References
1. Cordell HJ. Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Hum Mol Genet. 2002;11(20):2463-2468. doi:10.1093/hmg/11.20.2463
2. Whitlock MC, Phillips PC. MULTIPLE FITNESS PEAKS AND EPISTASIS. :31.
3. Moore JH. A global view of epistasis. Nat Genet. 2005;37(1):13-14. doi:10.1038/ng0105-13
4. Mackay TF, Moore JH. Why epistasis is important for tackling complex human disease genetics. Genome Med. 2014;6(6):125. doi:10.1186/gm561
5. Sanjuan R, Elena SF. Epistasis correlates to genomic complexity. Proc Natl Acad Sci. 2006;103(39):14402-14405. doi:10.1073/pnas.0604543103
6. Natarajan C, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF. Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin. Science. 2013;340(6138):1324-1327. doi:10.1126/science.1236862
7. Salverda MLM, Dellus E, Gorter FA, et al. Initial Mutations Direct Alternative Pathways of Protein Evolution. Zhang J, ed. PLoS Genet. 2011;7(3):e1001321. doi:10.1371/journal.pgen.1001321
8. Draghi JA, Plotkin JB. SELECTION BIASES THE PREVALENCE AND TYPE OF EPISTASIS ALONG ADAPTIVE TRAJECTORIES: SELECTION BIASES EPISTASIS ALONG ADAPTIVE TRAJECTORIES.Evolution. 2013;67(11):3120-3131. doi:10.1111/evo.12192
9. Kouyos RD, Silander OK, Bonhoeffer S. Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol Evol. 2007;22(6):308-315. doi:10.1016/j.tree.2007.02.014
10. Rokyta DR, Joyce P, Caudle SB, Miller C, Beisel CJ, Wichman HA. Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus. Malik HS, ed. PLoS Genet. 2011;7(6):e1002075. doi:10.1371/journal.pgen.1002075
11. Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife. 2013;2. doi:10.7554/eLife.00631
12. Bloom JD, Gong LI, Baltimore D. Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance. Science. 2010;328(5983):1272-1275. doi:10.1126/science.1187816
13. Lozovsky ER, Chookajorn T, Brown KM, et al. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci. 2009;106(29):12025-12030. doi:10.1073/pnas.0905922106
14. Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature. 2009;461(7263):515-519. doi:10.1038/nature08249
15. Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis. Science. 2007;317(5844):1544-1548. doi:10.1126/science.1142819
16. Weinreich DM. Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins. Science. 2006;312(5770):111-114. doi:10.1126/science.1123539
17. Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510
18. Kvitek DJ, Sherlock G. Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape. Zhang J, ed. PLoS Genet. 2011;7(4):e1002056. doi:10.1371/journal.pgen.1002056
19. Chou H-H, Chiu H-C, Delaney NF, Segre D, Marx CJ. Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation. Science. 2011;332(6034):1190-1192. doi:10.1126/science.1203799
20. Wei X, Zhang J. Patterns and Mechanisms of Diminishing Returns from Beneficial Mutations. Agashe D, ed. Mol Biol Evol. 2019;36(5):1008-1021. doi:10.1093/molbev/msz035
21. Kryazhimskiy S, Rice DP, Jerison ER, Desai MM. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science. 2014;344(6191):1519-1522. doi:10.1126/science.1250939
22. Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population. Science. 2011;332(6034):1193-1196. doi:10.1126/science.1203801
23. Shapiro B, Rambaut A, Pybus OG, Holmes EC. A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution.Mol Biol Evol. 2006;23(9):1724-1730. doi:10.1093/molbev/msl037
24. Sanjuán R, Cuevas JM, Moya A, Elena SF. Epistasis and the Adaptability of an RNA Virus.Genetics. 2005;170(3):1001-1008. doi:10.1534/genetics.105.040741
25. Burch CL, Chao L. Epistasis and Its Relationship to Canalization in the RNA Virus φ6.Genetics. 2004;167(2):559-567. doi:10.1534/genetics.103.021196
26. Michalakis Y. EVOLUTION: Epistasis in RNA Viruses. Science. 2004;306(5701):1492-1493. doi:10.1126/science.1106677
27. da Silva J, Coetzer M, Nedellec R, Pastore C, Mosier DE. Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region. Genetics. 2010;185(1):293-303. doi:10.1534/genetics.109.112458
28. Sanjuan R, Moya A, Elena SF. The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci. 2004;101(43):15376-15379. doi:10.1073/pnas.0404125101
29. Bonhoeffer S. Evidence for Positive Epistasis in HIV-1. Science. 2004;306(5701):1547-1550. doi:10.1126/science.1101786
30. Trindade S, Sousa A, Xavier KB, Dionisio F, Ferreira MG, Gordo I. Positive Epistasis Drives the Acquisition of Multidrug Resistance. Zhang J, ed. PLoS Genet. 2009;5(7):e1000578. doi:10.1371/journal.pgen.1000578
31. Moore JH. The Ubiquitous Nature of Epistasis in Determining Susceptibility to Common Human Diseases. Hum Hered. 2003;56(1-3):73-82. doi:10.1159/000073735
32. Swint-Kruse L. Using Evolution to Guide Protein Engineering: The Devil IS in the Details. Biophys J. 2016;111(1):10-18. doi:10.1016/j.bpj.2016.05.030
33. Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci. 2014;111(43):15426-15431. doi:10.1073/pnas.1410624111
34. Miton CM, Tokuriki N. How mutational epistasis impairs predictability in protein evolution and design: How Epistasis Impairs Predictability in Enzyme Evolution.Protein Sci. 2016;25(7):1260-1272. doi:10.1002/pro.2876
35. Reetz MT. The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering. Angew Chem Int Ed. 2013;52(10):2658-2666. doi:10.1002/anie.201207842
36. Wells JA. Additivity of mutational effects in proteins. Biochemistry. 1990;29(37):8509-8517. doi:10.1021/bi00489a001
37. Dellus-Gur E, Elias M, Caselli E, et al. Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme’s Conformational Freedom and Disorder. J Mol Biol. 2015;427(14):2396-2409. doi:10.1016/j.jmb.2015.05.011
38. Gonzalez CE, Ostermeier M. Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase. J Mol Biol. 2019;431(10):1981-1992. doi:10.1016/j.jmb.2019.03.020
39. Olson CA, Wu NC, Sun R. A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain. Curr Biol. 2014;24(22):2643-2651. doi:10.1016/j.cub.2014.09.072
40. Istomin AY, Gromiha MM, Vorov OK, Jacobs DJ, Livesay DR. New insight into long-range nonadditivity within protein double-mutant cycles. Proteins Struct Funct Bioinforma. 2007;70(3):915-924. doi:10.1002/prot.21620
41. Yu H, Dalby PA. Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics.Proc Natl Acad Sci. 2018;115(47):E11043-E11052. doi:10.1073/pnas.1810324115
42. Jemimah S, Gromiha MM. Exploring additivity effects of double mutations on the binding affinity of protein-protein complexes. Proteins Struct Funct Bioinforma. 2018;86(5):536-547. doi:10.1002/prot.25472
43. Justina Jankauskaite, Brian Jiménez-García, Justas Dapkūnas, Juan Fernández-Recio, Iain H Moal. “SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation”. Bioinformatics. bty635. doi:10.1093
44. Sarai A, Uedaira H, Bava KA, Kitajima K, Gromiha MM. ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res. 2004;32(suppl_1):D120-D121. doi:10.1093/nar/gkh082
45. Berman HM, Westbrook J, Feng Z, et al. The Protein Databank. Nucliec Acids Res. 2000;28:235-242.
46. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
47. Eastman P, Swails J, Chodera JD, et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Gentleman R, ed. PLOS Comput Biol. 2017;13(7):e1005659. doi:10.1371/journal.pcbi.1005659
48. The FoldX web server: an online force field. Nucleic Acids Res. 2005;33(Web Server):W382-W388. doi:10.1093/nar/gki387
49. Kabsch W, Sander C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22(12):2577-2637. doi:10.1002/bip.360221211
50. Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. Maximum Allowed Solvent Accessibilites of Residues in Proteins. PLoS ONE. 2013;8(11). doi:10.1371/journal.pone.0080635
51. Burnham KP, Anderson DR, Burnham KP. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. 2nd ed. Springer; 2002.
52. R Core Team.R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing; 2020. https://www.R-project.org/
53. Venables WN, Ripley BD. Modern Applied Statistics with S. Fourth. Springer; 2002. http://www.stats.ox.ac.uk/pub/MASS4
54. Mazerolle MJ.AICcmodavg: Model Selection and Multimodel Inference Based on (Q)AIC(c).; 2020. https://cran.r-project.org/package=AICcmodavg
55. Jacksod SE, Fersht AR. Contribution of Residues in the Reactive Site Loop of Chymotrypsin Inhibitor 2 to Protein Stability and Activityt. :8.
56. Pons J, Rajpal A, Kirsch JF. Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the hyhel-10/lysozyme interaction. Protein Sci. 1999;8(5):958-968. doi:10.1110/ps.8.5.958
57. Li Y, Li H, Smith-Gill SJ, Mariuzza RA. Three-Dimensional Structures of the Free and Antigen-Bound Fab from Monoclonal Antilysozyme Antibody HyHEL-63† , ‡. Biochemistry. 2000;39(21):6296-6309. doi:10.1021/bi000054l
58. Schreiber G, Fersht AR. Energetics of protein-protein interactions: Analysis ofthe Barnase-Barstar interface by single mutations and double mutant cycles.J Mol Biol. 1995;248(2):478-486. doi:10.1016/S0022-2836(95)80064-6
59. Goldman ER, Dall’Acqua W, Braden BC, Mariuzza RA. Analysis of Binding Interactions in an Idiotope−Antiidiotope Protein−Protein Complex by Double Mutant Cycles . Biochemistry. 1997;36(1):49-56. doi:10.1021/bi961769k
60. Pielak GJ, Wang X. Interactions between Yeast Iso-1-cytochrome c and Its Peroxidase. Biochemistry. 2001;40(2):422-428. doi:10.1021/bi002124u
61. Huang L-T, Gromiha MM. Reliable prediction of protein thermostability change upon double mutation from amino acid sequence. Bioinformatics. 2009;25(17):2181-2187. doi:10.1093/bioinformatics/btp370