Exothermicity Is Not a Necessary Condition for Enhanced Diffusion of Enzymes

Abstract

Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We perform measurements on the endothermic and relatively slow enzyme aldolase, which also shows substrate-induced enhanced diffusion. We propose a new physical paradigm, which reveals that the diffusion coefficient of a model enzyme hydrodynamically coupled to its environment increases significantly when undergoing changes in conformational fluctuations in a substrate-dependent manner, and is independent of the overall turnover rate of the underlying enzymatic reaction. Our results show that substrate-induced enhanced diffusion of enzyme molecules can be explained within an equilibrium picture, and that the exothermicity of the catalyzed reaction is not a necessary condition for the observation of this phenomenon.In a quest for understanding nonequilibrium processes encountered in biology and chemistry, the study of active matter, namely systems constituted of agents able to consume and convert energy extracted from their environment, has been a major focus of the contemporary physical sciences [1,2]. Recent progress led to the design, fabrication and characterization of synthetic micro-and nano-machines relying on different propulsion mechanisms, and able to reproduce functions inspired from molecular biology, such as cargo transport or chemical sensing [3,4]. Such autonomous objects could have major technological applications, provided that they are small enough and fully biocompatible. In this context, and going down in scale, enzyme molecules have received a lot of attention, as models of biological nanoscale transducers able to convert chemical energy into mechanical work. Biomolecules typically perform cyclic turnovers in which they bind to substrates and catalytically convert them to products while undergoing conformational changes [5][6][7][8]. Recently, in vitro studies of enzymes using fluorescence correlation spectroscopy (FCS) have revealed that their diffusion coefficient is enhanced in a substrate-dependent manner [9][10][11][12], and that the diffusion enhancement ∆D at substrate saturation was typically of the order of the bare diffusion coefficient of the enzyme D 0 measured in the absence of substrate molecules. This observation holds for a wide range of enzymes, which typically catalyze fast and exothermic chemical reactions, with reaction enthalpies that can reach 40k B T per molecule and catalytic rates up to ∼ 10 4 s −1 for the particular case of catalase [12].This intriguing phenomenon, that could have major implications in the spatial organisation of biological processes [13], was subsequently investigated from a theoretical point of view. It was first suggested that the enhancement of the * P.I. and X.Z. contributed equally to this work. † Present address: Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat 382 355, India. ‡ Corre...

Enzymatically Powered Surface‐Associated Self‐Motile Protocells

“…Enzymatically induced motility of inert particles and motion of enzymes themselves have been demonstrated in recent studies, but there is significant debate over the mechanism of force generation. Various proposed mechanisms include the idea that the reaction is exothermic; thus one possible theoretical model is collective heating that results from enzymatic turnover . Sen and co‐workers show that catalase‐ or urease‐coated PS microparticles exhibit enhancement of diffusivity within corresponding substrate solutions and attribute this enhancement to heat generation .…”

“…The flow most closely correlated not with the exothermicity of the reaction, but rather the difference in osmolarity between reactants and products. It is also possible that the conformational change of the enzymes during turnover leads to an impulsive force …”

“…We use the fundamental insights of Sen and co‐workers, who have identified the ability of enzymes to enhance the diffusivity of enzyme‐coated microparticles . The mechanism of enzyme‐associated enhancement of diffusion is somewhat in debate and involves some combination of self‐phoresis, enzyme shape fluctuation, and collective heating . For self‐phoresis, an asymmetric distribution of reaction products in vicinity of the enzyme creates corresponding shear or osmotic flows.…”

“…In enzyme fluctuation, the continuous deformation of enzymes during substrate turnover leads to a propulsive force. Sen and co‐workers experimentally demonstrated that periodic shape changes of an enzyme during substrate turnover create a mechanical force that can enhance diffusivity . In collective heating, exothermic enzymes such as catalase and urease convert chemical potential into thermal energy.…”

Molecular simulations of cellular processes

“…Whereas the effects of macromolecular crowding on protein internal dynamics, and translational and rotational diffusion have been studied employing a multiscale model by Trovato et al (2013), investigations on the influence of protein flexibility on diffusion are lacking, albeit they could be potentially relevant (Illien et al 2017). In part, this is a consequence of the limitations of most discussed models and, in part, it is due to the less frequent use of multiscale models.…”