Slow domain reconfiguration causes power-law kinetics in a two-state enzyme

Abstract

Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.

Membrane Chemistry Tunes the Structure of a Peptide Transporter

“…While these structures suggest models with well‐defined states, our results sketch DtpA as an ensemble of multiple conformers with rapid dynamics. Recent studies showed that enzymes obey structural dynamics much faster than the timescales required for turnover . Such dynamics are also prevalent in DtpA, irrespective of the lipid environment (Figure C,D and Figure C).…”

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope

“…Another interesting parallel was described very recently in the two-domain enzyme quiescin sulfhydryl oxidase from the parasite Trypanosoma brucei 37 . Here the two domains are joined by a short disordered linker, and the enzyme transitions between open and closed states in the course of the catalytic cycle.…”

“…Here the two domains are joined by a short disordered linker, and the enzyme transitions between open and closed states in the course of the catalytic cycle. Fuzzy and apparently non-specific interactions between the two domains, arising as a result of their high mutual effective concentration, give rise to a rugged energy landscape, sub-diffusive conformational dynamics and ultimately to unusual, non-exponential reaction kinetics in this enzyme 37 . Thus, non-specific interactions, occurring as a result of the high effective concentration ensured by tethering with a disordered linker, can modulate protein function in a range of ways.…”

The conformational distribution of a major facilitator superfamily peptide transporter is modulated by the membrane composition

“…This heterogeneity is expected to be static at the fast nanosecond time-scale of the donor fluorescence lifetime 65 , which is expected to cause deviations from the predicted linear dependence between donor lifetime and transfer efficiency 65,66 . This deviation is indeed observed experimentally ( Fig S17).…”

“…Numerous bacterial POT structures have been determined to date [41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58] . We focus on the E. coli peptide transporter DtpA 59,60 to explore the effect of different environments such as detergents and Saposin nanoparticles 61,62 (SapNPs) with different lipid compositions on the conformation of the protein using single molecule FRET (smFRET) [63][64][65][66][67][68] . DtpA is an ideal model system since its substrate specificity is remarkably similar to that of its homologs PepT1 and PepT2 from human 36,[69][70][71][72][73][74][75] .…”