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https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#1
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811600/exploring-leishmania-secretory-proteins-to-design-b-and-t-cell-multi-epitope-subunit-vaccine-using-immunoinformatics-approach
#2
Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Visceral leishmaniasis (VL) is a fatal form of leishmaniasis which affects 70 countries, worldwide. Increasing drug resistance, HIV co-infection, and poor health system require operative vaccination strategy to control the VL transmission dynamics. Therefore, a holistic approach is needed to generate T and B memory cells to mediate long-term immunity against VL infection. Consequently, immunoinformatics approach was applied to design Leishmania secretory protein based multi-epitope subunit vaccine construct consisting of B and T cell epitopes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811153/the-design-of-target-specific-antibodies-scfv-by-applying-de-novo-workflow-case-study-on-bmr1-antigen-from-brugia-malayi
#3
Bee Yin Khor, Theam Soon Lim, Rahmah Noordin, Yee Siew Choong
De novo approach was applied to design single chain fragment variable (scFv) for BmR1, a recombinant antigen from Bm17DIII gene which is the primary antigen used for the detection of anti-BmR1 IgG4 antibodies in the diagnostic of lymphatic filariasis. Three epitopes of the BmR1 was previously predicted form an ab initio derived three-dimensional structure. A collection of energetically favourable conformations was generated via hot-spot-centric approach. This resulted in a set of three different scFv scaffolds used to compute the high shape complementary conformations via dock-and-design approach with the predicted epitopes of BmR1...
July 19, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28808060/the-human-rna-binding-protein-and-e3-ligase-mex-3c-binds-the-mex-3-recognition-element-mre-motif-with-high-affinity
#4
Lingna Yang, Chongyuan Wang, Fudong Li, Jiahai Zhang, Anam Nayab, Jihui Wu, Yunyu Shi, Qingguo Gong
MEX-3 is a KH domain-containing RNA-binding protein, first identified as a translational repressor in Caenorhabditis elegans, while its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3' UTR and posttranscriptional regulation of MEX-3 target transcripts...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28807980/cd177-modulates-human-neutrophil-migration-through-activation-mediated-integrin-and-chemoreceptor-regulation
#5
Ming Bai, Ricardo Grieshaber-Bouyer, Junxia Wang, Angela B Schmider, Zachary S Wilson, Liling Zeng, Olha Halyabar, Matthew D Godin, Hung N Nguyen, Anaïs Levescot, Pierre Cunin, Craig T Lefort, Roy J Soberman, Peter A Nigrovic
CD177 is a GPI-anchored protein expressed by a variable proportion of human neutrophils that mediates surface expression of the anti-neutrophil cytoplasmic antibody (ANCA) antigen proteinase 3. CD177 associates with β2 integrins and recognizes PECAM-1, suggesting a role in neutrophil migration. However, CD177(pos) neutrophils exhibit no clear migratory advantage in vivo, despite interruption of transendothelial migration by in vitro CD177 ligation. We sought to understand this paradox. Using a PECAM-1-independent transwell system, we found that CD177(pos) and CD177(neg) neutrophils migrated comparably...
August 14, 2017: Blood
https://www.readbyqxmd.com/read/28805498/gingiskhan%C3%A2-protease-cleavage-allows-a-high-throughput-antibody-to-fab-conversion-enabling-direct-functional-assessment-during-lead-identification-of-human-monoclonal-and-bispecific-igg1-antibodies
#6
Jörg Moelleken, Manuel Endesfelder, Christian Gassner, Sabine Lingke, Simone Tomaschek, Oksana Tyshchuk, Stefan Lorenz, Ulrike Reiff, Michael Mølhøj
The determination of the binding strength of immunoglobulins (IgGs) to targets can be influenced by avidity when the targets are soluble di- or multimeric proteins, or associated to cell surfaces, including surfaces introduced from heterogeneous assays. However, for the understanding of the contribution of a second drug-to-target binding site in molecular design, or for ranking of monovalent binders during lead identification, affinity-based assessment of the binding strength is required. Typically, monovalent binders like antigen-binding fragments (Fabs) are generated by proteolytic cleavage with papain, which often results in a combination of under- and over-digestion, and requires specific optimization and chromatographic purification of the desired Fabs...
August 14, 2017: MAbs
https://www.readbyqxmd.com/read/28804556/anti-tumor-efficacy-evaluation-of-a-novel-monoclonal-antibody-targeting-neutral-amino-acid-transporter-asct2-using-patient-derived-xenograft-mouse-models-of-gastric-cancer
#7
Noriyuki Kasai, Aya Sasakawa, Kenta Hosomi, Tze Wei Poh, Bernadette Lynn Chua, Wei Peng Yong, Jimmy So, Shing Leng Chan, Richie Soong, Koji Kono, Toshihiko Ishii, Kazuya Yamano
ASC amino acid transporter 2 (ASCT2), also known as solute linked carrier family 1 member A5 (SLC1A5) is a Na+-dependent glutamine/neutral amino acid transporter. ASCT2 acts as a high-affinity transporter of L-glutamine (Gln) and has been reported to be up-regulated in a variety of cancerous tissues including stomach, liver, and kidney. In this study, we evaluated anti-tumor efficacy of a novel anti-ASCT2 humanized monoclonal antibody, KM8094, which has a neutralizing activity against glutamine uptake, as a therapeutic antibody against gastric cancer and explored clinical predictive biomarker candidates by utilizing patient-derived xenograft (PDX) mouse models...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28804489/normalized-synergy-predicts-that-cd8-co-receptor-contribution-to-t-cell-receptor-tcr-and-pmhc-binding-decreases-as-tcr-affinity-increases-in-human-viral-specific-t-cells
#8
Chad M Williams, Alexandra A Schonnesen, Shu-Qi Zhang, Ke-Yue Ma, Chenfeng He, Tori Yamamoto, S Gail Eckhardt, Christopher A Klebanoff, Ning Jiang
The discovery of naturally occurring T cell receptors (TCRs) that confer specific, high-affinity recognition of pathogen and cancer-associated antigens remains a major goal in cellular immunotherapies. The contribution of the CD8 co-receptor to the interaction between the TCR and peptide-bound major histocompatibility complex (pMHC) has previously been correlated with the activation and responsiveness of CD8(+) T cells. However, these studies have been limited to model systems of genetically engineered hybridoma TCRs or transgenic mouse TCRs against either a single epitope or an array of altered peptide ligands...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28802648/designing-binding-kinetic-assay-on-the-bio-layer-interferometry-bli-biosensor-to-characterize-antibody-antigen-interactions
#9
Vishal Kamat, Ashique Rafique
The Octet biosensors provide a high-throughput alternative to the well-established surface plasmon resonance (SPR) and SPR imaging (SPRi) biosensors to characterize antibody-antigen interactions. However, the utility of the Octet biosensors for the accurate and reproducible measurement of binding rate constants of monoclonal antibodies (mAbs) is limited due to challenges such as analyte rebinding, and mass transport limitation (MTL). This study focuses on addressing these challenges and provides experimental conditions to reliably measure kinetics of mAb-antigen interactions...
August 9, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28795601/poly-glutamic-dendrimer-based-conjugates-for-cancer-vaccination-a-computational-design-for-targeted-delivery-of-antigens
#10
L I F Moura, N Martinho, L C Silva, T S Barata, S Brocchini, H F Florindo, M Zloh
Computational techniques are useful to predict interaction models and molecular properties for the design of drug delivery systems, such as dendrimers. This work evaluated the impact of surface modifications of mannosamine-conjugated multifunctional poly(glutamic acid) (PG)-dendrimers as nanocarriers of the tumour associated antigens (TAA) MART-1, gp100:44 and gp100:209. Molecular dynamics simulations and docking studies were performed. Nitrobenzoxadiazole (NBD)-PG-G4-dendrimer displayed 64 carboxylic groups, however, the Frontier Molecular Orbital Theory study evidenced that only 32 of those were available to form covalent bonds...
August 10, 2017: Journal of Drug Targeting
https://www.readbyqxmd.com/read/28794178/potential-of-high-affinity-slow-off-rate-modified-aptamer-somamer-reagents-for-mycobacterium-tuberculosis-proteins-as-tools-for-infection-models-and-diagnostic-applications
#11
Theresa Russell, Louis S Green, Taylor Rice, Nicole A Kruh-Garcia, Karen Dobos, Mary A DeGroote, Thomas Hraha, David G Sterling, Nebojsa Janjic, Urs A Ochsner
Direct pathogen detection in blood to diagnose active tuberculosis (TB) has been difficult, due to low levels of circulating antigens or due to the lack of specific, high-affinity binding reagents and reliable assays with adequate sensitivity. We sought to determine whether slow off-rate modified aptamer (SOMAmer) reagents with sub-nanomolar affinity for M. tuberculosis (Mtb) proteins (antigen 85A, 85B, 85C, GroES, GroEL2, DnaK, CFP10, KAD, CFP2, RplL and Tpx) could be useful to diagnose tuberculosis. When incorporated into the multiplexed, array-based proteomic SOMAscan assay, limits of detection reached the sub-picomolar range in 40% serum...
August 9, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28791742/a-multispecific-monoclonal-antibody-g2-recognizes-at-least-three-completely-different-epitope-sequences-with-high-affinity
#12
Md Nuruddin Mahmud, Masayuki Oda, Daiki Usui, Yasuo Inoshima, Naotaka Ishiguro, Yuji O Kamatari
A monoclonal antibody (mAb) G2 possesses an unusual characteristic of reacting with at least three proteins (ATP6V1C1, SEPT3, and C6H10orf76) other than its original antigen, chicken prion protein (ChPrP). The epitopes on ChPrP and ATP6V1C1 have been identified previously. In this study, we identified the epitope in the third protein, SEPT3. Interestingly, there was no amino acid sequence similarity among the epitopes on the three proteins. These epitopes had high binding affinities to G2 (KD = ∼10(-7) M for monovalent binding and KD = ∼10(-9) M for divalent binding), as determined using a SPR biosensor...
August 9, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28791022/enhancing-stability-of-camelid-and-shark-single-domain-antibodies-an-overview
#13
REVIEW
Ellen R Goldman, Jinny L Liu, Dan Zabetakis, George P Anderson
Single domain antibodies (sdAbs) are gaining a reputation as superior recognition elements as they combine the advantages of the specificity and affinity found in conventional antibodies with high stability and solubility. Melting temperatures (Tms) of sdAbs cover a wide range from below 50 to over 80°C. Many sdAbs have been engineered to increase their Tm, making them stable until exposed to extreme temperatures. SdAbs derived from the variable heavy chains of camelid and shark heavy chain-only antibodies are termed VHH and VNAR, respectively, and generally exhibit some ability to refold and bind antigen after heat denaturation...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28789522/a-new-architecture-for-reagentless-protein-based-electro-chemical-biosensors
#14
Di Kang, Sheng Sun, Martin Kurnik, Demosthenes P Morales, Frederick Willis Dahlquist, Kevin W Plaxco
Here we demonstrate a new class of reagentless, single-step sensors for the detection of proteins and peptides that is the electro-chemical analog of fluorescence polarization (fluorescence anisotropy), a versatile optical approach widely employed to this same end. Our electrochemical sensors consist of a redox-reporter-modified protein (the "receptor") site-specifically anchored to an electrode via a short, flexible polypeptide linker. Interaction of the receptor with its binding partner alters the efficiency with which the reporter approaches the electrode surface, thus causing a change in redox current upon voltammetric interrogation...
August 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28774114/fc-binding-ligands-of-immunoglobulin-g-an-overview-of-high-affinity-proteins-and-peptides
#15
REVIEW
Weonu Choe, Trishaladevi A Durgannavar, Sang J Chung
The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies...
December 8, 2016: Materials
https://www.readbyqxmd.com/read/28772027/escherichia-coli-surface-display-for-the-selection-of-nanobodies
#16
REVIEW
Valencio Salema, Luis Ángel Fernández
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display)...
August 3, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28768709/co-stimulatory-function-in-primary-germinal-center-responses-cd40-and-b7-are-required-on-distinct-antigen-presenting-cells
#17
Masashi Watanabe, Chiharu Fujihara, Andrea J Radtke, Y Jeffrey Chiang, Sumeena Bhatia, Ronald N Germain, Richard J Hodes
T cell-dependent germinal center (GC) responses require coordinated interactions of T cells with two antigen-presenting cell (APC) populations, B cells and dendritic cells (DCs), in the presence of B7- and CD40-dependent co-stimulatory pathways. Contrary to the prevailing paradigm, we found unique cellular requirements for B7 and CD40 expression in primary GC responses to vaccine immunization with protein antigen and adjuvant: B7 was required on DCs but was not required on B cells, whereas CD40 was required on B cells but not on DCs in the generation of antigen-specific follicular helper T cells, antigen-specific GC B cells, and high-affinity class-switched antibody production...
August 2, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28765875/quantum-dot-pmhc-multimers-vs-phycoerythrin-pmhc-tetramers-for-identification-of-hla-a-0201-restricted-phbv-core-antigen18-27-specific-t-cells
#18
Jianmeng Zhu, Yong Huang, Jing Su, Jian He, Yating Yu, Yongxiang Zhao, Xiaoling Lu
Detection of human leukocyte antigens-A2-restricted p-hepatitis B virus (HBV) core antigen‑specific cytotoxic T lymphocytes (CTLs) is important in the study of HBV immunopathogenesis and vaccine design. Currently, major histocompatibility complex (MHC) class I/peptide‑(p) MHCI tetramers are considered the optimal tools to detect antigen‑specific CTLs. However, the MHC‑tetramer technique also has certain drawbacks and is under continuous development. The quantum dot (QD) bioconjugates nanotechnology with its unique inorganic‑biological properties has been developing fast...
August 1, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28765476/annexin-a11-is-targeted-by-igg4-and-igg1-autoantibodies-in-igg4-related-disease
#19
Lowiek M Hubers, Harmjan Vos, Alex R Schuurman, Robin Erken, Ronald P Oude Elferink, Boudewijn Burgering, Stan F J van de Graaf, Ulrich Beuers
OBJECTIVE: Immunoglobulin G4-related disease (IgG4-RD) is a multiorgan immune-mediated disease that predominantly affects the biliary tract (IgG4-associated cholangitis, IAC) and pancreas (autoimmune pancreatitis, AIP). We recently identified highly expanded IgG4+ B-cell receptor clones in blood and affected tissues of patients with IAC/AIP suggestive of specific (auto)antigenic stimuli involved in initiating and/or maintaining the inflammatory response. This study aimed to identify (auto)antigen(s) that are responsible for the clonal expansion of IgG4+ B cells in IgG4-RD...
August 1, 2017: Gut
https://www.readbyqxmd.com/read/28762497/t-cell-dependent-antigen-adjuvanted-with-dotap-cpg-b-but-not-dotap-cpg-a-induces-robust-germinal-center-responses-and-high-affinity-antibodies-in-mice
#20
Munir Akkaya, Billur Akkaya, Patrick W Sheehan, Pietro Miozzo, Mirna Pena, Chen-Feng Qi, Javier Manzella-Lapeira, Silvia Bolland, Susan K Pierce
The development of vaccines for infectious diseases for which we currently have none, including HIV, will likely require the use of adjuvants that strongly promote germinal center responses and somatic hypermutation to produce broadly neutralizing antibodies. Here we compared the outcome of immunization with the T-cell dependent antigen, NP-conjugated to chicken gamma globulin (NP-CGG) adjuvanted with the toll-like receptor 9 (TLR9) ligands, CpG-A or CpG-B, alone or conjugated with the cationic lipid carrier, DOTAP...
August 1, 2017: European Journal of Immunology
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