scholarly journals Neutralizing Epitopes and Residues Mediating the Potential Antigenic Drift of the Hemagglutinin-Esterase Protein of Influenza C Virus

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 417 ◽  
Author(s):  
Yoko Matsuzaki ◽  
Kanetsu Sugawara ◽  
Yuki Furuse ◽  
Yoshitaka Shimotai ◽  
Seiji Hongo ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Antigenic Site ◽  
Antigenic Drift ◽  
Receptor Binding Site ◽  
Ann Arbor ◽  
Influenza C Virus ◽  
Escape Mutants ◽  
Antigenic Epitopes

We mapped the hemagglutinin-esterase (HE) antigenic epitopes of the influenza C virus on the three-dimensional (3D) structure of the HE glycoprotein using 246 escape mutants that were selected by a panel of nine anti-HE monoclonal antibodies (MAbs), including seven of the C/Ann Arbor/1/50 virus and two of the C/Yamagata/15/2004 virus. The frequency of variant selection in the presence of anti-HE MAbs was very low, with frequencies ranging from 10−4.62 to 10−7.58 for the C/Ann Arbor/1/50 virus and from 10−7.11 to 10−9.25 for the C/Yamagata/15/2004 virus. Sequencing of mutant HE genes revealed 25 amino acid substitutions at 16 positions in three antigenic sites: A-1, A-2, and A-3, and a newly designated Y-1 site. In the 3D structure, the A-1 site was widely located around the receptor-binding site, the A-2 site was near the receptor-destroying enzyme site, and the Y-1 site was located in the loop on the topside of HE. The hemagglutination inhibition reactions of the MAbs with influenza C viruses, circulating between 1947 and 2016, were consistent with the antigenic-site amino acid changes. We also found some amino acid variations in the antigenic site of recently circulating strains with antigenic changes, suggesting that viruses that have the potential to alter antigenicity continue to circulate in humans.

scholarly journals Structural Differences among Hemagglutinins of Influenza A Virus Subtypes Are Reflected in Their Antigenic Architecture: Analysis of H9 Escape Mutants

2004 ◽  
Vol 78 (1) ◽  
pp. 240-249 ◽  
Author(s):  
Nikolai V. Kaverin ◽  
Irina A. Rudneva ◽  
Natalia A. Ilyushina ◽  
Aleksandr S. Lipatov ◽  
Scott Krauss ◽  
...  
Keyword(s):  
Hong Kong ◽  
Amino Acid ◽  
Influenza A ◽  
Three Dimensional ◽  
Antigenic Site ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Equivalent Site ◽  
Escape Mutants ◽  
Phenotypic Variations

ABSTRACT We used a panel of monoclonal antibodies to H9 hemagglutinin to select 18 escape mutants of mouse-adapted influenza A/Swine/Hong Kong/9/98 (H9N2) virus. Cross-reactions of the mutants with the antibodies and the sequencing of hemagglutinin genes revealed two minimally overlapping epitopes. We mapped the amino acid changes to two areas of the recently reported three-dimensional structure of A/Swine/Hong Kong/9/98 hemagglutinin. The grouping of the antigenically relevant amino acid positions in H9 hemagglutinin differs from the pattern observed in H3 and H5 hemagglutinins. Several positions in site B of H3 hemagglutinin are distributed in two sites of H9 hemagglutinin. Unlike any subtype analyzed so far, H9 hemagglutinin does not contain an antigenic site corresponding to site A in H3 hemagglutinin. Positions 145 and 193 (H3 numbering), which in H3 hemagglutinin belong to sites A and B, respectively, are within one site in H9 hemagglutinin. This finding is consistent with the peculiarity of the three-dimensional structure of the H9 molecule, that is, the absence from H9 hemagglutinin of the lateral loop that forms site A in H3 and the equivalent site in H5 hemagglutinins. The escape mutants analyzed displayed phenotypic variations, including decreased virulence for mice and changes in affinity for sialyl substrates. Our results demonstrate a correlation between intersubtype differences in three-dimensional structure and variations among subtypes in the distribution of antigenic areas. Our findings also suggest that covariation and pleiotropic effects of antibody-selected mutations may be important in the evolution of H9 influenza virus, a possible causative agent of a future pandemic.

scholarly journals Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018–2019

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 977
Author(s):  
Kobporn Boonnak ◽  
Chayasin Mansanguan ◽  
Dennis Schuerch ◽  
Usa Boonyuen ◽  
Hatairat Lerdsamran ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Seasonal Influenza ◽  
Influenza Viruses ◽  
Surface Proteins ◽  
Antigenic Drift ◽  
Influenza B ◽  
Receptor Binding Site ◽  
Antigenic Sites ◽  
Ha Protein

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.

scholarly journals Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp.

2017 ◽  
Vol 9 (2) ◽  
pp. 204-208 ◽  
Author(s):  
Emre SEVİNDİK
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
3D Structure ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Bisphosphate Carboxylase ◽  
Molecular Weights ◽  
Acid Ratio ◽  
Important Enzyme

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.

scholarly journals Epitope Mapping of the Hemagglutinin Molecule of a Highly Pathogenic H5N1 Influenza Virus by Using Monoclonal Antibodies

2007 ◽  
Vol 81 (23) ◽  
pp. 12911-12917 ◽  
Author(s):  
Nikolai V. Kaverin ◽  
Irina A. Rudneva ◽  
Elena A. Govorkova ◽  
Tatyana A. Timofeeva ◽  
Aleksandr A. Shilov ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
H5n1 Virus ◽  
Antigenic Site ◽  
H5n1 Influenza Virus ◽  
Highly Pathogenic ◽  
H5n1 Influenza ◽  
Antigenic Sites ◽  
Escape Mutants ◽  
Pathogenic H5n1

ABSTRACT We mapped the hemagglutinin (HA) antigenic epitopes of a highly pathogenic H5N1 influenza virus on the three-dimensional HA structure by characterizing escape mutants of a recombinant virus containing A/Vietnam/1203/04 (H5N1) ΔHA and neuraminidase genes in the genetic background of A/Puerto Rico/8/34 (H1N1) virus. The mutants were selected with a panel of eight anti-HA monoclonal antibodies (MAbs), seven to A/Vietnam/1203/04 (H5N1) virus and one to A/Chicken/Pennsylvania/8125/83 (H5N2) virus, and the mutants’ HA genes were sequenced. The amino acid changes suggested three MAb groups: four MAbs reacted with the complex epitope comprising parts of the antigenic site B of H3 HA and site Sa of H1 HA, two MAbs reacted with the epitope corresponding to the antigenic site A in H3 HA, and two MAbs displayed unusual behavior: each recognized amino acid changes at two widely separate antigenic sites. Five changes were detected in amino acid residues not previously reported as changed in H5 escape mutants, and four others had substitutions not previously described. The HA antigenic structure differs substantially between A/Vietnam/1203/04 (H5N1) virus and the low-pathogenic A/Mallard/Pennsylvania/10218/84 (H5N2) virus we previously characterized (N. V. Kaverin et al., J. Gen. Virol. 83:2497-2505, 2002). The hemagglutination inhibition reactions of the MAbs with recent highly pathogenic H5N1 viruses were consistent with the antigenic-site amino acid changes but not with clades and subclades based on H5 phylogenetic analysis. These results provide information on the recognition sites of the MAbs widely used to study H5N1 viruses and demonstrate the involvement of the HA antigenic sites in the evolution of highly pathogenic H5N1 viruses, findings that can be critical for characterizing pathogenesis and vaccine design.

scholarly journals Selection of neutralizing antibody escape mutants with type A influenza virus HA-specific polyclonal antisera: possible significance for antigenic drift

1997 ◽  
Vol 118 (2) ◽  
pp. 149-154 ◽  
Author(s):  
S. M. CLEVELAND ◽  
H. P. TAYLOR ◽  
N. J. DIMMOCK
Keyword(s):  
Haemagglutination Inhibition ◽  
Antigenic Site ◽  
Neutralizing Antibody ◽  
Type A ◽  
Antigenic Drift ◽  
Progeny Virus ◽  
Escape Mutant ◽  
Virus Growth ◽  
Escape Mutants ◽  
Selection Of

Ten antisera were produced in rabbits by two or three intravenous injections of inactivated whole influenza type A virions. All contained haemagglutination-inhibition (HI) antibody directed predominantly to an epitope in antigenic site B and, in addition, various amounts of antibodies to an epitope in site A and in site D. The ability of untreated antisera to select neutralization escape mutants was investigated by incubating virus possessing the homologous haemagglutinin with antiserum adjusted to contain anti-B epitope HI titres of 100, 1000 and 10000 HIU/ml. Virus-antiserum mixtures were inoculated into embryonated hen's eggs, and progeny virus examined without further selection. Forty percent of the antisera at a titre of 1000 HIU/ml selected neutralizing antibody escape mutants as defined by their lack of reactivity to Mab HC10 (site B), and unchanged reactivity to other Mabs to site A and site D epitopes. All escape mutant-selecting antisera had a ratio of anti-site B (HC10)-epitope antibody[ratio ]other antibodies of [ges ]2·0[ratio ]1. The antiserum with the highest ratio (7·4[ratio ]1) selected escape mutants in all eggs tested in four different experiments. No antiserum used at a titre of 10000 HIU/ml allowed multiplication of any virus. All antisera used at a titre of 100 HIU/ml permitted virus growth, but this was wild-type (wt) virus. We conclude that a predominant epitope-specific antibody response, a titre of [ges ]1000 HIU/ml, and a low absolute titre of other antibodies ([les ]500 HIU/ml) are three requirements for the selection of escape mutants. None of the antisera in this study could have selected escape mutants without an appropriate dilution factor, so the occurrence of an escape mutant-selecting antiserum in nature is likely to be a rare event.

scholarly journals The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition

Biomolecules ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 221 ◽  
Author(s):  
András Benedek ◽  
Fanni Temesváry-Kis ◽  
Tamjidmaa Khatanbaatar ◽  
Ibolya Leveles ◽  
Éva Viola Surányi ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Amino Acid Position ◽  
Terminal Segment ◽  
Inhibition Mechanism ◽  
Structural Explanation ◽  
E Coli ◽  
Repair Enzymes ◽  
Species Specific

Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E. coli dUTPase to StlSaPIbov1 inhibition. We solved the three-dimensional (3D) crystal structure of such a mutant in complex with the substrate analogue dUPNPP and surprisingly found that the C-terminal arm of the enzyme, containing the P-loop-like motif was ordered in the structure. This segment was never localized before in any other E. coli dUTPase crystal structures. The 3D structure in agreement with solution phase experiments suggested that ordering of the flexible C-terminal segment upon substrate binding is a major factor in defining the sensitivity of E. coli dUTPase for StlSaPIbov1 inhibition.

scholarly journals Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants

2002 ◽  
Vol 83 (10) ◽  
pp. 2497-2505 ◽  
Author(s):  
Nikolai V. Kaverin ◽  
Irina A. Rudneva ◽  
Natalia A. Ilyushina ◽  
Natalia L. Varich ◽  
Aleksandr S. Lipatov ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Haemagglutination Inhibition ◽  
Three Dimensional ◽  
Glycosylation Site ◽  
Dimensional Structure ◽  
Mouse Serum ◽  
Antigenic Sites ◽  
Escape Mutants ◽  
Influenza Virus Haemagglutinin

To elucidate the structure of the antigenic sites of avian H5 influenza virus haemagglutinin (HA) we analysed escape mutants of a mouse-adapted variant of the H5N2 strain A/Mallard/Pennsylvania/10218/84. A panel of five anti-H5 monoclonal antibodies (mAbs) was used to select 16 escape mutants. The mutants were tested by ELISA and haemagglutination inhibition with this panel of anti-H5 mAbs and the HA genes of the mutants were sequenced. The sequencing demonstrated that the amino acid changes were grouped in two antigenic sites. One corresponded to site A in the H3 HA. The other contained areas that are separated in the amino acid sequence but are topographically close in the three-dimensional structure and partially overlap in the reactions with mAbs. This site corresponds in part to site B in the H3 structure; it also includes a region not involved in site B that partially overlaps site Sa in the H1 HA and an antigenic area in H2 HA. Mutants with the amino acid change K152N, as well as those with the change D126N, showed reduced lethality in mice. The substitution D126N, creating a new glycosylation site, was accompanied by an increase in the sensitivity of the mutants to normal mouse serum inhibitors. Several amino acid changes in the H5 escape mutants occurred at the positions of reported changes in H2 drift variants. This coincidence suggests that the antigenic sites described and analysed here may be important for drift variation if H5 influenza virus ever appears as a pathogen circulating in humans.

scholarly journals Plasticity of Amino Acid Residue 145 Near the Receptor Binding Site of H3 Swine Influenza A Viruses and Its Impact on Receptor Binding and Antibody Recognition

2018 ◽  
Vol 93 (2) ◽  
Author(s):  
Jefferson J. S. Santos ◽  
Eugenio J. Abente ◽  
Adebimpe O. Obadan ◽  
Andrew J. Thompson ◽  
Lucas Ferreri ◽  
...  
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Influenza A ◽  
Antigenic Drift ◽  
Amino Acid Substitutions ◽  
Receptor Binding Site ◽  
Antibody Recognition ◽  
Antigenic Characterization ◽  
Antigenic Evolution

ABSTRACT The hemagglutinin (HA), a glycoprotein on the surface of influenza A virus (IAV), initiates the virus life cycle by binding to terminal sialic acid (SA) residues on host cells. The HA gradually accumulates amino acid substitutions that allow IAV to escape immunity through a mechanism known as antigenic drift. We recently confirmed that a small set of amino acid residues are largely responsible for driving antigenic drift in swine-origin H3 IAV. All identified residues are located adjacent to the HA receptor binding site (RBS), suggesting that substitutions associated with antigenic drift may also influence receptor binding. Among those substitutions, residue 145 was shown to be a major determinant of antigenic evolution. To determine whether there are functional constraints to substitutions near the RBS and their impact on receptor binding and antigenic properties, we carried out site-directed mutagenesis experiments at the single-amino-acid level. We generated a panel of viruses carrying substitutions at residue 145 representing all 20 amino acids. Despite limited amino acid usage in nature, most substitutions at residue 145 were well tolerated without having a major impact on virus replication in vitro. All substitution mutants retained receptor binding specificity, but the substitutions frequently led to decreased receptor binding. Glycan microarray analysis showed that substitutions at residue 145 modulate binding to a broad range of glycans. Furthermore, antigenic characterization identified specific substitutions at residue 145 that altered antibody recognition. This work provides a better understanding of the functional effects of amino acid substitutions near the RBS and the interplay between receptor binding and antigenic drift. IMPORTANCE The complex and continuous antigenic evolution of IAVs remains a major hurdle for vaccine selection and effective vaccination. On the hemagglutinin (HA) of the H3N2 IAVs, the amino acid substitution N 145 K causes significant antigenic changes. We show that amino acid 145 displays remarkable amino acid plasticity in vitro, tolerating multiple amino acid substitutions, many of which have not yet been observed in nature. Mutant viruses carrying substitutions at residue 145 showed no major impairment in virus replication in the presence of lower receptor binding avidity. However, their antigenic characterization confirmed the impact of the 145 K substitution in antibody immunodominance. We provide a better understanding of the functional effects of amino acid substitutions implicated in antigenic drift and its consequences for receptor binding and antigenicity. The mutation analyses presented in this report represent a significant data set to aid and test the ability of computational approaches to predict binding of glycans and in antigenic cartography analyses.

Search for conserved amino acid residues of the α-crystallin proteins of vertebrates

2016 ◽  
Vol 14 (02) ◽  
pp. 1641004 ◽  
Author(s):  
Nikita G. Shiliaev ◽  
Olga M. Selivanova ◽  
Oxana V. Galzitskaya
Keyword(s):  
Amino Acid ◽  
Bioinformatics Analysis ◽  
3D Structure ◽  
Three Dimensional ◽  
Aromatic Amino Acids ◽  
Small Heat Shock Protein ◽  
Lens Protein ◽  
Individual Amino Acid ◽  
Amino Acid Residues ◽  
Eye Lens Protein

[Formula: see text]-crystallin is the major eye lens protein and a member of the small heat-shock protein (sHsp) family. [Formula: see text]-crystallins have been shown to support lens clarity by preventing the aggregation of lens proteins. We performed the bioinformatics analysis of [Formula: see text]-crystallin sequences from vertebrates to find conserved amino acid residues as the three-dimensional (3D) structure of [Formula: see text]-crystallin is not identified yet. We are the first who demonstrated that the N-terminal region is conservative along with the central domain for vertebrate organisms. We have found that there is correlation between the conserved and structured regions. Moreover, amyloidogenic regions also correspond to the structured regions. We analyzed the amino acid composition of [Formula: see text]-crystallin A and B chains. Analyzing the occurrence of each individual amino acid residue, we have found that such amino acid residues as leucine, serine, lysine, proline, phenylalanine, histidine, isoleucine, glutamic acid, and valine change their content simultaneously in A and B chains in different classes of vertebrates. Aromatic amino acids occur more often in [Formula: see text]-crystallins from vertebrates than on the average in proteins among 17 animal proteomes. We obtained that the identity between A and B chains in the mammalian group is 0.35, which is lower than the published 0.60.

scholarly journals Identification of New Ocellatin Antimicrobial Peptides by cDNA Precursor Cloning in the Frame of This Family of Intriguing Peptides

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 751
Author(s):  
Mariela M. Marani ◽  
Silvana Aguilar ◽  
Ana P. Cuzziol Boccioni ◽  
Natalia L. Cancelarich ◽  
Néstor G. Basso ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Antimicrobial Peptides ◽  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Amino Acid Residues ◽  
Conserved Residues ◽  
Α Helix ◽  
In Silico Analyses

Ocellatins are a family of antimicrobial peptides found exclusively in the Leptodactylus genus. To date, 10 species have been studied and more than 23 peptides described. Here we report the sequences of five new peptides from the skin of the frog Leptodactylus latrans (Anura: Leptodactylidae) determined by cDNA cloning of the complete prepro-peptide structures. The mature peptides were characterized with in silico tools and compared with those previously described. With 21 amino acid residues, this new set of peptides not previously described in the Leptodactylus genus share between 100 and 76.2% similarity to ocellatin antimicrobial peptides. These novel peptides are cationic and their three-dimensional (3D) structure holds the highly conserved residues G1, D4, K7, and K11 and a high theoretical amphipathic α-helix content. Furthermore, in silico analyses of these new peptides predicted antimicrobial activity. This study is framed in the context of previous work published about ocellatins, and therefore, provides a review of this intriguing family of peptides.

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