scholarly journals Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains

2006 ◽  
Vol 87 (1) ◽  
pp. 129-138 ◽  
Author(s):  
Pia Laine ◽  
Soile Blomqvist ◽  
Carita Savolainen ◽  
Koen Andries ◽  
Tapani Hovi
Keyword(s):  
Amino Acids ◽  
Capsid Protein ◽  
Amino Acid Sequences ◽  
Human Rhinovirus ◽  
Complete Agreement ◽  
Species Classification ◽  
Conserved Motifs ◽  
Virus Structure ◽  
Capsid Protein Vp1 ◽  
Virus Strains

An alignment was made of the deduced amino acid sequences of the entire capsid protein VP1 of all human rhinovirus (HRV) prototype strains to examine conserved motifs in the primary structure. A set of previously proposed crucially important amino acids in the footprints of the two known receptor molecules was not conserved in a receptor group-specific way. In contrast, VP1 and VP3 amino acids in the minor receptor-group strains corresponding to most of the predicted ICAM-1 footprint definitely differed from those of the ICAM-1-using major receptor-group strains. Previous antiviral-sensitivity classification showed an almost-complete agreement with the species classification and a fair correlation with amino acids aligning in the antiviral pocket. It was concluded that systematic alignment of sequences of related virus strains can be used to test hypotheses derived from molecular studies of individual model viruses and to generate ideas for future studies on virus structure and replication.

scholarly journals Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses

2005 ◽  
Vol 86 (3) ◽  
pp. 697-706 ◽  
Author(s):  
Pia Laine ◽  
Carita Savolainen ◽  
Soile Blomqvist ◽  
Tapani Hovi
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Capsid Protein ◽  
Phylogenetic Trees ◽  
Amino Acid Sequences ◽  
Human Rhinovirus ◽  
Human Enterovirus ◽  
Coding Region ◽  
Coding Sequences ◽  
Capsid Protein Vp1

Phylogenetic analysis of the capsid protein VP1 coding sequences of all 101 human rhinovirus (HRV) prototype strains revealed two major genetic clusters, similar to that of the previously reported VP4/VP2 coding sequences, representing the established two species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Pairwise nucleotide identities varied from 61 to 98 % within and from 46 to 55 % between the two HRV species. Interserotypic sequence identities in both HRV species were more variable than those within any Human enterovirus (HEV) species in the same family. This means that unequivocal serotype identification by VP1 sequence analysis used for HEV strains may not always be possible for HRV isolates. On the other hand, a comprehensive insight into the relationships between VP1 and partial 2A sequences of HRV and HEV revealed a genus-like situation. Distribution of pairwise nucleotide identity values between these genera varied from 41 to 54 % in the VP1 coding region, similar to those between heterologous members of the two HRV species. Alignment of the deduced amino acid sequences revealed more fully conserved amino acid residues between HRV-B and polioviruses than between the two HRV species. In phylogenetic trees, where all HRVs and representatives from all HEV species were included, the two HRV species did not cluster together but behaved like members of the same genus as the HEVs. In conclusion, from a phylogenetic point of view, there are no good reasons to keep these two human picornavirus genera taxonomically separated.

scholarly journals Primary structure of OXA-3 and phylogeny of oxacillin-hydrolyzing class D beta-lactamases.

1995 ◽  
Vol 39 (4) ◽  
pp. 887-893 ◽  
Author(s):  
F Sanschagrin ◽  
F Couture ◽  
R C Levesque
Keyword(s):  
Amino Acids ◽  
Structure And Function ◽  
Amino Acid Sequences ◽  
Specific Class ◽  
Conserved Motifs ◽  
Beta Lactamases ◽  
Class A ◽  
Class D ◽  
And Function ◽  
Conserved Amino Acids

We determined the nucleotide sequence of the blaOXA-3(pMG25) gene from Pseudomonas aeruginosa. The bla structural gene encoded a protein of 275 amino acids representing one monomer of 31,879 Da for the OXA-3 enzyme. Comparisons between the OXA-3 nucleotide and amino acid sequences and those of class A, B, C, and D beta-lactamases were performed. An alignment of the eight known class D beta-lactamases including OXA-3 demonstrated the presence of conserved amino acids. In addition, conserved motifs composed of identical amino acids typical of penicillin-recognizing proteins and specific class D motifs were identified. These conserved motifs were considered for possible roles in the structure and function of oxacillinases. On the basis of the alignment and identity scores, a dendrogram was constructed. The phylogenetic data obtained revealed five groups of class D beta-lactamases with large evolutionary distances between each group.

scholarly journals Replacement of Loop II of VP1 of the DA Strain with Loop II of the GDVII Strain of Theiler’s Murine Encephalomyelitis Virus Alters Neurovirulence, Viral Persistence, and Demyelination

1998 ◽  
Vol 72 (9) ◽  
pp. 7557-7562 ◽  
Author(s):  
Yoshiaki Wada ◽  
Ingeborg J. McCright ◽  
Frank G. Whitby ◽  
Ikuo Tsunoda ◽  
Robert S. Fujinami
Keyword(s):  
Amino Acids ◽  
Central Nervous System ◽  
Nervous System ◽  
Capsid Protein ◽  
Inflammatory Disease ◽  
Viral Persistence ◽  
Theiler’S Murine Encephalomyelitis Virus ◽  
Encephalomyelitis Virus ◽  
Capsid Protein Vp1

ABSTRACT Theiler’s murine encephalomyelitis viruses, which are murine picornaviruses, can cause central nervous system inflammatory disease. To study the role of loop II in capsid protein VP1, two mutant viruses of strain DA in which DA loop II amino acids were replaced with strain GDVII amino acids were constructed. Infection of mice with the two mutant viruses led to dramatically different patterns of disease.

scholarly journals Characterization and Construction of Functional cDNA Clones of Pariacoto Virus, the First Alphanodavirus Isolated outside Australasia

2000 ◽  
Vol 74 (11) ◽  
pp. 5123-5132 ◽  
Author(s):  
Karyn N. Johnson ◽  
Jean-Louis Zeddam ◽  
L. Andrew Ball
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Capsid Protein ◽  
Cultured Cells ◽  
Geographic Origin ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Homologous Proteins ◽  
Genomic Rnas ◽  
Rna Genome

ABSTRACT Pariacoto virus (PaV) was recently isolated in Peru from the Southern armyworm (Spodoptera eridania). PaV particles are isometric, nonenveloped, and about 30 nm in diameter. The virus has a bipartite RNA genome and a single major capsid protein with a molecular mass of 39.0 kDa, features that support its classification as aNodavirus. As such, PaV is the firstAlphanodavirus to have been isolated from outside Australasia. Here we report that PaV replicates in wax moth larvae and that PaV genomic RNAs replicate when transfected into cultured baby hamster kidney cells. The complete nucleotide sequences of both segments of the bipartite RNA genome were determined. The larger genome segment, RNA1, is 3,011 nucleotides long and contains a 973-amino-acid open reading frame (ORF) encoding protein A, the viral contribution to the RNA replicase. During replication, a 414-nucleotide long subgenomic RNA (RNA3) is synthesized which is coterminal with the 3′ end of RNA1. RNA3 contains a small ORF which could encode a protein of 90 amino acids similar to the B2 protein of other alphanodaviruses. RNA2 contains 1,311 nucleotides and encodes the 401 amino acids of the capsid protein precursor α. The amino acid sequences of the PaV capsid protein and the replicase subunit share 41 and 26% identity with homologous proteins of Flock house virus, the best characterized of the alphanodaviruses. These and other sequence comparisons indicate that PaV is evolutionarily the most distant of the alphanodaviruses described to date, consistent with its novel geographic origin. Although the PaV capsid precursor is cleaved into the two mature capsid proteins β and γ, the amino acid sequence at the cleavage site, which is Asn/Ala in all other alphanodaviruses, is Asn/Ser in PaV. To facilitate the investigation of PaV replication in cultured cells, we constructed plasmids that transcribed full-length PaV RNAs with authentic 5′ and 3′ termini. Transcription of these plasmids in cells recreated the replication of PaV RNA1 and RNA2, synthesis of subgenomic RNA3, and translation of viral proteins A and α.

scholarly journals Conservation of Amino Acids in Human Rhinovirus 3C Protease Correlates with Broad-Spectrum Antiviral Activity of Rupintrivir, a Novel Human Rhinovirus 3C Protease Inhibitor

2005 ◽  
Vol 49 (2) ◽  
pp. 619-626 ◽  
Author(s):  
S. L. Binford ◽  
F. Maldonado ◽  
M. A. Brothers ◽  
P. T. Weady ◽  
L. S. Zalman ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Antiviral Activity ◽  
Broad Spectrum ◽  
Amino Acid Sequences ◽  
Human Rhinovirus ◽  
Clinical Isolates ◽  
Sequence Analyses ◽  
3C Protease

ABSTRACT The picornavirus 3C protease is required for the majority of proteolytic cleavages that occur during the viral life cycle. Comparisons of published amino acid sequences from 6 human rhinoviruses (HRV) and 20 human enteroviruses (HEV) show considerable variability in the 3C protease-coding region but strict conservation of the catalytic triad residues. Rupintrivir (formerly AG7088) is an irreversible inhibitor of HRV 3C protease with potent in vitro activity against all HRV serotypes (48 of 48), HEV strains (4 of 4), and untyped HRV field isolates (46 of 46) tested. To better understand the relationship between in vitro antiviral activity and 3C protease-rupintrivir binding interactions, we performed nucleotide sequence analyses on an additional 21 HRV serotypes and 11 HRV clinical isolates. Antiviral activity was also determined for 23 HRV clinical isolates and four additional HEV strains. Sequence comparison of 3C proteases (n = 58) show that 13 and 11 of the 14 amino acids that are involved in side chain interactions with rupintrivir are strictly conserved among HRV and HEV, respectively. These sequence analyses are consistent with the comparable in vitro antiviral potencies of rupintrivir against all HRV serotypes, HRV isolates, and HEV strains tested (50% effective concentration range, 3 to 183 nM; n = 125). In summary, the conservation of critical amino acid residues in 3C protease and the observation of potent, broad-spectrum antipicornavirus activity of rupintrivir highlight the advantages of 3C protease as an antiviral target.

scholarly journals Site-saturation mutagenesis of the PALTAVETG motif in coxsackievirus A9 capsid protein VP1 reveals evidence of conservation of a periodic hydrophobicity profile

1999 ◽  
Vol 80 (8) ◽  
pp. 1919-1927 ◽  
Author(s):  
Antero Airaksinen ◽  
Merja Roivainen ◽  
Glyn Stanway ◽  
Tapani Hovi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Capsid Protein ◽  
Amino Acid Substitution ◽  
Saturation Mutagenesis ◽  
Single Amino Acid ◽  
Site Saturation ◽  
Coxsackievirus A9 ◽  
Capsid Protein Vp1 ◽  
Hydrophobicity Profile

Enteroviruses possess a highly conserved 9 amino acid stretch of mainly hydrophobic character in the capsid protein VP1. A novel strategy, combining site-saturation mutagenesis and a single-tube cloning and transfection procedure, has been developed for the analysis of this motif in coxsackievirus A9 (CAV-9). Four individual amino acids were separately mutated. Mutagenesis of three of the four positions in CAV-9 resulted in a number of viable but impaired mutant strains, each containing a single amino acid substitution. In contrast, no mutants with amino acid substitutions at leucine 31 were isolated, although three different leucine codons were found among the viruses recovered. Small plaque size was regularly associated with reduced yields of infectious virus and an amino acid substitution at the target site in the viruses isolated from the site-saturated virus pools. From the range of amino acids observed in viable mutants, it was possible to estimate the characteristics that are required at individual amino acid positions. It seems that in the motif studied here, a periodic hydrophobicity profile needs to be conserved. The constraints observed on the ranges of acceptable amino acids presumably reflect the structural–functional requirements that have resulted in the conservation of the motif.

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