用于底物分析的位置扫描合成组合文库。
Positional scanning synthetic combinatorial libraries for substrate profiling.
作者信息
Schneider Eric L, Craik Charles S
机构信息
Department of Pharmaceutical Chemistry, The University of California, San Francisco, San Francisco, CA, USA.
出版信息
Methods Mol Biol. 2009;539:59-78. doi: 10.1007/978-1-60327-003-8_4.
Abstract
Determining the preferred substrate cleavage sequence of proteases is an important step toward understanding their roles in cancer development and progression. Knowledge of this sequence can aid in the design of new experimental tools for study as well as aid in the identification of endogenous protease substrates and signaling pathways. Various investigators have demonstrated a number of techniques to uncover these sequences, but most can be very time consuming. We have designed and successfully implemented a complete diverse ACC tetrapeptide positional scanning synthetic combinatorial library that allows for the rapid screening of proteases to determine their preferred residues at positions P1-P4. These sequences can be readily verified through kinetic measurements on single peptide substrates and utilized to further knowledge of the role of proteases in cancer.
摘要
确定蛋白酶的首选底物切割序列是理解其在癌症发展和进程中作用的重要一步。了解该序列有助于设计新的研究实验工具，并有助于识别内源性蛋白酶底物和信号通路。许多研究人员已经展示了多种揭示这些序列的技术，但大多数技术可能非常耗时。我们设计并成功实施了一个完整的多样化丙氨酸-半胱氨酸-半胱氨酸（ACC）四肽位置扫描合成组合文库，该文库可快速筛选蛋白酶，以确定其在P1 - P4位置的首选残基。通过对单个肽底物的动力学测量可以很容易地验证这些序列，并用于进一步了解蛋白酶在癌症中的作用。
相似文献
1
Positional scanning synthetic combinatorial libraries for substrate profiling.
Methods Mol Biol. 2009;539:59-78. doi: 10.1007/978-1-60327-003-8_4.
2
Mixture-based peptide libraries for identifying protease cleavage motifs.
Methods Mol Biol. 2009;539:79-91. doi: 10.1007/978-1-60327-003-8_5.
3
Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries.
Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7754-9. doi: 10.1073/pnas.140132697.
4
DNA-Encoded Noncanonical Substrate Library for Protease Profiling.
Chembiochem. 2024 Dec 2;25(23):e202400559. doi: 10.1002/cbic.202400559. Epub 2024 Nov 4.
5
Synthetic substrates for measuring activity of autophagy proteases: autophagins (Atg4).
Autophagy. 2010 Oct;6(7):936-47. doi: 10.4161/auto.6.7.13075. Epub 2010 Oct 19.
6
Substrate optimization and clinical validation of reporter peptides for MS-based protease profiling in serum specimens: a new approach for diagnosis of malignant disease.
Int J Oncol. 2011 Jul;39(1):145-54. doi: 10.3892/ijo.2011.1009. Epub 2011 Apr 18.
7
Synthesis of a HyCoSuL peptide substrate library to dissect protease substrate specificity.
Nat Protoc. 2017 Oct;12(10):2189-2214. doi: 10.1038/nprot.2017.091. Epub 2017 Sep 21.
8
Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities.
J Biol Chem. 2006 May 5;281(18):12824-32. doi: 10.1074/jbc.M513331200. Epub 2006 Mar 6.
9
Screening for protease substrate by polyvalent phage display.
Comb Chem High Throughput Screen. 2005 Mar;8(2):197-203. doi: 10.2174/1386207053258541.
10
Using peptide libraries to identify optimal cleavage motifs for proteolytic enzymes.
Methods. 2004 Apr;32(4):398-405. doi: 10.1016/j.ymeth.2003.10.003.
引用本文的文献
1
Engineered MSC-EVs loaded with BDNF-enhancing neuropeptides via a non-disruptive method enhance post-stroke neuroregeneration via intranasal delivery.
J Nanobiotechnology. 2025 Aug 29;23(1):594. doi: 10.1186/s12951-025-03654-x.
2
TCR-T cell therapy: current development approaches, preclinical evaluation, and perspectives on regulatory challenges.
J Transl Med. 2024 Oct 4;22(1):897. doi: 10.1186/s12967-024-05703-9.
3
Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin.
Protein Sci. 2024 Aug;33(8):e5110. doi: 10.1002/pro.5110.
4
Multiplex substrate profiling by mass spectrometry for proteases.
Methods Enzymol. 2023;682:375-411. doi: 10.1016/bs.mie.2022.09.009. Epub 2022 Dec 21.
5
Embracing enzyme promiscuity with activity-based compressed biosensing.
Cell Rep Methods. 2022 Dec 30;3(1):100372. doi: 10.1016/j.crmeth.2022.100372. eCollection 2023 Jan 23.
6
-Derived Conotoxins: Novel Therapeutic Opportunities from a Marine Organism.
Mar Drugs. 2022 Dec 10;20(12):773. doi: 10.3390/md20120773.
7
Activity-Based Probes for Proteases Pave the Way to Theranostic Applications.
Pharmaceutics. 2022 Apr 30;14(5):977. doi: 10.3390/pharmaceutics14050977.
8
Universal Access to Protease Chemiluminescent Probes through Solid-Phase Synthesis.
Bioconjug Chem. 2021 Oct 20;32(10):2134-2140. doi: 10.1021/acs.bioconjchem.1c00384. Epub 2021 Sep 22.
9
Enhanced Antibiofilm Effects of N Plasma-Treated Buffer Combined with Antimicrobial Hexapeptides Against Plant Pathogens.
Polymers (Basel). 2020 Sep 1;12(9):1992. doi: 10.3390/polym12091992.
10
Coumarin as a structural component of substrates and probes for serine and cysteine proteases.
Biochim Biophys Acta Proteins Proteom. 2020 Sep;1868(9):140445. doi: 10.1016/j.bbapap.2020.140445. Epub 2020 May 13.
本文引用的文献
1
The macrophage-stimulating protein pathway promotes metastasis in a mouse model for breast cancer and predicts poor prognosis in humans.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7570-5. doi: 10.1073/pnas.0702095104. Epub 2007 Apr 24.
2
Coordinate expression and functional profiling identify an extracellular proteolytic signaling pathway.
Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5771-6. doi: 10.1073/pnas.0606514104. Epub 2007 Mar 27.
3
Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities.
J Biol Chem. 2006 May 5;281(18):12824-32. doi: 10.1074/jbc.M513331200. Epub 2006 Mar 6.
4
Selective chemical functional probes of granzymes A and B reveal granzyme B is a major effector of natural killer cell-mediated lysis of target cells.
Chem Biol. 2005 May;12(5):567-77. doi: 10.1016/j.chembiol.2005.03.006.
5
Communication between the active sites and dimer interface of a herpesvirus protease revealed by a transition-state inhibitor.
Proc Natl Acad Sci U S A. 2004 May 4;101(18):6870-5. doi: 10.1073/pnas.0401613101. Epub 2004 Apr 26.
6
Scanning the prime-site substrate specificity of proteolytic enzymes: a novel assay based on ligand-enhanced lanthanide ion fluorescence.
Bioorg Med Chem Lett. 2002 Dec 16;12(24):3619-23. doi: 10.1016/s0960-894x(02)00786-2.
7
Expedient solid-phase synthesis of fluorogenic protease substrates using the 7-amino-4-carbamoylmethylcoumarin (ACC) fluorophore.
J Org Chem. 2002 Feb 8;67(3):910-5. doi: 10.1021/jo016140o.
8
Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries.
Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7754-9. doi: 10.1073/pnas.140132697.
9
Cellular localization of membrane-type serine protease 1 and identification of protease-activated receptor-2 and single-chain urokinase-type plasminogen activator as substrates.
J Biol Chem. 2000 Aug 25;275(34):26333-42. doi: 10.1074/jbc.M002941200.
10
A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis.
J Biol Chem. 1997 Jul 18;272(29):17907-11. doi: 10.1074/jbc.272.29.17907.
Zotero 插件