-by-deep-sequencing
#2
Tyler Lopez, Dong Hyun Nam, Evan Kaihara, Zahid Mustafa, Xin Ge
Matrix metalloproteinase (MMP)-14 is an important target for cancer treatment due to its critical roles in tumor invasion and metastasis. Previous failures of all compound-based broad-spectrum MMP inhibitors in clinical trials suggest that selectivity is the key for a successful therapy. With inherent high specificity, monoclonal antibodies (mAbs) therefore arise as attractive inhibitors able to target the particular MMP of interest. As a routine screening method, enzyme-linked immunosorbent assays (ELISA) have been applied to panned phage libraries for the isolation of mAbs inhibiting MMP-14...
January 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28076422/monoclonal-antibody-against-g-glycoprotein-increases-respiratory-syncytial-virus-clearance-in-vivo-and-prevents-vaccine-enhanced-diseases
#3
Hyo-Jeong Lee, Jeong-Yoon Lee, Min-Hee Park, Joo-Young Kim, Jun Chang
Respiratory syncytial virus (RSV) is a common cause of lower respiratory tract illness in infants, young children, and the elderly. The G glycoprotein plays a role in host cell attachment and also modulates the host immune response, thereby inducing disease pathogenesis. We generated two monoclonal antibodies (mAbs; 5H6 and 3A5) against G protein core fragment (Gcf), which consisted of amino acid residues 131 to 230 from RSV A2 G protein. Epitope mapping study revealed that 5H6 specifically binds to the G/164-176 peptide that includes conserved sequences shared by both RSV A and B subtypes, and 3A5 binds to the G/190-204 peptide...
2017: PloS One
https://www.readbyqxmd.com/read/28072528/triosephosphate-isomerase-and-filamin-c-share-common-epitopes-as-novel-allergens-of-procambarus-clarkii
#4
Yang Yang, Yong-Xia Zhang, Meng Liu, Soheila J Maleki, Ming-Li Zhang, Qingmei Liu, Min-Jie Cao, Wen-Jin Su, Guang-Ming Liu
Triosephosphate isomerase (TIM) is a key enzyme in glycolysis and has been identified as an allergen in saltwater products. In this study, TIM with the molecular mass of 28 kDa was purified from the freshwater crayfish (Procambarus clarkii) muscle. A 90-kDa protein showed IgG/IgE cross-reactivity with TIM was purified and identified as filamin C (FLN c), which is an actin-binding proteins. TIM showed similar thermal and pH stability while better digestion resistant compared with FLN c. Result of surface plasmon resonance (SPR) experiment demonstrated the infinity of anti-TIM polyclonal antibody (pAb) to both TIM and FLN c...
January 10, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28065804/limited-naturally-occurring-escape-in-broadly-neutralizing-antibody-epitopes-in-hepatitis-c-glycoprotein-e2-and-constrained-sequence-usage-in-acute-infection
#5
Chaturaka Rodrigo, Melanie R Walker, Preston Leung, Auda A Eltahla, Jason Grebely, Gregory J Dore, Tanya Applegate, Kimberly Page, Sunita Dwivedi, Julie Bruneau, Meghan D Morris, Andrea L Cox, William Osburn, Arthur Y Kim, Janke Schinkel, Naglaa H Shoukry, Georg M Lauer, Lisa Maher, Margaret Hellard, Maria Prins, Fabio Luciani, Andrew R Lloyd, Rowena A Bull
Broadly neutralizing antibodies have been associated with spontaneous clearance of the hepatitis C infection as well as viral persistence by immune escape. Further study of neutralizing antibody epitopes is needed to unravel pathways of resistance to virus neutralization, and to identify conserved regions for vaccine design. All reported broadly neutralizing antibody (BNAb) epitopes in the HCV Envelope (E2) glycoprotein were identified. The critical contact residues of these epitopes were mapped onto the linear E2 sequence...
January 5, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28061503/correction-epitope-mapping-of-antibodies-suggests-the-novel-membrane-topology-of-b-cell-receptor-associated-protein-31-on-the-cell-surface-of-embryonic-stem-cells-the-novel-membrane-topology-of-bap31
#6
Won-Tae Kim, Hong Seo Choi, Hyo Jeong Hwang, Han-Sung Jung, Chun Jeih Ryu
[This corrects the article DOI: 10.1371/journal.pone.0130670.].
2017: PloS One
https://www.readbyqxmd.com/read/28060819/an-anti-human-lutheran-glycoprotein-phage-antibody-inhibits-cell-migration-on-laminin-511-epitope-mapping-of-the-antibody
#7
Yurie Enomoto-Okawa, Yuka Maeda, Nozomi Harashima, Yumika Sugawara, Fumihiko Katagiri, Kentaro Hozumi, Kam Man Hui, Motoyoshi Nomizu, Yuji Ito, Yamato Kikkawa
The Lutheran glycoprotein (Lu), also known as basal cell adhesion molecule (B-CAM), is an Ig superfamily (IgSF) transmembrane receptor for laminin α5. Although Lu is not present in normal hepatocytes, its expression is significantly increased in hepatocellular carcinoma (HCC). In this study, we isolated thirteen phage antibodies to Lu from a phage library of peripheral blood from HCC patients, suggesting that these patients produced autoantibodies against endogenous Lu. To characterize the phage antibodies, we determined the Lu domains they recognize...
2017: PloS One
https://www.readbyqxmd.com/read/28057002/prediction-of-anti-inflammatory-proteins-peptides-an-insilico-approach
#8
Sudheer Gupta, Ashok K Sharma, Vibhuti Shastri, Midhun K Madhu, Vineet K Sharma
BACKGROUND: The current therapy for inflammatory and autoimmune disorders involves the use of nonspecific anti-inflammatory drugs and other immunosuppressant, which are often accompanied with potential side effects. As an alternative therapy, anti-inflammatory peptides are recently being exploited as anti-inflammatory agents for treatment of various inflammatory diseases such as Alzheimer's disease and rheumatoid arthritis. Thus, understanding the correlation between amino acid sequence and its potential anti-inflammatory property is of great importance for the discovery of novel and efficient anti-inflammatory peptide-based therapeutics...
January 6, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28053669/mycobacterium-avium-subsp-paratuberculosis-and-associated-risk-factors-for-inflammatory-bowel-disease-in-iranian-patients
#9
Samin Zamani, Mohammad Reza Zali, Hamid Asadzadeh Aghdaei, Leonardo Antonio Sechi, Magdalena Niegowska, Elisa Caggiu, Rouhollah Keshavarz, Nader Mosavari, Mohammad Mehdi Feizabadi
BACKGROUND: Inflammatory bowel disease (IBD) is described as a relapsing condition with high morbidity and uncertain complex pathogenesis. The association of Mycobacterium avium ssp. paratuberculosis (MAP) with Crohn's disease (CD) in human has been debated for decades, however there is no confirmed data to verify such relations in Iran. The aim of this study was to investigate risk factors and a possible role of MAP in Iranian patients with CD. METHODS: Anti-MAP antibodies were detected in serum of IBD patients and subjects without IBD (nIBD) through ELISA; MAP DNA and viable MAP cells were identified in patients' biopsies through nested PCR and direct culture methods, respectively...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28052137/mapping-polyclonal-hiv-1-antibody-responses-via-next-generation-neutralization-fingerprinting
#10
Nicole A Doria-Rose, Han R Altae-Tran, Ryan S Roark, Stephen D Schmidt, Matthew S Sutton, Mark K Louder, Gwo-Yu Chuang, Robert T Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S Abdool Karim, James M Binley, Mark Connors, Barton F Haynes, Malcolm A Martin, David C Montefiori, Lynn Morris, Julie Overbaugh, Peter D Kwong, John R Mascola, Ivelin S Georgiev
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially novel epitope specificities...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28051320/correlation-of-antibody-responses-to-a-peptide-antigen-gp120-c5-sup-501-512-sup-gp41-sup-732-744-sup-with-hiv-disease-progression
#11
Birger Sørensen, Maja A Sommerfelt, Grete Stjernholm, Peter Lawrence Smith, Mats Ökvist, Arnt-Ove Hovden, Gunnar Hoddevik, Robert R Redfield, Valentina Ustina, Øyvind Jelmert, Jerome Zeldis, Angus Dalgleish
Antibodies to the carboxyterminal constant (C5) region 5 of the HIV-1 envelope glycoprotein gp120 have previously been associated with slow disease progression. This is one of the regions on gp120 that interact with the transmembrane glycoprotein, gp41, anchoring it to the viral and infected cell membrane. This study analyzed humoral responses to a novel heterodimeric peptide construct comprising the C5<sup>501-512</sup> region and a compatible region on gp41<sup>732-744</sup>. Antibody prevalence to C5<sup>501-512</sup>/gp41<sup>732-744</sup> was associated with slow disease progression in a treatment naive historical longitudinal cohort from Norway (n=32; p=0...
January 4, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28031369/mapping-the-human-memory-b-cell-and-serum-neutralizing-antibody-responses-to-denv4-infection-and-vaccination
#12
Usha K Nivarthi, Nurgun Kose, Gopal Sapparapu, Douglas Widman, Emily Gallichotte, Jennifer M Pfaff, Benjamin J Doranz, Daniela Weiskopf, Alessandro Sette, Anna P Durbin, Steve S Whitehead, Ralph Baric, James E Crowe, Aravinda M de Silva
: The four dengue virus (DENV) serotypes are mosquito-borne flaviviruses responsible for dengue fever and dengue hemorrhagic fever. People exposed to DENV develop antibodies that strongly neutralize the serotype responsible for infection. Historically, infection with DENV serotype 4 (DENV4) has been less common and understudied in comparison to the other three serotypes. However, DENV4 has been responsible for recent large and sustained epidemics in Asia and Latin America. The neutralizing antibody responses and the epitopes targeted against DENV4 are not characterized in human infection...
December 28, 2016: Journal of Virology
https://www.readbyqxmd.com/read/28028735/mapping-of-surface-exposed-epitopes-of-in-vitro-and-in-vivo-aggregated-species-of-alpha-synuclein
#13
Leire Almandoz-Gil, Veronica Lindström, Jessica Sigvardson, Philipp J Kahle, Lars Lannfelt, Martin Ingelsson, Joakim Bergström
Aggregated alpha-synuclein is the main component of Lewy bodies, intraneuronal deposits observed in Parkinson's disease and dementia with Lewy bodies. The objective of the study was to identify surface-exposed epitopes of alpha-synuclein in vitro and in vivo formed aggregates. Polyclonal immunoglobulin Y antibodies were raised against short linear peptides of the alpha-synuclein molecule. An epitope in the N-terminal region (1-10) and all C-terminal epitopes (90-140) were found to be exposed in an indirect enzyme-linked immunosorbent assay (ELISA) using recombinant monomeric, oligomeric, and fibrillar alpha-synuclein...
December 27, 2016: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28026090/the-mesenchymal-precursor-cell-marker-antibody-stro-1-binds-to-cell-surface-heat-shock-cognate-70
#14
Stephen Fitter, Stan Gronthos, Soo Siang Ooi, Andrew C W Zannettino
Since its discovery more than 25 years ago, the STRO-1 antibody has played a fundamental role in defining the hierarchical nature of mesenchymal precursor cells (MPC) and their progeny. STRO-1 antibody binding remains a hallmark of immature pluripotent MPC. Despite the significance of STRO-1 in the MPC field, the identity of the antigen has remained elusive. Using a combination of 2-dimensional gel electrophoresis, coupled with Western blotting and Tandem mass spectroscopy, we have identified the STRO-1 antigen as heat shock cognate 70 (HSC70;HSPA8)...
December 27, 2016: Stem Cells
https://www.readbyqxmd.com/read/28013368/lectins-a-primer-for-histochemists-and-cell-biologists
#15
REVIEW
Joachim C Manning, Antonio Romero, Felix A Habermann, Gabriel García Caballero, Herbert Kaltner, Hans-Joachim Gabius
An experimental observation on selecting binding partners underlies the introduction of the term 'lectin'. Agglutination of erythrocytes depending on their blood-group status revealed the presence of activities in plant extracts that act in an epitope-specific manner like antibodies. As it turned out, their binding partners on the cell surface are carbohydrates of glycoconjugates. By definition, lectins are glycan-specific (mono- or oligosaccharides presented by glycoconjugates or polysaccharides) receptors, distinguished from antibodies, from enzymes using carbohydrates as substrates and from transporters of free saccharides...
December 24, 2016: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28005336/mapping-of-molecular-structure-of-the-nanoscale-surface-in-bionanoparticles
#16
Luciana M Herda, Delyan R Hristov, Maria Cristina Lo Giudice, Ester Polo, Kenneth A Dawson
Characterizing the orientation of covalently conjugated proteins on nanoparticles, produced for in vitro and in vivo targeting, though an important feature of such a system, has proved challenging. Although extensive physicochemical characterization of targeting nanoparticles can be addressed in detail, relevant biological characterization of the nanointerface is crucial in order to select suitable nanomaterials for further in vitro or in vivo experiments. In this work, we adopt a methodology using antibody fragments (Fab) conjugated to gold nanoparticles (immunogold) to map the available epitopes on a transferrin grafted silica particle (SiO2-PEG8-Tf) as a proxy methodology to predict nanoparticle biological function, and therefore cellular receptor engagement...
December 29, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28004095/epitope-mapping-of-mono-and-polyclonal-antibodies-by-screening-phage-displayed-random-peptide-libraries
#17
Peter Molek, Tomaž Bratkovič
Detailed knowledge of antigenic determinants is crucial when characterizing therapeutic and diagnostic antibodies, assessing vaccine effectiveness and developing epitope-based vaccines. Most epitope mapping approaches are labor intensive and costly. In this study, we evaluated panning of phage-displayed random peptide libraries against antibodies as a tool for cognate epitope identification. We used six antibodies directed to three model protein antigens as targets to show that the approach is applicable to both mono- and polyclonal antibodies...
December 2016: Acta Chimica Slovenica
https://www.readbyqxmd.com/read/28000709/characterization-of-a-novel-inhibitory-human-monoclonal-antibody-directed-against-plasmodium-falciparum-apical-membrane-antigen-1
#18
Dominika J Maskus, Michał Królik, Susanne Bethke, Holger Spiegel, Stephanie Kapelski, Melanie Seidel, Otchere Addai-Mensah, Andreas Reimann, Torsten Klockenbring, Stefan Barth, Rainer Fischer, Rolf Fendel
Malaria remains a major challenge to global health causing extensive morbidity and mortality. Yet, there is no efficient vaccine and the immune response remains incompletely understood. Apical Membrane Antigen 1 (AMA1), a leading vaccine candidate, plays a key role during merozoite invasion into erythrocytes by interacting with Rhoptry Neck Protein 2 (RON2). We generated a human anti-AMA1-antibody (humAbAMA1) by EBV-transformation of sorted B-lymphocytes from a Ghanaian donor and subsequent rescue of antibody variable regions...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27997997/the-structure-of-the-mite-allergen-blo-t-1-explains-the-limited-antibody-cross-reactivity-to-der-p-1
#19
Kåre H Meno, Jette S Kastrup, I-Chun Kuo, Kaw Yan Chua, Michael Gajhede
The Blomia tropicalis (Blo t) mite species is considered a storage mite in temperate climate zones and an important source of indoor allergens causing allergic asthma and rhinitis in tropical and subtropical regions. Here, we report the crystal structure of one of the allergens from Blo t, recombinant proBlo t 1 (rproBlo t 1), determined at 2.1 Å resolution. Overall, the fold of rproBlo t 1 is characteristic for the pro-form of cysteine proteases from the C1A class. Structural comparison of experimentally mapped Der f 1/Der p1 IgG epitopes to the same surface patch on Blo t 1, as well as of sequence identity of surface exposed residues, suggests limited cross-reactivity between these allergens and Blo t 1...
December 20, 2016: Allergy
https://www.readbyqxmd.com/read/27995897/neurodegenerative-disease-mutations-in-trem2-reveal-a-functional-surface-and-distinct-loss-of-function-mechanisms
#20
Daniel L Kober, Jennifer M Alexander-Brett, Celeste M Karch, Carlos Cruchaga, Marco Colonna, Michael J Holtzman, Thomas J Brett
Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer's disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer's risk variants impact binding to a TREM2 ligand...
December 20, 2016: ELife
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