Literature DB >> 25075907

Deep mutational scanning: a new style of protein science.

Douglas M Fowler1, Stanley Fields2.   

Abstract

Mutagenesis provides insight into proteins, but only recently have assays that couple genotype to phenotype been used to assess the activities of as many as 1 million mutant versions of a protein in a single experiment. This approach-'deep mutational scanning'-yields large-scale data sets that can reveal intrinsic protein properties, protein behavior within cells and the consequences of human genetic variation. Deep mutational scanning is transforming the study of proteins, but many challenges must be tackled for it to fulfill its promise.

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Year:  2014        PMID: 25075907      PMCID: PMC4410700          DOI: 10.1038/nmeth.3027

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  52 in total

1.  Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing.

Authors:  Andreas Ernst; David Gfeller; Zhengyan Kan; Somasekar Seshagiri; Philip M Kim; Gary D Bader; Sachdev S Sidhu
Journal:  Mol Biosyst       Date:  2010-08-11

2.  Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning.

Authors:  Yasuhiro Fujino; Risako Fujita; Kouichi Wada; Kotomi Fujishige; Takashi Kanamori; Lindsey Hunt; Yoshihiro Shimizu; Takuya Ueda
Journal:  Biochem Biophys Res Commun       Date:  2012-10-26       Impact factor: 3.575

3.  Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

Authors:  Jacob A Tennessen; Abigail W Bigham; Timothy D O'Connor; Wenqing Fu; Eimear E Kenny; Simon Gravel; Sean McGee; Ron Do; Xiaoming Liu; Goo Jun; Hyun Min Kang; Daniel Jordan; Suzanne M Leal; Stacey Gabriel; Mark J Rieder; Goncalo Abecasis; David Altshuler; Deborah A Nickerson; Eric Boerwinkle; Shamil Sunyaev; Carlos D Bustamante; Michael J Bamshad; Joshua M Akey
Journal:  Science       Date:  2012-05-17       Impact factor: 47.728

4.  Computational design of ligand-binding proteins with high affinity and selectivity.

Authors:  Christine E Tinberg; Sagar D Khare; Jiayi Dou; Lindsey Doyle; Jorgen W Nelson; Alberto Schena; Wojciech Jankowski; Charalampos G Kalodimos; Kai Johnsson; Barry L Stoddard; David Baker
Journal:  Nature       Date:  2013-09-04       Impact factor: 49.962

Review 5.  A guide for functional analysis of BRCA1 variants of uncertain significance.

Authors:  Gaël A Millot; Marcelo A Carvalho; Sandrine M Caputo; Maaike P G Vreeswijk; Melissa A Brown; Michelle Webb; Etienne Rouleau; Susan L Neuhausen; Thomas v O Hansen; Alvaro Galli; Rita D Brandão; Marinus J Blok; Aneliya Velkova; Fergus J Couch; Alvaro N A Monteiro
Journal:  Hum Mutat       Date:  2012-07-16       Impact factor: 4.878

6.  The spatial architecture of protein function and adaptation.

Authors:  Richard N McLaughlin; Frank J Poelwijk; Arjun Raman; Walraj S Gosal; Rama Ranganathan
Journal:  Nature       Date:  2012-10-07       Impact factor: 49.962

7.  Analyses of the effects of all ubiquitin point mutants on yeast growth rate.

Authors:  Benjamin P Roscoe; Kelly M Thayer; Konstantin B Zeldovich; David Fushman; Daniel N A Bolon
Journal:  J Mol Biol       Date:  2013-01-30       Impact factor: 5.469

8.  Epistasis among adaptive mutations in deer mouse hemoglobin.

Authors:  Chandrasekhar Natarajan; Noriko Inoguchi; Roy E Weber; Angela Fago; Hideaki Moriyama; Jay F Storz
Journal:  Science       Date:  2013-06-14       Impact factor: 47.728

9.  Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing.

Authors:  Michael W Traxlmayr; Christoph Hasenhindl; Matthias Hackl; Gerhard Stadlmayr; Jakub D Rybka; Nicole Borth; Johannes Grillari; Florian Rüker; Christian Obinger
Journal:  J Mol Biol       Date:  2012-07-27       Impact factor: 5.469

10.  Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein.

Authors:  Daniel Melamed; David L Young; Caitlin E Gamble; Christina R Miller; Stanley Fields
Journal:  RNA       Date:  2013-09-24       Impact factor: 4.942

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  323 in total

1.  High-throughput identification of protein mutant stability computed from a double mutant fitness landscape.

Authors:  Nicholas C Wu; C Anders Olson; Ren Sun
Journal:  Protein Sci       Date:  2015-12-08       Impact factor: 6.725

2.  Landscape-Based Biology.

Authors:  Andrew D Ellington
Journal:  J Mol Evol       Date:  2015-10-19       Impact factor: 2.395

3.  How mutational epistasis impairs predictability in protein evolution and design.

Authors:  Charlotte M Miton; Nobuhiko Tokuriki
Journal:  Protein Sci       Date:  2016-01-22       Impact factor: 6.725

4.  Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses.

Authors:  Nicholas C Wu; Andrew J Thompson; Juhye M Lee; Wen Su; Britni M Arlian; Jia Xie; Richard A Lerner; Hui-Ling Yen; Jesse D Bloom; Ian A Wilson
Journal:  Science       Date:  2020-06-19       Impact factor: 47.728

5.  High-throughput discovery of trafficking-deficient variants in the cardiac potassium channel KV11.1.

Authors:  Krystian A Kozek; Andrew M Glazer; Chai-Ann Ng; Daniel Blackwell; Christian L Egly; Loren R Vanags; Marcia Blair; Devyn Mitchell; Kenneth A Matreyek; Douglas M Fowler; Bjorn C Knollmann; Jamie I Vandenberg; Dan M Roden; Brett M Kroncke
Journal:  Heart Rhythm       Date:  2020-06-06       Impact factor: 6.343

6.  Unbiased Fitness Estimation of Pooled Barcode or Amplicon Sequencing Studies.

Authors:  Fangfei Li; Marc L Salit; Sasha F Levy
Journal:  Cell Syst       Date:  2018-11-01       Impact factor: 10.304

7.  Gene-specific features enhance interpretation of mutational impact on acid α-glucosidase enzyme activity.

Authors:  Aashish N Adhikari
Journal:  Hum Mutat       Date:  2019-08-07       Impact factor: 4.878

8.  Modulation of FadR binding capacity for acyl-CoA fatty acids through structure-guided mutagenesis.

Authors:  John-Paul Bacik; Chris M Yeager; Scott N Twary; Ricardo Martí-Arbona
Journal:  Protein J       Date:  2015-10       Impact factor: 2.371

9.  Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships.

Authors:  Christopher M Jakobson; Daniel F Jarosz
Journal:  Cell Syst       Date:  2019-05-01       Impact factor: 10.304

Review 10.  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

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