Literature DB >> 21561674

Deep mutational scanning: assessing protein function on a massive scale.

Carlos L Araya1, Douglas M Fowler.   

Abstract

Analysis of protein mutants is an effective means to understand their function. Protein display is an approach that allows large numbers of mutants of a protein to be selected based on their activity, but only a handful with maximal activity have been traditionally identified for subsequent functional analysis. However, the recent application of high-throughput sequencing (HTS) to protein display and selection has enabled simultaneous assessment of the function of hundreds of thousands of mutants that span the activity range from high to low. Such deep mutational scanning approaches are rapid and inexpensive with the potential for broad utility. In this review, we discuss the emergence of deep mutational scanning, the challenges associated with its use and some of its exciting applications.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21561674      PMCID: PMC3159719          DOI: 10.1016/j.tibtech.2011.04.003

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  68 in total

1.  Rapid construction of empirical RNA fitness landscapes.

Authors:  Jason N Pitt; Adrian R Ferré-D'Amaré
Journal:  Science       Date:  2010-10-15       Impact factor: 47.728

2.  A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Authors:  Marc Sultan; Marcel H Schulz; Hugues Richard; Alon Magen; Andreas Klingenhoff; Matthias Scherf; Martin Seifert; Tatjana Borodina; Aleksey Soldatov; Dmitri Parkhomchuk; Dominic Schmidt; Sean O'Keeffe; Stefan Haas; Martin Vingron; Hans Lehrach; Marie-Laure Yaspo
Journal:  Science       Date:  2008-07-03       Impact factor: 47.728

Review 3.  Colloquium papers: Adaptive landscapes and protein evolution.

Authors:  Maurício Carneiro; Daniel L Hartl
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-30       Impact factor: 11.205

4.  Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.

Authors:  Emmanuel Dias-Neto; Diana N Nunes; Ricardo J Giordano; Jessica Sun; Gregory H Botz; Kuan Yang; João C Setubal; Renata Pasqualini; Wadih Arap
Journal:  PLoS One       Date:  2009-12-17       Impact factor: 3.240

5.  Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis.

Authors:  B Virnekäs; L Ge; A Plückthun; K C Schneider; G Wellnhofer; S E Moroney
Journal:  Nucleic Acids Res       Date:  1994-12-25       Impact factor: 16.971

6.  Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Authors:  Arttu Jolma; Teemu Kivioja; Jarkko Toivonen; Lu Cheng; Gonghong Wei; Martin Enge; Mikko Taipale; Juan M Vaquerizas; Jian Yan; Mikko J Sillanpää; Martin Bonke; Kimmo Palin; Shaheynoor Talukder; Timothy R Hughes; Nicholas M Luscombe; Esko Ukkonen; Jussi Taipale
Journal:  Genome Res       Date:  2010-04-08       Impact factor: 9.043

7.  Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library.

Authors:  Michael J Feldhaus; Robert W Siegel; Lee K Opresko; James R Coleman; Jane M Weaver Feldhaus; Yik A Yeung; Jennifer R Cochran; Peter Heinzelman; David Colby; Jeffrey Swers; Christilyn Graff; H Steven Wiley; K Dane Wittrup
Journal:  Nat Biotechnol       Date:  2003-01-21       Impact factor: 54.908

8.  High-throughput sequencing of the zebrafish antibody repertoire.

Authors:  Joshua A Weinstein; Ning Jiang; Richard A White; Daniel S Fisher; Stephen R Quake
Journal:  Science       Date:  2009-05-08       Impact factor: 47.728

9.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

10.  The Human Gene Mutation Database: 2008 update.

Authors:  Peter D Stenson; Matthew Mort; Edward V Ball; Katy Howells; Andrew D Phillips; Nick St Thomas; David N Cooper
Journal:  Genome Med       Date:  2009-01-22       Impact factor: 11.117

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  80 in total

1.  Next-generation protein engineering targets influenza.

Authors:  Shoshana J Wodak
Journal:  Nat Biotechnol       Date:  2012-06-07       Impact factor: 54.908

2.  Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5.

Authors:  Glenna Wink Foight; Amy E Keating
Journal:  Protein Sci       Date:  2016-02-03       Impact factor: 6.725

3.  High-throughput analysis of in vivo protein stability.

Authors:  Ikjin Kim; Christina R Miller; David L Young; Stanley Fields
Journal:  Mol Cell Proteomics       Date:  2013-07-29       Impact factor: 5.911

4.  A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers.

Authors:  Justin D Smith; Kimberly F McManus; Hunter B Fraser
Journal:  Mol Biol Evol       Date:  2013-07-30       Impact factor: 16.240

5.  Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis.

Authors:  Alex Nisthal; Connie Y Wang; Marie L Ary; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-01       Impact factor: 11.205

6.  Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits.

Authors:  Jihye Park; Balaji Selvam; Keisuke Sanematsu; Noriatsu Shigemura; Diwakar Shukla; Erik Procko
Journal:  J Biol Chem       Date:  2019-02-05       Impact factor: 5.157

7.  Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts.

Authors:  Joshua T Atkinson; Alicia M Jones; Vikas Nanda; Jonathan J Silberg
Journal:  Protein Eng Des Sel       Date:  2019-12-31       Impact factor: 1.650

8.  Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.

Authors:  Justin R Klesmith; John-Paul Bacik; Emily E Wrenbeck; Ryszard Michalczyk; Timothy A Whitehead
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-14       Impact factor: 11.205

Review 9.  The power of fission: yeast as a tool for understanding complex splicing.

Authors:  Benjamin Jung Fair; Jeffrey A Pleiss
Journal:  Curr Genet       Date:  2016-09-14       Impact factor: 3.886

10.  Mapping Proteome-Wide Targets of Environmental Chemicals Using Reactivity-Based Chemoproteomic Platforms.

Authors:  Daniel Medina-Cleghorn; Leslie A Bateman; Breanna Ford; Ann Heslin; Karl J Fisher; Esha D Dalvie; Daniel K Nomura
Journal:  Chem Biol       Date:  2015-10-22
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