Multiple mutations are typically required to significantly improve protein stability or aggregation kinetics. However, when several substitutions are made in a single protein, the mutations can potentially interact in a nonadditive manner, resulting in epistatic effects, which can hamper protein-engineering strategies to improve thermostability or aggregation kinetics. Here, we have examined the role of protein dynamics in mediating epistasis between pairs of mutations. With Escherichia coli transketolase (TK) as a model, we explored the epistatic interactions between two single variants H192P and A282P, and also between the double-mutant H192P/A282P and two single variants, I365L or G506A. Epistasis was determined for several measures of protein stability, including the following: the free-energy barrier to kinetic inactivation, ∆∆G ‡; thermal transition midpoint temperatures, T m; and aggregation onset temperatures, T agg Nonadditive epistasis was observed between neighboring mutations as expected, but also for distant mutations located in the surface and core regions of different domains. Surprisingly, the epistatic behaviors for each measure of stability were often different for any given pairwise recombination, highlighting that kinetic and thermodynamic stabilities do not always depend on the same structural features. Molecular-dynamics simulations and a pairwise cross-correlation analysis revealed that mutations influence the dynamics of their local environment, but also in some cases the dynamics of regions distant in the structure. This effect was found to mediate epistatic interactions between distant mutations and could therefore be exploited in future protein-engineering strategies.
Submitter: Shu-Ching Ou
Submission Date: March 27, 2019, 4:37 p.m.
ND: not determined.
|Number of data points||146|
|Assays/Quantities/Protocols||Experimental Assay: Tagg: Aggregation Onset Temperature ; Experimental Assay: Tm ; Experimental Assay: ΔSvh ; Experimental Assay: f60 ; Experimental Assay: kd: Inactivation rate constant ; Experimental Assay: t1/2 ; Experimental Assay: T50^15 ; Experimental Assay: Km ; Experimental Assay: kcat ; Experimental Assay: kcat/Km|
|Libraries||Variants for TK|
|Structure ID||Release Date||Resolution||Structure Title|
|1QGD||1999-04-23T00:00:00+0000||1.9||TRANSKETOLASE FROM ESCHERICHIA COLI|
|2R5N||2007-09-04T00:00:00+0000||1.6||Crystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate|
|2R8O||2007-09-11T00:00:00+0000||1.47||Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate|
|2R8P||2007-09-11T00:00:00+0000||1.65||Transketolase from E. coli in complex with substrate D-fructose-6-phosphate|
|5HHT||2016-01-11T00:00:00+0000||1.5||Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln|
|6RJC||2019-04-26T00:00:00+0000||1.05||E.coli transketolase apoenzyme|
|6TJ8||2019-11-25T00:00:00+0000||0.92||Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine diphosphate|
|6TJ9||2019-11-25T00:00:00+0000||0.95||Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine and substrate xylulose 5-phosphate|
|Percent Identity||Matching Chains||Protein||Accession||Entry Name|