scholarly journals Comparison of Antigenic Regions Identified on IgG1Fc Using Bioinformatics vs Pepscan Analysis

2008 ◽  
Vol 1 ◽  
pp. CMAMD.S514 ◽  
Author(s):  
Paul N. Nelson ◽  
Olwyn M.R. Westwood ◽  
Graham Freimanis ◽  
Denise Roden ◽  
Samir Sissaoui ◽  
...  
Keyword(s):  
Rheumatoid Factor ◽  
Epitope Mapping ◽  
Bioinformatics Analysis ◽  
Entire Length ◽  
The Other ◽  
Antigenic Determinants ◽  
Amino Acid Residues ◽  
Antibody Recognition ◽  
Ch2 Domain ◽  
Protein Macromolecule

Epitope mapping allowed the location of antigenic determinants on a protein macromolecule to be identified. In particular, pepscan techniques that utilize a series of overlapping peptides, help detect key amino acid residues that are important in antibody recognition and binding. In a previous study, we employed 15-mer peptides spanning the entire length of IgG1Fc to ascertain successfully the target epitopes of isotypic/allotypic monoclonal reagents. As an extension to this work we have used these peptides to evaluate the location of epitope targets of five IgM rheumatoid factor antibodies (RFAbs). Overall, 2 antibodies, RFAb TS2 and TS1, detected a similar epitope within the CH3 domain (360-KNQVSLTCLVKGFYP-374), whilst 1 (RFAb SJ1) recognised an epitope in the CH2 domain (294-EQYNSTYRVVSVLTV-308). In contrast, 2 RFAbs, PRSJ2 and PRTS1 detected four and five epitopes respectively within the Fc region. RFAb PRSJ2 recognised epitopes detected by RFAB TS2 and TS1 but also further epitopes in the CH2 domain (256-TPEVTCVVVDVSHED-270) and CH3 domain (418-QQGNVFSCSVMHEAL-432). Similarly, RFAb PRTS1 detected all four epitopes plus a fifth in the CH3 domain (382-ESNGQPENNYKTTPP-396). In essence there was a consensus of target epitopes identified by these rheumatoid factor antibodies. Interestingly, two epitopes (256–270, CH2 domain and 360–374, CH3 domain) were novel in that they had not been identified in previous pepscan studies. The other epitopes recognised, either overlapped or were immediately adjacent to previous epitopes detected by poly/monoclonal rheumatoid factor antibodies. Molecular modelling (PCImdad) of IgG1Fc showed that all five epitopes were exposed and surface accessible for antibody interaction. In addition, a bioinformatics analysis of the Fc region using ExPASy was employed to identify key antigenic determinants. This ‘in silico’ approach may provide a means of determining key regions without the need to develop overlapping peptides spanning the entire length of a macromolecule.

scholarly journals Epitope Mapping of Immunogenic and Adhesive Structures in Repetitive Domains of Mycoplasma bovis Variable Surface Lipoproteins

2000 ◽  
Vol 68 (2) ◽  
pp. 680-687 ◽  
Author(s):  
K. Sachse ◽  
J. H. Helbig ◽  
I. Lysnyansky ◽  
C. Grajetzki ◽  
W. Müller ◽  
...  
Keyword(s):  
Epitope Mapping ◽  
Antigenic Determinants ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mycoplasma Bovis ◽  
Amino Acid Residues ◽  
Adhesion Sites ◽  
Variable Surface ◽  
The Family ◽  
Immunodominant Epitopes ◽  
Frequency Phase

ABSTRACT The family of variable surface lipoproteins (Vsps) of the bovine pathogen Mycoplasma bovis includes some of the most immunogenic antigens of this microorganism. Vsps were shown to undergo high-frequency phase and size variations and to possess extensive reiterated coding sequences extending from the N-terminal end to the C-terminal end of the Vsp molecule. In the present study, mapping experiments were conducted to detect regions with immunogenicity and/or adhesion sites in repetitive domains of four Vsp antigens of M. bovis, VspA, VspB, VspE, and VspF. In enzyme-linked immunosorbent assay experiments, sera obtained from naturally infected cattle showed antibodies to different repeating peptide units of the Vsps, particularly to units RA1, RA2, RA4.1, RB2.1, RE1, and RF1, all of which were found to contain immunodominant epitopes of three to seven amino acids. Competitive adherence trials revealed that a number of oligopeptides derived from various repeating units of VspA, VspB, VspE, and VspF partially inhibited cytoadhesion ofM. bovis PG45 to embryonic bovine lung cells. Consequently, putative adherence sites were identified in the same repeating units (RA1, RA2, RA4.1, RB2.1, RE1, and RF1) and in RF2. The positions and lengths of the antigenic determinants were mostly identical to those of adhesion-mediating sites in all short repeating units, whereas in the considerably longer RF1 unit (84 amino acid residues), there was only one case of identity among four immunogenic epitopes and six adherence sites. The identification of epitopes and adhesive structures in repetitive domains of Vsp molecules is consistent with the highly immunogenic nature observed for several members of the Vsp family and suggests a possible function for these Vsp molecules as complex adherence-mediating regions in pathogenesis.

Oxytocin analogues with non-coded amino acid residues in position 8: [8-Neopentylglycine]oxytocin and [8-cycloleucine]oxytocin

1987 ◽  
Vol 52 (9) ◽  
pp. 2317-2325 ◽  
Author(s):  
Jan Hlaváček ◽  
Jan Pospíšek ◽  
Jiřina Slaninová ◽  
Walter Y. Chan ◽  
Victor J. Hruby
Keyword(s):  
Amino Acid ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
The Other ◽  
Amino Acid Residues ◽  
Phase Synthesis ◽  
Other Hand ◽  
Fragment Condensation

[8-Neopentylglycine]oxytocin (II) and [8-cycloleucine]oxytocin (III) were prepared by a combination of solid-phase synthesis and fragment condensation. Both analogues exhibited decreased uterotonic potency in vitro, each being about 15-30% that of oxytocin. Analogue II also displayed similarly decreased uterotonic potency in vivo and galactogogic potency. On the other hand, analogue III exhibited almost the same potency as oxytocin in the uterotonic assay in vivo and in the galactogogic assay.

Immunochemical Studies on Antithrombin III

1979 ◽  
Author(s):  
E.J. McKay
Keyword(s):  
Antithrombin Iii ◽  
The Other ◽  
Antigenic Determinants ◽  
Immunochemical Analysis ◽  
Paradoxical Effect ◽  
Test Protocol ◽  
Agar Gel ◽  
High Affinity ◽  
Time Required ◽  
Antigen Antibody

Depressed Antithrombin III (AT) levels Increase thrombic tendency in man, therefore value in assaying this protein has been established. Immunochemical analysis of AT in clinical disease has however proved controversial, consequently systematic studies were undertaken to rationalize the requirements necessary to optimise these methods in particular electro-Immunoassay. The known binding affinity of AT for heparin has been exploited to differentiate high affinity AT from its inhibitor - protease complexes and has resulted in reports stating that heparin added to the agar gel prior to electrophoresis significantly reduces the time required for completion of antigen/antibody complexes. Our studies however have demonstrated that the antibody required for quantitative analysis must be capable of not only reacting with “native” antigenic determinants of AT but also with “neo” antigens that are exposed when inhibitor-protease complexes are formed. Heparin should not be used in the test protocol, for it has a paradoxical effect on Immunopreclpltation in gels, masking some antigenic determinants of unbound - high affinity AT on one hand, and appear to disrupt the Immunoprecipitin “rocket” formed with the inhibitor-protease complexes during electrophoresis on the other.

scholarly journals Amino Acids 1055 to 1192 in the S2 Region of Severe Acute Respiratory Syndrome Coronavirus S Protein Induce Neutralizing Antibodies: Implications for the Development of Vaccines and Antiviral Agents

2005 ◽  
Vol 79 (6) ◽  
pp. 3289-3296 ◽  
Author(s):  
Choong-Tat Keng ◽  
Aihua Zhang ◽  
Shuo Shen ◽  
Kuo-Ming Lip ◽  
Burtram C. Fielding ◽  
...  
Keyword(s):  
Amino Acids ◽  
Severe Acute Respiratory Syndrome ◽  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Antiviral Agents ◽  
Host Cells ◽  
Heptad Repeat ◽  
Antigenic Determinants ◽  
Amino Acid Residues ◽  
S Protein

ABSTRACT The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) interacts with cellular receptors to mediate membrane fusion, allowing viral entry into host cells; hence it is recognized as the primary target of neutralizing antibodies, and therefore knowledge of antigenic determinants that can elicit neutralizing antibodies could be beneficial for the development of a protective vaccine. Here, we expressed five different fragments of S, covering the entire ectodomain (amino acids 48 to 1192), as glutathione S-transferase fusion proteins in Escherichia coli and used the purified proteins to raise antibodies in rabbits. By Western blot analysis and immunoprecipitation experiments, we showed that all the antibodies are specific and highly sensitive to both the native and denatured forms of the full-length S protein expressed in virus-infected cells and transfected cells, respectively. Indirect immunofluorescence performed on fixed but unpermeabilized cells showed that these antibodies can recognize the mature form of S on the cell surface. All the antibodies were also able to detect the maturation of the 200-kDa form of S to the 210-kDa form by pulse-chase experiments. When the antibodies were tested for their ability to inhibit SARS-CoV propagation in Vero E6 culture, it was found that the anti-SΔ10 antibody, which was targeted to amino acid residues 1029 to 1192 of S, which include heptad repeat 2, has strong neutralizing activities, suggesting that this region of S carries neutralizing epitopes and is very important for virus entry into cells.

Precipitin Inhibition of Candida stellatoidea Antiserum with Oligosaccharides Obtained from the Parent Mannan

1970 ◽  
Vol 1 (1) ◽  
pp. 61-63
Author(s):  
William O. Mitchell ◽  
H. F. Hasenclever
Keyword(s):  
Inhibitory Activity ◽  
The Other ◽  
Antigenic Determinants ◽  
Effective Inhibitor ◽  
Structural Configuration ◽  
Immune Precipitation

Inhibition of immune precipitation with oligosaccharides obtained from Candida stellatoidea mannan has been used to provide more information about the haptenic groups of this serologically active polysaccharide. The oligosaccharides di-, tri-, tetra-, and a mixture of penta- and hexasaccharides were studied. The inhibitory activity of these materials was tested with two immune sera. With one serum, 0.8 μmole of the mixture of penta- and hexasaccharides inhibited the reaction by 87%, and, with the other serum, 0.4 μmole of the mixture inhibited the reaction by 99%. Monosaccharides were also tested with each antiserum and found to be noninhibitory. It is apparent that the mixture of oligosaccharides containing 5 to 6 mannose units was the most effective inhibitor. Since it is known that these oligosaccharides contain a predominance of α 1-2 linkages and lesser numbers of α 1-3 linkages, it is likely that these are important in the structural configuration of the antigenic determinants.

scholarly journals Identification of antigenic epitopes for Guertu virus nucleocapsid protein

2021 ◽  
Author(s):  
Siyuan Wang ◽  
Xihong Yue ◽  
Alai Shalitanati ◽  
Abulimiti Moming ◽  
Shu Shen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Epitope Mapping ◽  
Virus Detection ◽  
Polyclonal Antiserum ◽  
Detection Methods ◽  
Amino Acid Residues ◽  
High Conservation ◽  
Potential Pathogenicity ◽  
Severe Fever ◽  
Antigenic Epitopes

Abstract Guertu virus (GTV), a novel tick-borne virus with potential pathogenicity, was first isolated from Dermacentor nuttalli in Xinjiang, China, in 2014. GTV has been shown to infect animal and human cell lines and to be pathogenic in mice. The viral nucleoprotein (NP) is the most conserved immunogenic protein. Elucidating the B-cell epitopes (BCEs) in the immunodominant region of the NP is important for the development of virus detection methods and vaccines. In order to identify the minimal motifs of linear BCEs in the NP of the GTV DXM strain, we used an improved biosynthetic peptide (BSP) method to truncate GTV NP into 30 16mer-peptides with 8 overlapping amino acid residues spanning the full length of the protein. The peptides were analyzed by western blot using rabbit anti-GTV NP polyclonal antiserum, and four positive 16mer-peptides were obtained. The 16mer-peptides were then truncated into 31 8mer-peptides with 7 overlapping amino acid residues and 10mer-peptides with 9 overlapping amino acid residues to screen for BCEs that can react with the rabbit anti-GTV NP polyclonal antiserum. The results showed that there were 6 minimal BCE motifs, namely, Enp1, 88EKYGLVER95; Enp2, 88EKYGLVER95; Enp3, 162TTKILMEA169; Enp4, 187GASKAEVY194; Enp5, 191AEVYNSFR198; and Enp6, 236ETAAAAYRNL245. Positive sheep sera could recognize all six BCEs with anti-GTV antibodies. The BCEs were aligned with the sequences of eight representative severe fever with thrombocytopenia syndrome phlebovirus strains from different countries and regions that were evolutionarily closely related to GTV. The sequence identity of the BCEs ranged from 80–100%, thus showing high conservation. The fine epitope mapping of GTV NP can be used to explore the biological and immunological properties of GTV NP antigens and serve as basic data for the development of multi-epitope detection reagents and vaccine design for GTV.

A sensitive and practical immunoradiometric assay of thyrotropin.

1986 ◽  
Vol 32 (3) ◽  
pp. 514-518 ◽  
Author(s):  
T Helenius ◽  
S Tikanoja
Keyword(s):  
Monoclonal Antibodies ◽  
Thyroid Cancer ◽  
Detection Limit ◽  
Cancer Patients ◽  
The Other ◽  
Antigenic Determinants ◽  
Immunoradiometric Assay ◽  
Chloramine T ◽  
Hyperthyroid Patients ◽  
Mean Concentration

Abstract We describe a two-site immunoradiometric assay for thyrotropin (TSH) in serum, based on use of two monoclonal antibodies directed against two separate antigenic determinants on the TSH molecule. One antibody is immobilized on polystyrene beads; the other is radioiodinated by a modified Chloramine T method. The detection limit of the assay is 0.02 milli-int. unit/L. The working range (CV less than 10%) is from 0.1 to greater than 50 milli-int. units/L. The log mean concentration of TSH in sera collected from 100 euthyroid subjects between 08:00 and 11:00 hours was 1.9 milli-int. units/L, the range 0.4-5.4 milli-int. units/L. Values for hyperthyroid patients and thyroid-cancer patients being treated with thyroxin were much lower than those for euthyroid persons. Results by this new assay correlated excellently with those by our conventional radioimmunoassay (r = 0.99) and also with a sensitive immunofluorometric TSH method (Delfia TSH) (r = 0.99).

New Antibiotic Uperin Peptides From the Dorsal Glands of the Australian Toadlet Uperoleia mjobergii

1996 ◽  
Vol 49 (12) ◽  
pp. 1325 ◽  
Author(s):  
AM Bradford ◽  
JH Bowie ◽  
MJ Tyler ◽  
JC Wallace
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Related Species ◽  
Antibiotic Activity ◽  
Amino Acid Sequences ◽  
The Other ◽  
Cationic Peptides ◽  
Amino Acid Residues ◽  
Skin Glands ◽  
Edman Sequencing

The dorsal glandular extract of the toadlet Uperoleia mjobergii contains more than 20 peptides. We report the amino acid sequences of the seven major peptides: these were determined by a combination of mass spectrometry and automated Edman sequencing. Three of these peptides have 19 amino acid residues and belong to the uperin 2 group of peptides [e.g. uperin 2.6, Gly Ile Leu Asp Ile Ala Lys Lys Leu Val Gly Gly Ile Arg Asn Val Leu Gly Ile (OH)], while the other four have 17 residues and are classified as uperins 3 [e.g. Uperin 3.4, Gly Val Gly Asp Leu Ile Arg Lys Ala Val Ala Ala Ile Lys Asn Ile Val (NH2)]. Several of these cationic peptides have been synthesized in order for bioassays to be carried out: they show significant antibiotic activity against a range of Gram-positive microorganisms. A major skin peptide from the related species Uperoleia inundata is a powerful neuropeptide named uperin 1.1 ([Ala2] uperolein ): no corresponding neuropeptide is detected in the skin glands of Uperoleia mjobergii.

Conformational Alterations of α2-Antiplasmin Induced by Complex Formation with Plasmin

1979 ◽  
Author(s):  
E.F. Plow ◽  
B. Wiman ◽  
D. Collen
Keyword(s):  
Complex Formation ◽  
Structural Changes ◽  
Limited Proteolysis ◽  
Terminal Region ◽  
The Other ◽  
Antigenic Determinants ◽  
Chemical Analyses ◽  
Large Fragment ◽  
Reactive Site ◽  
Immunodiffusion Analysis

The conformational and structural changes induced in the α2-antiplasmin (AP) molecule by complex formation with plasmin have been analyzed utilizing quantitative radioimmuno-chemical analyses. Complexes prepared in plasmin excess -(PAP-P) and therefore subjected to limited proteolysis and complexes prepared in AP excess (PAP-A) have been compared with free AP. With AP antiserum, PAP-A, PAP-P and AP yielded reactions of complete identity by immunodiffusion analysis. In radioimmunoassay, however, these were clearly distinguished, and four distinct sets of antigenic determinants were delineated. Set I determinants were expressed equivalently by PAP-P, PAP-A and AP and were, therefore, not altered by complex formation. This set was recognized by 90% of the antibodies, and the determinants were all included within a large fragment of Mr 60,000 derived from the NH2-terminal region of AP. The other three sets of determinants were modulated by complex formation. Set II was expressed by PAP-A and AP but not by PAP-P, and these were sensitive to proteolysis by plasmin. Set III determinants were expressed only by AP and were localized to a peptide of Mr 8,000 derived from the COOH-terminal region of AP. Set IV determinants were also present only on AP but were not present in the peptide and required an intact reactive site in AP for expression. Thus, there is evidence for multiple conformational modulations in AP induced by complex formation, and these modulations can be pinpointed to specific loci within the AP molecule.

Plural Origins of Molecular Homochirality in Our Biota Part II. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides

1997 ◽  
Vol 52 (1-2) ◽  
pp. 89-96 ◽  
Author(s):  
Thereza Amélia Soares ◽  
Roberto Dias Lins ◽  
Ricardo Longo ◽  
Richard Garratt ◽  
Ricardo Ferreira
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Mechanics ◽  
Computer Simulations ◽  
The Other ◽  
Amino Acid Residues ◽  
Relative Stabilities ◽  
Amber Force Field ◽  
Cross Inhibition

Abstract By computer simulations -molecular mechanics and molecular dynamics with the amber force field (Weiner et al., (1986), J. Comp. Chem. 7, 2 30-252) -we have determined the stabilities of oligoribotide strands built with ᴅ -and ʟ-riboses, and of peptide chains with ᴅ -and ʟ-amino acid residues. In particular, complementary double-chains of oligoribotides were studied, since they are an important feature of the growing mechanism of modern nucleic acids. Peptide chains on the other hand, grow without need of a template. We found that mixed oligoribotides are less stable than homochiral ones, and that this chiral effect is less noticeable in peptide chains. The results support the interpretation that ʟ-riboses act as terminators to the template-assisted growth of oligo-r-Gᴅ (enantiomeric cross-inhibition; Joyce et al., (1987), Proc. Natl. Acad. Sci. USA 84, 4398-4402). Based on this effect, a chemical pathway is proposed which could, under assumed prebiotic conditions, bypass the hindrance of homochiral growth.

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