Stability effects of mutations and protein evolvability.

By Nobuhiko Tokuriki, Dan S. Tawfik. 2009

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Citations in the corpus

Exploring protein fitness landscapes by directed evolution (2009, positive): “Several studies have revealed a key link between stability and epistasis, where the effect of a mutation can be conditional on the stability of the parent sequenc”
Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast (2014, methodology): “These structural analyses are consistent with the chemical intuition that the functional sensitivity of a position to mutation is primarily determined by direct binding interfaces 39 as well as structural integrity 40 and dynamics 41 .”
Toward the solution of the protein structure prediction problem (2021, background): “The key reason for the success of TASSER is its effective combination of multiple templates (20 – 50) and its optimized simulation strategy that combines ef ﬁ cient conformational movements with an effective knowledge and template-based energy function.”
Selection for Protein Stability Enriches for Epistatic Interactions (2018, background): “But, with some 24 exceptions [7], this view has been largely replaced with a more parsimonious explanation based on 25 the high dimensionality of sequence space: marginal stabilities are observed because, simply, far 26 more sequences are marginally stable than maximally stable [8].”
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations (2015, background): “In general, the current state-of-the-art experimental mappings artificially widen the threshold for acceptance of mutations, such that the early accumulating mutations have no apparent effect on the protein’s fitness [73].”
How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme (2015, result): “for ampicillin hydrolysis by TEM-1 but consistent with several other studies suggesting this is a rather general effect [3,34,35].”
STRUM: structure-based prediction of protein stability changes upon single-point mutation (2016, background): “Experimental measurements showed that nearly one-third of nsSNP mutations are deleterious to human health (Tokuriki and Tawfik, 2009).”
Enzyme promiscuity: a mechanistic and evolutionary perspective. (2010, background): “Thus, when drifting in the absence of any selection, loss of all functions (nonfunctionalization) because of (162, 170) is orders of magnitude likely than neofunctionalization (171). www.annualreviews.org • Enzyme Promiscuity 495 utilization parts The above observations prompted a number of…”
Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels (2013, background): “Under these conditions, selection results in stably-folded proteins [19,20], such that modestly destabilizing mutations can be tolerated without dramatic changes to the fraction of natively folded protein molecules and hence function.”
Epistasis in protein evolution (2016, background): “This kind of epistasis fits a model by which stability maps nonlinearly to function and fitness: in the simplest case, suppose that the biological function of a protein scales linearly with the quantity of folded protein in the cell.(84) Two mutations that independently affect protein stability will”
The genetic landscape of a physical interaction (2018, background): “Additional non-linearities occur in the folding of individual proteins or RNAs (‘threshold robustness’) (Bershtein et al., 2006; Olson et al., 2014; Tokuriki and Tawfik, 2009), in saturating enzyme flux (Kacser and Burns, 1973; Stiffler et al., 2015), and in regulatory dynamics (Gjuvsland et al.,…”
Mega-scale experimental analysis of protein folding stability in biology and design (2023, background): “However, the challenge of measuring stability has made it difficult to experimentally distinguish selection for stability from other selective pressures on a global level 36– 38 .”