Biology subjects

Prentice, E. J.

Publications and source records attributed to Prentice, E. J..

3 recordsLinked to original sources

bioRxiv2025

Correlated dynamics, reactive conformations and non-Arrhenius behaviour in the temperature-dependence of enzyme activity: triosephosphate isomerase

Heat capacity changes are increasingly recognised as crucial for understanding the temperature dependence of enzyme-catalysed reaction rates. Here, we combine experiments and molecular dynamics simulations to investigate triosephosphate isomerase (TIM, TPI) from psychrophilic, mesophilic and thermophilic organisms. Kinetic data show clear curvature in rate-temperature plots, particularly for the cold-adapted enzyme, independent of unfolding. This non-Arrhenius behaviour is accounted for by Macromolecular Rate Theory (MMRT), implying an activation heat capacity, largest for the psychrophile. Simulations reveal the molecular origins of these differences, showing significant conformational and dynamical changes between reactant and transition states in the cold-adapted enzyme, with a smaller activation heat capacity in the mesophilic enzyme, and near-zero for the thermophile. Transition-state-like conformations and reorganized correlated dynamics underlie these adaptations. These results demonstrate that dynamical differences between crucial states along the reaction pathway play a key role in determining the optimum temperature of activity for this archetypal enzyme.

biochemistry↗

bioRxiv2023

Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Many enzymes display non-Arrhenius behaviour with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behaviour and recently the role of the activation heat capacity [Formula] has been widely discussed. If enzyme-catalysed reactions occur with appreciable negative values of [Formula] (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalysed rate. We use these data to test a range of models including macromolecular rate theory (MMRT) and an equilibrium model. In addition, we have performed extensive molecular dynamics (MD) simulations to characterise the conformational landscape traversed by MalL in the enzyme-substrate complex and an enzyme-transition state complex. We have crystallised the enzyme in a transition state-like conformation in the absence of a ligand and determined an X-ray crystal structure at very high resolution (1.10 [A]). We show (using simulation) that this enzyme-transition state conformation has a more restricted conformational landscape than the wildtype enzyme. We coin the term "transition state-like conformation (TLC)" to apply to this state of the enzyme. Together, these results imply a cooperative conformational transition between an enzyme-substrate conformation (ES) and a transition-state-like conformation (TLC) that precedes the chemical step. We present a two-state model as an extension of MMRT (MMRT-2S) that describes the data along with a convenient approximation with linear temperature dependence of the activation heat capacity (MMRT-1L) that can be used where fewer data points are available. Our model rationalises disparate behaviour seen for MalL and a thermophilic alcohol dehydrogenase and is consistent with a raft of data for other enzymes. Our model can be used to characterise the conformational changes required for enzyme catalysis and provides insights into the role of cooperative conformational changes in transition state stabilisation that are accompanied by changes in heat capacity for the system along the reaction coordinate. TLCs are likely to be of wide importance in understanding the temperature dependence of enzyme activity, and other aspects of enzyme catalysis.

biochemistry↗

bioRxiv2017

Dynamical origins of heat capacity changes in enzyme catalysed reactions

Heat capacity changes are emerging as essential for explaining the temperature dependence of enzyme-catalysed reaction rates. This has important implications for enzyme kinetics, thermoadaptation and evolution, but the physical basis of these heat capacity changes is unknown. Here we show by a combination of experiment and simulation, for two quite distinct enzymes (dimeric ketosteroid isomerase and monomeric alpha-glucosidase), that the activation heat capacity change for the catalysed reaction can be predicted through atomistic molecular dynamics simulations. The simulations reveal subtle and surprising underlying dynamical changes: tightening of loops around the active site is observed as expected, but crucially, changes in energetic fluctuations are evident across the whole enzyme including important contributions from oligomeric neighbours and domains distal to the active site. This has general implications for understanding enzyme catalysis and demonstrating a direct connection between functionally important microscopic dynamics and macroscopically measurable quantities.

biochemistry↗