Erratum to: Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature: Fitness Effects of Protein Mutations (Protein Science, (2016), 25, 7, (1219-1226), 10.1002/pro.2928);Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

Protein Science

Volumn 28, Issue 3, 2016, Pages 1219-1226

  Boucher, Jeffrey I ^a   Bolon, Daniel N A ^a   Tawfik, Dan S ^b  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

mutational scan; polymorphism; protein evolution; SNP; systematic mutational mapping

Indexed keywords

MUTANT PROTEIN;

GENE FREQUENCY; GENE MAPPING; HUMAN; MOLECULAR EVOLUTION; NATURAL POPULATION; NONHUMAN; PERSONALIZED MEDICINE; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FUNCTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARDIZATION;

EID: 84976593316     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.3476     Document Type: Erratum

References (35)

1. Fowler DM, Fields S (2014) Deep mutational scanning: a new style of protein science. Nat Methods 11:801–807.
2. Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E (2015) Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Rep 11:645–656.
3. Huang W, Petrosino J, Hirsch M, Shenkin PS, Palzkill T (1996) Amino acid sequence determinants of beta-lactamase structure and activity. J Mol Biol 258:688–703.
4. Loeb DD, Swanstrom R, Everitt L, Manchester M, Stamper SE, Hutchison CAIII (1989) Complete mutagenesis of the HIV-1 protease. Nature 340:397–400.
5. Rennell D, Bouvier SE, Hardy LW, Poteete AR (1991) Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol 222:67–88.
6. Orr HA (2009) Fitness and its role in evolutionary genetics. Nat Rev Genet 10:531–539.
7. Dessau M, Goldhill D, McBride R, Turner PE, Modis Y (2012) Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzyme. PLoS Genet 8:e1003102.
8. Roscoe BP, Thayer KM, Zeldovich KB, Fushman D, Bolon DN (2013) Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J Mol Biol 425:1363–1377.
9. Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444:929–932.
10. Firnberg E, Labonte JW, Gray JJ, Ostermeier M (2014) A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol 31:1581–1592.
11. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159.
12. Jiang L, Mishra P, Hietpas RT, Zeldovich KB, Bolon DN (2013) Latent effects of Hsp90 mutants revealed at reduced expression levels. PLoS Genet 9:e1003600.
13. Rockah-Shmuel L, Toth-Petroczy A, Tawfik DS (2015) Systematic mapping of protein mutational space by prolonged drift reveals the deleterious effects of seemingly neutral mutations. PLoS Comput Biol 11:e1004421.
14. Dykhuizen DE, Dean AM, Hartl DL (1987) Metabolic flux and fitness. Genetics 115:25–31.
15. Kacser H, Burns JA (1981) The molecular basis of dominance. Genetics 97:639–666.
16. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008. (2006)
17. Newton MS, Arcus VL, Patrick WM (2015) Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. J R Soc Interface 12: 2015036.
18. Bershtein S, Mu W, Shakhnovich EI (2012) Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proc Natl Acad Sci USA 109:4857–4862.
19. Boucher JI, Cote P, Flynn J, Jiang L, Laban A, Mishra P, Roscoe BP, Bolon DNA (2014) Viewing protein fitness landscapes through a next-gen lens. Genetics 198:461–471.
20. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ (2000) Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25:333–337.
21. Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA (2011) Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci USA 108:680–685.
22. Kowalsky CA, Klesmith JR, Stapleton JA, Kelly V, Reichkitzer N, Whitehead TA (2015) High-resolution sequence-function mapping of full-length proteins. PLoS One 10:e0118193.
23. Mayr E, Provine WB (1998) The evolutionary synthesis: perspectives on the unification of biology. Harvard University Press, Cambridge, MA.
24. Otto SP, Whitlock MC (1997) The probability of fixation in populations of changing size. Genetics 146:723–733.
25. Buri P (1956) Gene frequency in small populations of mutant Drosophila. Evolution 10:367–402.
26. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 13:635–643.
27. Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci USA 109:18488–18492.
28. Hietpas RT, Jensen JD, Bolon DN (2011) Experimental illumination of a fitness landscape. Proc Natl Acad Sci USA 108:7896–7901.
29. Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DNA (2016) A balance between inhibitor binding and substrate processing confers influenza drug resistance. J Mol Biol 428:538–553.
30. Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI (2013) Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Mol Cell 49:133–144.
31. Lunzer M, Golding GB, Dean AM (2010) Pervasive cryptic epistasis in molecular evolution. PLoS Genet 6:e1001162.
32. Rosenberg AB, Patwardhan RP, Shendure J, Seelig G (2015) Learning the sequence determinants of alternative splicing from millions of random sequences. Cell 163:698–711.
33. Wagenaar TR, Ma L, Roscoe B, Park SM, Bolon DN, Green MR (2014) Resistance to vemurafenib resulting from a novel mutation in the BRAFV600E kinase domain. Pigment Cell Melanoma Res 27:124–133.
34. Hoogstraat M, Gadellaa-van Hooijdonk CG, Ubink I, Besselink NJM, Pieterse M, Veldhuis W, van Stralen M, Meijer EFJ, Willems SM, Hadders MA, Kuilman T, Krijgsman O, Peeper DS, Koudijs MJ, Cuppen E, Voest EE, Lolkema MP (2015) Detailed imaging and genetic analysis reveal a secondary BRAF(L505H) resistance mutation and extensive intrapatient heterogeneity in metastatic BRAF mutant melanoma patients treated with vemurafenib. Pigment Cell Melanoma Res 28:318–323.
35. Young DL, Fields S (2015) The role of functional data in interpreting the effects of genetic variation. Mol Biol Cell 26:3904–3908.