Missense meanderings in sequence space: a biophysical view of protein evolution

By Mark A. DePristo, Daniel M. Weinreich, Daniel L. Hartl. 2005

646 citations recorded by the source corpus.

Subfields: Cell Biology, Genetics, Molecular Biology

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Citations in the corpus

Revealing evolutionary constraints on proteins through sequence analysis (2018, background): “For instance, protein thermal stability, measured through folding free energy, is approximately additive [8, 13].”
A biophysical protein folding model accounts for most mutational fitness effects in viruses (2011, background): “Such tradeoffs often result from mutations to an enzyme’s active site (16-18) when evolving a new function, i.”
Stability effects of mutations and protein evolvability. (2009, background): “Indeed, understanding and predicting the effects of mutations on the organismal level is a major challenge of evolutionary biology [1 ,6,7].”
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks (2020, methodology): “0 kcal/mol around the optimal stability in stability space, and mutations whose impact 390 on stability fall within the neutral zone will have little effect on fitness (46).”
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations (2015, background): “Phylogenetic analyses enable insights regarding how protein sequences diverge [1, 2] and what dictates the purging of mutations [3, 4].”
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins (2011, background): “Yet, numerous studies of protein evolution in vitro [27–29] as well as studies in bacteria [30] and viruses [20,31,32] have shown that beneficial mutations are often pleiotropic: in addition to their original beneficial effect, they cause some, usually negative, side effects on other protein propert”
Mutational effects on stability are largely conserved during protein evolution (2013, background): “Epistasis at the level of function and fitness can arise even if stability is fully site independent due to counterbalancing stabilizing and destabilizing mutations (11, 12), and stability is only one mechanism of epistasis (13, 14).”
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics (2014, background): “The entire population is subject to mutation, drift, and purifying selection [65]. designed ones [21]) therefore implies a ‘stability-activity tradeoff’ [22] or provides the evidence against selection for stability altogether [23 (cid:2) ].”
How Protein Stability and New Functions Trade Off (2008, background): “It also follows, that increasing the initial stability of the starting point enzyme will enable the subsequent acquisition of function altering mutations that are otherwise not tolerated [1,2,6,34,58].”
Stability-mediated epistasis constrains the evolution of an influenza protein (2013, background): “The first explanation holds that evolution actively selects for marginal stability because both insufficient and excess stability are deleterious (DePristo et al., 2005; Tokuriki and Tawfik, 2009).”
Evolvability as a function of purifying selection in TEM-1 β-lactamase. (2015, neutral): “, on protein stability), supporting a view that most mutations are not neutral at the biochemical level (DePristo et al., 2005; Tokuriki and Tawfik, 2009).”