title: Predicting serpin/protease interactions.
abstract: Proteases are tightly regulated by specific inhibitors, such as serpins, which are able to undergo considerable and irreversible conformational changes in order to trap their targets. There has been a considerable effort to investigate serpin structure and functions in the past few decades; however, the specific interactions between proteases and serpins remain elusive. In this chapter, we describe detailed experimental protocols to determine and characterize the extended substrate specificity of proteases based on a substrate phage display technique. We also describe how to employ a bioinformatics system to analyze the substrate specificity data obtained from this technique and predict the potential inhibitory serpin partners of a protease (in this case, the immune protease, granzyme B) in a step-by-step manner. The method described here could also be applied to other proteases for more generalized substrate specificity analysis and substrate discovery.
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.
authors.forename: Jiangning
authors.initials: J
authors.lastname: Song
authors.forename: Antony Y
authors.initials: AY
authors.lastname: Matthews
authors.forename: Cyril F
authors.initials: CF
authors.lastname: Reboul
authors.forename: Dion
authors.initials: D
authors.lastname: Kaiserman
authors.forename: Robert N
authors.initials: RN
authors.lastname: Pike
authors.forename: Phillip I
authors.initials: PI
authors.lastname: Bird
authors.forename: James C
authors.initials: JC
authors.lastname: Whisstock
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D053804:Granzymes / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D011485:Protein Binding / Q000187:drug effects; D054730:Protein Interaction Domains and Motifs / Q000187:drug effects; D017433:Protein Structure, Secondary / Q000187:drug effects; D059748:Proteolysis / Q000187:drug effects*; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015843:Serpins / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D013379:Substrate Specificity
chemical_list: D019151:Peptide Library; D020543:Proteome; D015843:Serpins; D053804:Granzymes