Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains.
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.
Laine
Pia
P
Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, 00300 Helsinki, Finland.
Blomqvist
Soile
S
Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, 00300 Helsinki, Finland.
Savolainen
Carita
C
Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, 00300 Helsinki, Finland.
Andries
Koen
K
Johnson & Johnson Pharmaceutical Research and Development, Beerse, Belgium.
Hovi
Tapani
T
Enterovirus Laboratory, Department of Viral Diseases and Immunology, National Public Health Institute (KTL), Mannerheimintie 166, 00300 Helsinki, Finland.
D002213:Capsid / Q000737:chemistry; D017124:Conserved Sequence; D006801:Humans; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis* / Q000235:genetics; D012229:Rhinovirus / Q000737:chemistry / Q000235:genetics* / Q000502:physiology; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D014764:Viral Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*
D012367:RNA, Viral; D014764:Viral Proteins; C074995:viral protein 1, rhinovirus