scholarly journals Sequence Conservation and Antigenic Variation of the Structural Proteins of Equine Rhinitis A Virus

2001 ◽  
Vol 75 (21) ◽  
pp. 10550-10556 ◽  
Author(s):  
Annalisa Varrasso ◽  
Heidi E. Drummer ◽  
Jin-an Huang ◽  
Rachel A. Stevenson ◽  
Nino Ficorilli ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Antigenic Variation ◽  
Amino Acid Sequences ◽  
Sequence Conservation ◽  
Structural Proteins ◽  
Serum Neutralization ◽  
Prototype Virus

ABSTRACT The nucleotide and deduced amino acid sequences of the P1 region of the genomes of 10 independent equine rhinitis A virus (ERAV) isolates were determined and found to be very closely related. A panel of seven monoclonal antibodies to the prototype virus ERAV.393/76 that bound to nonneutralization epitopes conserved among all 10 isolates was raised. In serum neutralization assays, rabbit polyclonal sera and sera from naturally and experimentally infected horses reacted in a consistent and discriminating manner with the 10 isolates, which indicated the existence of variation in the neutralization epitopes of these viruses.

scholarly journals Comparative Analysis of Two Meningococcal Immunotyping Monoclonal Antibodies by Resonant Mirror Biosensor and Antibody Gene Sequencing

1999 ◽  
Vol 6 (6) ◽  
pp. 838-843 ◽  
Author(s):  
Bambos M. Charalambous ◽  
Janet Evans ◽  
Ian M. Feavers ◽  
Martin C. J. Maiden
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Antigenic Variation ◽  
Gene Sequencing ◽  
Amino Acid Sequences ◽  
Heavy Chains ◽  
Sequence Identity ◽  
Differential Binding ◽  
Major Surface ◽  
Antibody Gene

ABSTRACT Lipooligosaccharide (LOS) is a major surface component of the cell walls of Neisseria meningitidis, which is important for its roles in pathogenesis and antigenic variation, as a target for immunological typing, and as a possible vaccine component. Although the structures of many antigenic variants have been determined, routine immunological typing of these molecules remains problematic. Resonant mirror analysis was combined with gene sequencing to characterize two monoclonal antibodies (MAbs) used in typing panels that were raised against the same LOS immunotype, L3,7,9. The two MAbs (MAb 4A8-B2 and MAb 9-2-L379) were of the same immunoglobulin subtype, but while MAb 9-2-L379 was more than a 1,000-fold more sensitive in immunotyping assays of both whole meningococcal cells and purified LOS, MAb 4A8-B2 was more specific for immunotype L3,7,9. The differences in sensitivity were a consequence of MAb 9-2-L379 having a 44-fold-faster association constant than MAb 4A8-B2. Comparison of the amino acid sequences of the variable chains of the MAbs revealed that they had very similar heavy chains (81% amino acid sequence identity) but diverse light chains (54% sequence identity). The differential binding kinetics and specificities observed with these MAbs were probably due to differences in the epitopes recognized, and these were probably a consequence of the different immunization protocols used in their production.

scholarly journals Location of antigenic sites recognized by monoclonal antibodies in the influenza A virus nucleoprotein molecule

2009 ◽  
Vol 90 (7) ◽  
pp. 1730-1733 ◽  
Author(s):  
Natalia L. Varich ◽  
Konstantin S. Kochergin-Nikitsky ◽  
Evgeny V. Usachev ◽  
Olga V. Usacheva ◽  
Alexei G. Prilipov ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Influenza A Virus ◽  
Influenza A ◽  
Antigenic Variation ◽  
Strain Differences ◽  
Antigenic Structure ◽  
Amino Acid Residues ◽  
Mutant Proteins ◽  
Antigenic Sites

The locations of amino acid positions relevant to antigenic variation in the nucleoprotein (NP) of influenza virus are not conclusively known. We analysed the antigenic structure of influenza A virus NP by introducing site-specific mutations at amino acid positions presumed to be relevant for the differentiation of strain differences by anti-NP monoclonal antibodies. Mutant proteins were expressed in a prokaryotic system and analysed by performing ELISA with monoclonal antibodies. Four amino acid residues were found to determine four different antibody-binding sites. When mapped in a 3D X-ray model of NP, the four antigenically relevant amino acid positions were found to be located in separate physical sites of the NP molecule.

Highland games: A benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences

2020 ◽  
Vol 117 (7) ◽  
pp. 2100-2115 ◽  
Author(s):  
Jonathan Coffman ◽  
Bruno Marques ◽  
Raquel Orozco ◽  
Minni Aswath ◽  
Hasan Mohammad ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Amino Acid Sequences

scholarly journals Cloning and Sequence Analysis of Genes Encoding Staphylococcus hyicus Exfoliative Toxin Types A, B, C, and D

2004 ◽  
Vol 186 (6) ◽  
pp. 1833-1837 ◽  
Author(s):  
Peter Ahrens ◽  
Lars Ole Andresen
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Serine Proteases ◽  
Amino Acid Sequences ◽  
Coding Sequence ◽  
Exfoliative Toxin ◽  
Genes Encoding

ABSTRACT Exfoliative toxins produced by certain strains of Staphylococcus hyicus mediate exudative epidermitis in pigs. In this study the genes coding for four different exfoliative toxin from S. hyicus (ExhA, ExhB, ExhC, and ExhD) were cloned and sequenced. The coding sequence of the four toxin genes ranged from 816 to 834 bp. The amino acid sequences of these four toxins were homologous to the earlier described exfoliative toxins SHETB from S. hyicus and ETA, ETB, and ETD from Staphylococcus aureus. The homology between the S. hyicus toxins was at the same level as the homology to the exfoliative toxins from S. aureus. The toxins showed similarity to serine proteases, including preservation of the catalytic tract in ExhA, ExhB, and ExhC. However, in ExhD, Asp in the putative catalytic tract was replaced with Glu. The recombinant toxins could be expressed in Escherichia coli, and three of the four toxins were recognized by monoclonal antibodies raised against native exfoliative toxins.

scholarly journals Expression and characterisation of the ryegrass mottle virus non-structural proteins

2010 ◽  
Vol 64 (5-6) ◽  
pp. 215-222
Author(s):  
Ina Baļķe ◽  
Gunta Resēviča ◽  
Dace Skrastiņa ◽  
Andris Zeltiņš
Keyword(s):  
Amino Acid ◽  
Expression System ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Mottle Virus ◽  
Expression Vectors ◽  
Structural Protein ◽  
E Coli

Expression and characterisation of the ryegrass mottle virus non-structural proteins The Ryegrass mottle virus (RGMoV) single-stranded RNA genome is organised into four open reading frames (ORF) which encode several proteins: ORF1 encodes protein P1, ORF2a contains the membrane-associated 3C-like serine protease, genome-linked protein VPg and a P16 protein gene. ORF2b encodes replicase RdRP and the only structural protein, coat protein, is synthesised from ORF3. To obtain the non-structural proteins in preparative quantities and to characterise them, the corresponding RGMoV gene cDNAs were cloned in pET- and pColdI-derived expression vectors and overexpressed in several E. coli host cells. For protease and RdRP, the best expression system containing pColdI vector and E. coli WK6 strain was determined. VPg and P16 proteins were obtained from the pET- or pACYC- vectors and E. coli BL21 (DE3) host cells and purified using Ni-Sepharose affinity chromatography. Attempts to crystallize VPg and P16 were unsuccessful, possibly due to non-structured amino acid sequences in both protein structures. Methods based on bioinformatic analysis indicated that the entire VPg domain and the C-terminal part of the P16 contain unstructured amino acid stretches, which possibly prevented the formation of crystals.

scholarly journals Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site

2002 ◽  
Vol 83 (12) ◽  
pp. 3075-3084 ◽  
Author(s):  
Afjal Hossain Khan ◽  
Kouichi Morita ◽  
Maria del Carmen Parquet ◽  
Futoshi Hasebe ◽  
Edward G. M. Mathenge ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chikungunya Virus ◽  
Genomic Sequence ◽  
Adenine Nucleotides ◽  
Repeated Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Sequence Elements

In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3′ non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5′ cap nucleotide, an I-poly(A) tract and the 3′ poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5′ NTR and repeated sequence elements (RSEs) within the 3′ NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o’nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as ‘polymerase slippage’, as has been reported for vesicular stomatitis virus.

scholarly journals The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

2020 ◽  
Vol 19 (2) ◽  
pp. 13-30
Author(s):  
E. Р. Kharchenko
Keyword(s):  
Amino Acid ◽  
Close Contact ◽  
Amino Acid Content ◽  
Infection Process ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Structural Proteins ◽  
Subunit Structure ◽  
S Protein ◽  
Immune Epitope

Relevance. Coronavirus SARS-Cov-2 is a novel virus demonstrating the ability to be trans¬mitted from human-to-human, via respiratory droplets or close contact, and cause the severe acute respiratory syndrome (SARS). The role of its structural proteins in the SARS pathogenesis is unknown.Aim is to characterize the features of the SARS-Cov-2 structural proteins and their changes associated with acquiring other way of transmission and analyze the possibility of heterologous immunity emergence in its infection. Materials and method. For the computer analysis and alignment, the gene sequences of SARS-Cov-2 , SARS-CoV , MERS-CoV и bat CoV HKU3 reference strains were used from the Internet. From the primary structure of their genes it were translated their structural proteins: spike (S), envelope (E),membrane (M), and nucleocapsid (N). The genetic code of structural proteins was also defined. The search of homologous sequences in the SARS-Cov-2 S-protein, surface proteins of other viruses, and human proteins was made to find immune epitope continuum of protein relationships.Results. In the SARS-Cov-2 structural proteins amino acid sequences of M, E, and N-proteins are conservative. The S1 subunit of the S-protein contains some large insertions, significant changes of the amino acid content with the predominance of arginine and lysine which is typical for the surface glycoproteins in the viruses possessing high contagiousness. The S2 subunit is rather conservative and retain negative polarity. The S-protein exhibits the immune epitope relationships with many proteins of viruses and human which may be associated with immune collisions.Conclusion: The SARSCov-2 features are determined by marked changes of the S1 subunit structure in the S-protein which may be responsible for its contagiousness and many immune collisions aggravating infection process.

N-Terminal Amino Acid Sequences of Vaccinia Virus Structural Proteins

Virology ◽  
1994 ◽  
Vol 202 (2) ◽  
pp. 844-852 ◽  
Author(s):  
Tetsuya Takahashi ◽  
Masayasu Oie ◽  
Yasuo Ichihashi
Keyword(s):  
Amino Acid ◽  
Vaccinia Virus ◽  
Amino Acid Sequences ◽  
Structural Proteins ◽  
Terminal Amino Acid ◽  
Terminal Amino
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