Abstract
BackgroundSerine protease inhibitors belonging to the Potato type-II Inhibitor family Protease Inhibitors (Pin-II type PIs) are essential plant defense molecules. They are characterized by multiple inhibitory repeat domains, conserved disulfide bond pattern, and a tripeptide reactive center loop. These features of Pin-II type PIs make them potential molecules for protein engineering and designing inhibitors for agricultural and therapeutic applications. However, the diversity in these PIs remains unexplored due to the lack of annotated protein sequences and their functional attributes in the available databases.ResultsWe have developed a database, PINIR (Pin-II type PIs Information Resource), by systematic collection and manual annotation of 415 Pin-II type PI protein sequences. For each PI, the number and position for signature sequences are specified: 695 domains, 75 linkers, 63 reactive center loops, and 10 disulfide bond patterns are identified and mapped. Database analysis revealed novel subcategories of PIs, species-correlated occurrence of inhibitory domains, reactive center loops, and disulfide bond patterns. By analyzing linker regions, we predict that alternative processing at linker regions could generate PI variants in the Solanaceae family.ConclusionPINIR (https://pinir.ncl.res.in) provides a web interface for browsing and analyzing the protein sequences of Pin-II type PIs. Information about signature sequences, spatio-temporal expression, biochemical properties, gene sequences, and literature references are provided. Analysis of PINIR depicts conserved species-specific features of Pin-II type PI protein sequences. Diversity in the sequence of inhibitory domains and reactive loops directs potential applications to engineer Pin-II type PIs. The PINIR database will serve as a comprehensive information resource for further research into Pin-II type PIs.
Highlights
Serine protease inhibitors belonging to the Potato type-II Inhibitor family Protease Inhibitors (Pin-II type Protease inhibitors (PIs)) are essential plant defense molecules
The unique feature of Pin-II type PIs is the presence of multiple inhibitory repeat domains (IRDs)
IRD-7 and IRD-9 (IRD-145 and IRD-143 in the Pin-II type PIs Information Resource (PINIR) database) from Capsicum annuum are more than 90% similar in the protein sequence but show a significant difference in the inhibitory activity towards serine proteases [15]
Summary
Serine protease inhibitors belonging to the Potato type-II Inhibitor family Protease Inhibitors (Pin-II type PIs) are essential plant defense molecules They are characterized by multiple inhibitory repeat domains, conserved disulfide bond pattern, and a tripeptide reactive center loop. These features of Pin-II type PIs make them potential molecules for protein engineering and designing inhibitors for agricultural and therapeutic applications. IRD-7 and IRD-9 (IRD-145 and IRD-143 in the PINIR database) from Capsicum annuum are more than 90% similar in the protein sequence but show a significant difference in the inhibitory activity towards serine proteases [15] This difference is attributed to the replacement of two cysteine residues in IRD-7 by serine in IRD-9, which causes the loss of two disulfide bonds. RCL is the primary interaction site for target serine protease and functions as an inhibitory tripeptide independent of the native IRD scaffold [18]
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