Comparison of human VDAC1 with streptococcal streptokinase and bovine bactericidal permeability increasing protein: role of structural information in identifying functionally significant domains.
Comparison of the primary amino acid sequence of the human X-linked voltage-dependent anion channel, with other sequences in data base searches, identified regions of similarity in streptococcal streptokinase and bovine bactericidal permeability increasing protein. These regions of similarity were in different areas of the protein and were relatively short. However, examination of an empirically derived structural model of the channel showed that each region of similarity in streptokinase and bovine bactericidal permeability increasing protein corresponded to contiguous transmembrane domains within the channel protein. We speculate that these transmembrane domains may be functionally significant for streptokinase and bovine bactericidal permeability increasing protein. These investigations demonstrate the need for incorporation of information regarding secondary, tertiary, and quaternary structures, as well as function, in algorithms used for database searches.
McCabe
K M
KM
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
Wheeler
D A
DA
Adams
V
V
McCabe
E R
ER
D000595:Amino Acid Sequence; D000818:Animals; D023181:Antimicrobial Cationic Peptides; D001798:Blood Proteins / Q000737:chemistry*; D002417:Cattle; D006801:Humans; D007473:Ion Channels / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D018272:Porins; D017386:Sequence Homology, Amino Acid; D013291:Streptococcus / Q000201:enzymology*; D013300:Streptokinase / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D050995:Voltage-Dependent Anion Channel 1; D050994:Voltage-Dependent Anion Channels
D023181:Antimicrobial Cationic Peptides; D001798:Blood Proteins; D007473:Ion Channels; D008565:Membrane Proteins; D018272:Porins; C494762:VDAC1 protein, human; D050994:Voltage-Dependent Anion Channels; C021623:bactericidal permeability increasing protein; D050995:Voltage-Dependent Anion Channel 1; D013300:Streptokinase