Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics.


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.

Submission Details

ID: GQfc7tAJ4

Submitter: Shu-Ching Ou

Submission Date: March 27, 2019, 4:37 p.m.

Version: 1

Publication Details
Yu H;Dalby PA,Proc Natl Acad Sci U S A (2018) Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics. PMID:30404916
Additional Information

ND: not determined.

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)

Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
6RJC 2019-09-11 1.05 E.coli transketolase apoenzyme
2R8O 2007-12-11 1.47 Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate
5HHT 2016-11-02 1.5 Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln
2R5N 2007-11-06 1.6 Crystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate
2R8P 2007-12-11 1.65 Transketolase from E. coli in complex with substrate D-fructose-6-phosphate

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
199.6 A,B Transketolase 1 P27302 TKT1_ECOLI