How Protein Stability and New Functions Trade Off

By Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik. PLoS Comput. Biol., 2008

569 citations recorded by the source corpus.

Numerous studies have noted that the evolution of new enzymatic specificities is accompanied by loss of the protein's thermodynamic stability (ΔΔG), thus suggesting a tradeoff between the acquisition of new enzymatic functions and stability. However, since most mutations are destabilizing (ΔΔG>0), one should ask how destabilizing mutations that confer new or altered enzymatic functions relative to all other mutations are. We applied ΔΔG computations by FoldX to analyze the effects of 548 mutations that arose from the directed evolution of 22 different enzymes. The stability effects, location, and type of function-altering mutations were compared to ΔΔG changes arising from all possible point mutations in the same enzymes. We found that mutations that modulate enzymatic functions are mostly destabilizing (average ΔΔG = +0.9 kcal/mol), and are almost as destabilizing as the “average” mutation in these enzymes (+1.3 kcal/mol). Although their stability effects are not as dramatic as in key catalytic residues, mutations that modify the substrate binding pockets, and thus mediate new enzymatic specificities, place a larger stability burden than surface mutations that underline neutral, non-adaptive evolutionary changes. How are the destabilizing effects of functional mutations balanced to enable adaptation? Our analysis also indicated that many mutations that appear in directed evolution variants with no obvious role in the new function exert stabilizing effects that may compensate for the destabilizing effects of the crucial function-altering mutations. Thus, the evolution of new enzymatic activities, both in nature and in the laboratory, is dependent on the compensatory, stabilizing effect of apparently “silent” mutations in regions of the protein that are irrelevant to its function.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fa4356c56194b7f4d1abb6e0d736ff7407782694

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Citations in the corpus

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality (2011, background): “This observation indicates that many residues playing an essential role in protein function are not detrimental to stability, which somewhat relativizes the well-known trade-off between stability and function [33,34,55].”
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites (2014, background): “…of evolutionary rate at protein level (Drummond & Wilke 2008, Serohijos et al. 2012), the evolution of novel function (Bloom et al. 2006, Tokuriki et al. 2008), and the expected equilibrium distributions of stability and the explanation of marginal stability (Taverna & Goldstein 2002,…”
Exploring protein fitness landscapes by directed evolution (2009, unknown): “Clearly, such proteins are far rarer than highly active, marginally stable proteins and, without a good reason, natural sequences would not exhibit both feature”
Optimizing protein stability in vivo. (2009, background): “Alternatively, it has been discussed that marginal stability may be functionally beneficial or that stability and function trade off (Bahar et al., 2007; DePristo et al., 2005; Ferreiro et al., 2007; Tsou, 1998; Beadle and Shoichet, 2002; Schreiber et al., 1994: Tokuriki et al., 2008).”
Enzyme promiscuity: a mechanistic and evolutionary perspective. (2010, background): “Stability Trade-offs An important facet of the l y . trade-off that is not are destabilizing, and mutations that affect function e r s a l s e often exhibit even higher destabilizing effects (136).”
How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme (2015, unknown): “Like other programs of its kind, FoldX performs poorly at quantitatively reproducing experimental changes in stability but is considered to correctly reflect trends [34,35,39,40], which could potentially fit our goal by helping to explain the ΔΔG distributions of residues under complex constraints.”
Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding (2020, unknown): “Several ACE2-contact residues exhibit binding-stability tradeoffs, as has been seen in the active sites and binding interfaces of other proteins (Julian et al., 2017; Tokuriki et al., 2008; Wang et al., 2002).”
Capturing the mutational landscape of the beta-lactamase TEM-1 (2013, methodology): “Predictions of ΔΔG derived from foldX were kindly provided by Nobuhiko Tokuriki (Vancouver, British Columbia, Canada) (34).”
Stability effects of mutations and protein evolvability. (2009, background): “Compensatory stabilizing mutations—uphill divergence Compensatory mutations, also called global suppressors owing to their ability to suppress the deleterious effects of a wide range of mutations, have been observed in natural [3 ,41 ] and in vitro evolution [50], and therefore play a key role in ev”
Consensus protein design (2016, background): “The mechanism by which this occurs is not fully understood, although is thought to involve a combination of raw stability and ‘global suppressor’ residues that buffer the effect of deleterious mutations (Poteete et al., 1997; Steipe, 1999; Nikolova et al., 2000; Tokuriki et al., 2008).”
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (2020, unknown): “Several ACE2-contact residues exhibit binding-stability tradeoffs, as has been seen in the active sites and binding interfaces of other proteins (Julian et al., 2017; Tokuriki et al., 2008; Wang et al., 2002).”
The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database (2022, unknown): “Not only will the intrinsic disorder proteins (or regions) exhibit high dynamical plasticity, as shown in previous research (Meier and Özbek 2007; Tokuriki et al. 2008; Tokuriki and Tawfik 2009; Marsh and Teichmann 2014), but they may also exhibit high evolvability (towards more specialized…”