Epistasis in protein evolution

By Tyler N. Starr, Joseph W. Thornton. 2016

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Citations in the corpus

Revealing evolutionary constraints on proteins through sequence analysis (2018, background): “This phenomenon is known as global [10,14] or nonspecific [9] epistasis, and its relevance has been shown in evolution experiments [14], over and above contributions from specific epistasis [9, 15].”
Direct coupling analysis of epistasis in allosteric materials (2018, unknown): “This “interaction” between mutations can span long-range positional combinations [6], results in either beneficial or detrimental effects to fitness [7], and shapes protein evolutionary paths [8].”
Experimental assay of a fitness landscape on a macroevolutionary scale (2017, background): “In other words, the presence of deleterious intermediate genotypes between highly fit ones leads to inaccessibility of some evolutionary trajectories between extant or ancestral sequences 6,20-22 , 44 .”
Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding (2020, unknown): “This shift in the effects of mutations between more distantly related RBDs is consistent with other studies of protein evolution demonstrating that epistastic entrenchment causes amino-acid preferences to change as homologous proteins become increasingly diverged (Hilton and Bloom, 2018; Lee et al.,”
Efficient generative modeling of protein sequences using simple autoregressive models (2021, methodology): “To predict contacts using arDCA, we need to go back to the biological interpretation of DCA couplings: they represent epistatic couplings between pairs of mutations [50].”
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (2020, unknown): “This shift in the effects of mutations between more distantly related RBDs is consistent with studies of protein evolution demonstrating that epistastic entrenchment causes amino acid preferences to change as proteins diverge (Hilton and Bloom, 2018; Lee et al., 2018; Pollock et al., 2012; Povolotsk”
Inferring the shape of global epistasis (2018, background): “Today, the idea that epistatic interactions are the result of a nonlinear mapping from an underlying additive trait has been called “unidimensional” (26, 27), “nonspecific” (28), or “global” (29) epistasis, and several heuristic techniques have been proposed to infer epistasis of this form (30–33).”