利用与酵母表面展示相结合的深度测序来表征蛋白质-蛋白质相互作用
Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display.
作者信息
Medina-Cucurella Angelica V, Whitehead Timothy A
机构信息
Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, USA.
出版信息
Methods Mol Biol. 2018;1764:101-121. doi: 10.1007/978-1-4939-7759-8_7.
Abstract
In this chapter, we discuss a method to determine the affinity and specificity of nearly all single-point mutants for a full-length protein binder. This method combines deep sequencing, comprehensive mutagenesis, yeast surface display, and fluorescence-activated cell sorting. This approach has been used to study sequence-function relationships for protein-protein interactions. The data can be used to determine the fine conformational epitope on the protein binder.
摘要
在本章中，我们讨论一种用于确定几乎所有单点突变体与全长蛋白质结合剂的亲和力和特异性的方法。该方法结合了深度测序、全面诱变、酵母表面展示和荧光激活细胞分选。此方法已被用于研究蛋白质-蛋白质相互作用的序列-功能关系。这些数据可用于确定蛋白质结合剂上的精细构象表位。
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本文引用的文献
1
Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.
Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2265-2270. doi: 10.1073/pnas.1614437114. Epub 2017 Feb 14.
2
Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves.
Elife. 2016 Dec 30;5:e23156. doi: 10.7554/eLife.23156.
3
Plasmid-based one-pot saturation mutagenesis.
Nat Methods. 2016 Nov;13(11):928-930. doi: 10.1038/nmeth.4029. Epub 2016 Oct 10.
4
Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing.
Proteins. 2016 Dec;84(12):1914-1928. doi: 10.1002/prot.25175. Epub 2016 Oct 26.
5
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J Biol Chem. 2015 Oct 30;290(44):26457-70. doi: 10.1074/jbc.M115.676635. Epub 2015 Aug 20.
6
High-resolution sequence-function mapping of full-length proteins.
PLoS One. 2015 Mar 19;10(3):e0118193. doi: 10.1371/journal.pone.0118193. eCollection 2015.
7
Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing.
J Mol Biol. 2015 Jan 30;427(2):328-40. doi: 10.1016/j.jmb.2014.10.024. Epub 2014 Nov 7.
8
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9
Deep mutational scanning: a new style of protein science.
Nat Methods. 2014 Aug;11(8):801-7. doi: 10.1038/nmeth.3027.
10
Yeast surface display for antibody isolation: library construction, library screening, and affinity maturation.
Methods Mol Biol. 2014;1131:151-81. doi: 10.1007/978-1-62703-992-5_10.
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