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Epitope mapping

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https://www.readbyqxmd.com/read/28904177/limited-proteolysis-as-a-tool-to-probe-the-tertiary-conformation-of-dysferlin-and-structural-consequences-of-patient-missense-variant-l344p
#1
Natalie Woolger, Adam Bournazos, Reece A Sophocleous, Frances J Evesson, Angela Lek, Birgit Driemer, R Bryan Sutton, Sandra T Cooper
Dysferlin is a large transmembrane protein that plays a key role in cell membrane repair, and underlies a recessive form of inherited muscular dystrophy. Dysferlinopathy is characterized by absence or marked reduction of dysferlin protein, with 43% of reported pathogenic variants being missense variants that span the length of the dysferlin protein. The unique structure of dysferlin, with seven tandem C2-domains separated by linkers, suggest dysferlin may dynamically associate with phospholipid membranes in response to Ca2+ signaling...
September 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28894095/atomic-structures-of-coxsackievirus-a6-and-its-complex-with-a-neutralizing-antibody
#2
Longfa Xu, Qingbing Zheng, Shaowei Li, Maozhou He, Yangtao Wu, Yongchao Li, Rui Zhu, Hai Yu, Qiyang Hong, Jie Jiang, Zizhen Li, Shuxuan Li, Huan Zhao, Lisheng Yang, Wangheng Hou, Wei Wang, Xiangzhong Ye, Jun Zhang, Timothy S Baker, Tong Cheng, Z Hong Zhou, Xiaodong Yan, Ningshao Xia
Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses...
September 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28892361/immunopurification-of-acetylcholinesterase-from-red-blood-cells-for-detection-of-nerve-agent-exposure
#3
Alicia J Dafferner, Lawrence M Schopfer, Gaoping Xiao, John R Cashman, Udaya Yerramalla, Rudolph C Johnson, Thomas A Blake, Oksana Lockridge
Nerve agents and organophosphorus pesticides make a covalent bond with the active site serine of acetylcholinesterase (AChE), resulting in inhibition of AChE activity and toxic symptoms. AChE in red blood cells (RBC) serves as a surrogate for AChE in the nervous system. Mass spectrometry analysis of adducts on RBC AChE could provide evidence of exposure. Our goal was to develop a method of immunopurifying human RBC AChE in quantities adequate for detecting exposure by mass spectrometry. For this purpose we immobilized 3 commercially available anti-human acetylcholinesterase monoclonals (AE-1, AE-2, and HR2) plus 3 new monoclonals...
September 11, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28888625/fine-mapping-and-conservation-analysis-of-linear-b-cell-epitopes-of-peste-des-petits-ruminants-virus-hemagglutinin-protein
#4
Ruisong Yu, Rui Zhu, Weixiang Gao, Ming Zhang, Shijuan Dong, Bingqing Chen, Li Yu, Chunfang Xie, Fengying Jiang, Zhen Li
Hemagglutinin protein (H), one of the two glycoproteins of peste des petits ruminants virus (PPRV), binds to its receptor on the host cell and acts as a major antigen that induces and confers highly protective immunity in the host. In order to delineate the epitopes on H protein, fine epitope mapping and conservation analysis of linear B-cell epitopes (BCEs) on PPRV H has been undertaken using biosynthetic peptides and rabbit anti-PPRV H sera. Thirteen linear BCEs were identified and their corresponding minimal motifs were located on the H protein of PPRV China/Tibet/Geg/07-30...
September 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28887429/nfm-cross-reactivity-to-mog-does-not-expand-a-critical-threshold-level-of-high-affinity-t-cells-necessary-for-onset-of-demyelinating-disease
#5
Lori Blanchfield, Joseph J Sabatino, Laurel Lawrence, Brian D Evavold
Of interest to the etiology of demyelinating autoimmune disease is the potential to aberrantly activate CD4(+) T cells due to cross-recognition of multiple self-epitopes such as has been suggested for myelin oligodendrocyte glycoprotein epitope 35-55 (MOG35-55) and neurofilament medium protein epitope 15-35 (NFM15-35). NFM15-35 is immunogenic in C57BL/6 mice but fails to induce demyelinating disease by polyclonal T cells despite having the same TCR contact residues as MOG35-55, a known encephalitogenic Ag...
September 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28883462/mapping-a-type-specific-epitope-by-monoclonal-antibody-against-vp3-protein-of-duck-hepatitis-a-type-1-virus
#6
Xiaoying Wu, Tingting Zhang, Fanyi Meng, Dongchun Guo, Xiuchen Yin, Shaozhou Wulin, Chenxi Li, Qingshan Zhang, Ming Liu, Yun Zhang
Duck hepatitis A subtype 1 virus (DHAV-1) infection causes high mortality in ducklings, resulting in significant losses to duck industries. VP3 is a structural protein of DHAV-1. However, B-cell epitopes on VP3 have not been investigated. To stimulate VP3 antibody response, eukaryotic expression plasmid pCI-neo-VP3 was constructed and used as DNA immunogen to prepare mAbs. Western blot showed that 25.5 kDa VP3 could be detected by mAbs in duck embryo fibroblast (DEF) cells transfected with pCI-neo-VP3. Immunofluorescence assay showed that mAbs could specifically bind to DEF cells infected with DHAV-1...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28875466/native-mass-spectrometry-ion-mobility-and-collision-induced-unfolding-categorize-malaria-antigen-antibody-binding
#7
Yining Huang, Nichole D Salinas, Edwin Chen, Niraj H Tolia, Michael L Gross
Plasmodium vivax Duffy Binding Protein (PvDBP) is a promising vaccine candidate for P. vivax malaria. Recently, we reported the epitopes on PvDBP region II (PvDBP-II) for three inhibitory monoclonal antibodies (2D10, 2H2, and 2C6). In this communication, we describe the combination of native mass spectrometry and ion mobility (IM) with collision induced unfolding (CIU) to study the conformation and stabilities of three malarial antigen-antibody complexes. These complexes, when collisionally activated, undergo conformational changes that depend on the location of the epitope...
September 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28836259/cartilage-matrix-remodelling-differs-by-disease-state-and-joint-type
#8
M-F Hsueh, V B Kraus, P Önnerfjord
Dramatic alterations in mechanical properties have been documented for osteoarthritic (OA) cartilage. However, the matrix composition underlying these changes has not been mapped and their aetiology is not entirely understood. We hypothesised that an understanding of the cartilage matrix heterogeneity could provide insights into the origin of these OA-related alterations. We generated serial transverse cryo sections for 7 different cartilage conditions: 2 joint sites (knee and hip), 2 disease states (healthy and OA) and 3 tissue depths (superficial, middle and deep)...
August 24, 2017: European Cells & Materials
https://www.readbyqxmd.com/read/28827189/prediction-of-antibody-structural-epitopes-via-random-peptide-library-screening-and-next-generation-sequencing
#9
Kelly N Ibsen, Patrick S Daugherty
Next generation sequencing (NGS) is widely applied in immunological research, but has yet to become common in antibody epitope mapping. A method utilizing a 12-mer random peptide library expressed in bacteria coupled with magnetic-based cell sorting and NGS correctly identified >75% of epitope residues on the antigens of two monoclonal antibodies (trastuzumab and bevacizumab). PepSurf, a web-based computational method designed for structural epitope mapping was utilized to compare peptides in libraries enriched for monoclonal antibody (mAb) binders to antigen surfaces (HER2 and VEGF-A)...
August 18, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28826780/towards-a-peptide-based-vaccine-against-shigella-sonnei-a-subtractive-reverse-vaccinology-based-approach
#10
Shehneela Baseer, Sajjad Ahmad, Kara E Ranaghan, Syed Sikander Azam
Shigella sonnei is one of the major causes of shigellosis in technically advanced countries and reports of its unprecedented increase are published from the Middle East, Latin America, and Asia. The pathogen exhibits resistance against first and second line antibiotics which highlights the need for the development of an effective broad-spectrum vaccine. A computational based approach comprising subtractive reverse vaccinology was used for the identification of potential peptide-based vaccine candidates in the proteome of S...
August 18, 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28823097/epitope-mapping-of-histo-blood-group-antigens-bound-to-norovirus-vlps-using-std-nmr-experiments-reveals-fine-details-of-molecular-recognition
#11
Brigitte Fiege, Mila Leuthold, Francisco Parra, Kevin P Dalton, Peter J Meloncelli, Todd L Lowary, Thomas Peters
Attachment of human noroviruses to histo blood group antigens (HBGAs) is thought to be critical for the infection process. Therefore, we have determined binding epitopes of synthetic type 1 to 6 blood group A- and B-tetrasaccharides binding to GII.4 human Norovirus virus like particles (VLPs) using STD NMR experiments. So far, little information is available from crystal structure analysis studies on the interactions of the reducing-end sugars with the protruding domain (P-domain) of the viral coat protein VP1...
August 19, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28818423/design-and-synthesis-of-multiple-antigenic-peptides-and-their-application-for-dengue-diagnosis
#12
Reeta Rai, Sameer Dubey, K V Santosh, Ashutosh Biswas, Vinit Mehrotra, D N Rao
Major difficulty in development of dengue diagnostics is availability of suitable antigens. To overcome this, we made an attempt to develop a peptide based diagnosis which offers significant advantage over other methods. With the help of in silico methods, two epitopes were selected from envelope protein and three from NS1 protein of dengue virus. These were synthesized in combination as three multiple antigenic peptides (MAPs). We have tested 157 dengue positive sera confirmed for NS1 antigen. MAP1 showed 96...
September 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28811514/differential-epitope-recognition-in-the-immunodominant-staphylococcal-antigen-a-of-staphylococcus-aureus-by-mouse-versus-human-igg-antibodies
#13
Dennis G A M Koedijk, Francisco Romero Pastrana, Hedzer Hoekstra, Sanne van den Berg, Jaap Willem Back, Carolien Kerstholt, Rianne C Prins, Irma A J M Bakker-Woudenberg, Jan Maarten van Dijl, Girbe Buist
The immunodominant staphylococcal antigen A (IsaA) is a potential target for active or passive immunization against the important human pathogen Staphylococcus aureus. Consistent with this view, monoclonal antibodies against IsaA were previously shown to be protective against S. aureus infections in mouse models. Further, patients with the genetic blistering disease epidermolysis bullosa (EB) displayed high IsaA-specific IgG levels that could potentially be protective. Yet, mice actively immunized with IsaA were not protected against S...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800361/identification-of-a-common-ara-h-3-epitope-recognized-by-both-the-capture-and-the-detection-monoclonal-antibodies-in-an-elisa-detection-kit
#14
Lipei Zhao, Liang Zhao, Buchang Zhang, Jason M Robotham, Kenneth H Roux, Hengli Tang
Allergy to peanuts has become a common and severe problem, especially in westernized countries. In this study, we evaluated the target and epitope specificity of the capture and detection mouse monoclonal antibodies (mAbs) used in a commercial peanut allergen detection platform. We first identified the target of these antibodies as Ara h 3 and then used an overlapping peptide array of Ara h 3 to determine the antibody-binding epitopes. Further amino acids critical for the binding via alanine substitutions at individual amino acid residues within the epitope were mapped...
2017: PloS One
https://www.readbyqxmd.com/read/28798301/kinetic-and-structural-characterization-of-the-effects-of-membrane-on-the-complex-of-cytochrome-b-5-and-cytochrome-c
#15
Katherine A Gentry, Elke Prade, Carlo Barnaba, Meng Zhang, Mukesh Mahajan, Sang-Choul Im, G M Anantharamaiah, Satoshi Nagao, Lucy Waskell, Ayyalusamy Ramamoorthy
Cytochrome b 5 (cytb 5) is a membrane protein vital for the regulation of cytochrome P450 (cytP450) metabolism and is capable of electron transfer to many redox partners. Here, using cyt c as a surrogate for cytP450, we report the effect of membrane on the interaction between full-length cytb 5 and cyt c for the first time. As shown through stopped-flow kinetic experiments, electron transfer capable cytb 5 - cyt c complexes were formed in the presence of bicelles and nanodiscs. Experimentally measured NMR parameters were used to map the cytb 5-cyt c binding interface...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28791419/mapping-of-the-binding-sites-of-human-histamine-n-methyltransferase-hnmt-monoclonal-antibodies
#16
Hubert G Schwelberger, Johannes Feurle, Gunnar Houen
OBJECTIVE: Recently, we characterized mouse monoclonal antibodies that allow the specific and sensitive detection of human histamine N-methyltransferase (HNMT). To understand differences in binding characteristics and recognition of enzyme variants we mapped the antibody binding sites. METHODS: Fragments of human HNMT were expressed as glutathione S-transferase fusion proteins that were used for testing antibody binding on immunoblots. Combined information from species cross-reactivity, sequence comparison, protein structure, and binding site prediction software were used to localize the epitope recognized by each antibody...
August 8, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28790847/combined-detection-of-dickkopf-1-subtype-classification-autoantibodies-as-biomarkers-for-the-diagnosis-and-prognosis-of-non-small-cell-lung-cancer
#17
Lei Shen, Xiaoguang Wu, Jinjing Tan, Meng Gu, Yu Teng, Zitong Wang, Wentao Yue
PURPOSE: This study aims to identify the clinical significance of serum autoantibodies against dickkopf-1 (DKK1) and evaluate their feasibility in the immunodiagnosis and prognosis of non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN: Epitope mapping by peptide microarray-based serum screening of NSCLC patients (n=72) and healthy controls (n=16) was performed. Indirect ELISA with peptides was used to measure the serum levels of autoantibodies in 206 NSCLC patients and 99 healthy controls...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28783665/structural-basis-for-potent-antibody-mediated-neutralization-of-human-cytomegalovirus
#18
Sumana Chandramouli, Enrico Malito, TuongVi Nguyen, Kate Luisi, Danilo Donnarumma, Yi Xing, Nathalie Norais, Dong Yu, Andrea Carfi
Human cytomegalovirus (HCMV) is the leading viral cause of birth defects and organ transplant rejection. The HCMV gH/gL/UL128/UL130/UL131A complex (Pentamer) is the main target of humoral responses and thus a key vaccine candidate. We report two structures of Pentamer bound to human neutralizing antibodies, 8I21 and 9I6, at 3.0 and 5.9 Å resolution, respectively. The HCMV gH/gL architecture is similar to that of Epstein-Barr virus (EBV) except for amino-terminal extensions on both subunits. The extension of gL forms a subdomain composed of a three-helix bundle and a β hairpin that acts as a docking site for UL128/UL130/UL131A...
June 30, 2017: Science Immunology
https://www.readbyqxmd.com/read/28770632/an-overview-of-hydrogen-deuterium-exchange-mass-spectrometry-hdx-ms-in-drug-discovery
#19
Glenn R Masson, Meredith L Jenkins, John E Burke
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered: This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions...
August 17, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28768817/cxcr4-specific-nanobodies-as-potential-therapeutics-for-whim-syndrome
#20
Raymond H de Wit, Raimond Heukers, Hendrik Brink, Angela Arsova, David Maussang, Pasquale Cutolo, Beatrijs Strubbe, Henry Vischer, Francoise Bachelerie, Martine J Smit
WHIM syndrome is a rare congenital immunodeficiency disease, named after its main clinical manifestations: Warts, Hypogammaglobulinemia, Infections and Myelokathexis. The disease is primarily caused by C-terminal truncation mutations of the chemokine receptor CXCR4. Consequently, these CXCR4-WHIM mutants have a gain of function in response to its ligand CXCL12, which results in abnormal leukocyte migration and thereby immune system dysfunctions. Treatment of WHIM patients currently consists of symptom relief, leading to unsatisfactory clinical responses...
August 2, 2017: Journal of Pharmacology and Experimental Therapeutics
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