Predicting serpin/protease interactions

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

5 Citations (Scopus)

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.
Original languageEnglish
Title of host publicationMethods in Enzymology, Volume 501: Serpin Structure and Evolution
EditorsJames C Whisstock, Philip I Bird
Place of PublicationUSA
PublisherAcademic Press
Pages237 - 273
Number of pages37
ISBN (Print)9780123859501
DOIs
Publication statusPublished - 2011

Cite this

Song, J., Matthews, A., Reboul, C. F., Kaiserman, D., Pike, R. N., Bird, P. I., & Whisstock, J. C. (2011). Predicting serpin/protease interactions. In J. C. Whisstock, & P. I. Bird (Eds.), Methods in Enzymology, Volume 501: Serpin Structure and Evolution (pp. 237 - 273). USA: Academic Press. https://doi.org/10.1016/B978-0-12-385950-1.00012-2
Song, Jiangning ; Matthews, Antony ; Reboul, Cyril F ; Kaiserman, Dion ; Pike, Robert N ; Bird, Phillip I ; Whisstock, James C. / Predicting serpin/protease interactions. Methods in Enzymology, Volume 501: Serpin Structure and Evolution. editor / James C Whisstock ; Philip I Bird. USA : Academic Press, 2011. pp. 237 - 273
@inbook{b96ea2a0bc094204b386d03cdc9ca081,
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.",
author = "Jiangning Song and Antony Matthews and Reboul, {Cyril F} and Dion Kaiserman and Pike, {Robert N} and Bird, {Phillip I} and Whisstock, {James C}",
year = "2011",
doi = "10.1016/B978-0-12-385950-1.00012-2",
language = "English",
isbn = "9780123859501",
pages = "237 -- 273",
editor = "Whisstock, {James C} and Bird, {Philip I}",
booktitle = "Methods in Enzymology, Volume 501: Serpin Structure and Evolution",
publisher = "Academic Press",
address = "United States of America",

}

Song, J, Matthews, A, Reboul, CF, Kaiserman, D, Pike, RN, Bird, PI & Whisstock, JC 2011, Predicting serpin/protease interactions. in JC Whisstock & PI Bird (eds), Methods in Enzymology, Volume 501: Serpin Structure and Evolution. Academic Press, USA, pp. 237 - 273. https://doi.org/10.1016/B978-0-12-385950-1.00012-2

Predicting serpin/protease interactions. / Song, Jiangning; Matthews, Antony; Reboul, Cyril F; Kaiserman, Dion; Pike, Robert N; Bird, Phillip I; Whisstock, James C.

Methods in Enzymology, Volume 501: Serpin Structure and Evolution. ed. / James C Whisstock; Philip I Bird. USA : Academic Press, 2011. p. 237 - 273.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

TY - CHAP

T1 - Predicting serpin/protease interactions

AU - Song, Jiangning

AU - Matthews, Antony

AU - Reboul, Cyril F

AU - Kaiserman, Dion

AU - Pike, Robert N

AU - Bird, Phillip I

AU - Whisstock, James C

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=22078538

U2 - 10.1016/B978-0-12-385950-1.00012-2

DO - 10.1016/B978-0-12-385950-1.00012-2

M3 - Chapter (Book)

SN - 9780123859501

SP - 237

EP - 273

BT - Methods in Enzymology, Volume 501: Serpin Structure and Evolution

A2 - Whisstock, James C

A2 - Bird, Philip I

PB - Academic Press

CY - USA

ER -

Song J, Matthews A, Reboul CF, Kaiserman D, Pike RN, Bird PI et al. Predicting serpin/protease interactions. In Whisstock JC, Bird PI, editors, Methods in Enzymology, Volume 501: Serpin Structure and Evolution. USA: Academic Press. 2011. p. 237 - 273 https://doi.org/10.1016/B978-0-12-385950-1.00012-2