R. W. Marriott, Astronomer

Kamp, Peter van de

doi:10.1126/science.123.3196.536

Cited by 2 publications

(8 citation statements)

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“…Previously, we have used extensive molecular dynamics simulations to characterise the conformational landscape in two states (ES and E-TS) for the model enzymes ketosteroid isomerase (KSI) and MalL and designer Kemp eliminase enzymes including an evolved variant. 14,30 This involved repeated independent simulations (x10) of 500 ns each to characterise the enzyme bound to either the substrate (ES complex) or a transition state analogue (E-TS complex). The difference in heat capacity between these states was calculated from the difference in fluctuations in the enthalpy for the two conformational ensembles.…”

Section: Two Conformations On the Pathway For The Enzyme-catalysed Re...mentioning

confidence: 99%

“…The latter is simulated by binding a (physical) transition-state analogue. 14 Simulations were also performed for the mutant MalL S536R (see below). Principal component analysis was used to characterise the conformational landscape in each of the two states (Figure 4).…”

Section: Two Conformations On the Pathway For The Enzyme-catalysed Re...mentioning

confidence: 99%

“…Their reduced mobility in the E-TS complex makes the greatest contribution to the calculated ∆𝐶 # ‡ from the WT simulations. 14 To check whether these shortened H-bonds are simply a function of the higher resolution of the S566R structure, we refined the S536R structure after truncating the diffraction data to a resolution equivalent to the WT structure (2.30 Å). We repeated the comparison and this also showed a significant shortening of 26 H-bonds at this resolution, confirming that the analysis was not biased based on the very high resolution of the S536R structure.…”

Section: Very High Resolution Structure Of Apo-s536r That Favours The...mentioning

confidence: 99%

“…13 The importance of activation heat capacity for enzyme kinetics has been the subject of debate recently. 3,5,6,14 The origin of this phenomenon lies in differences in fluctuations and populations of conformations between the enzyme-substrate complex (ES) and the enzyme-transition state complex (E-TS). We have argued that a consensus is emerging whereby the enzyme-substrate complex fluctuates between at least two conformations, one that favours the substrate and one that favours the transition state and that there is a difference in heat capacity between these two conformations.…”

Section: Introductionmentioning

confidence: 99%

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Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Walker

Hamill

Crean

et al. 2023

Preprint

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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 (∆CP≠) has been widely discussed. If enzyme-catalysed reactions occur with appreciable negative values of ∆CP≠(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 Å). 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.

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Section: Two Conformations On the Pathway For The Enzyme-catalysed Re...mentioning

confidence: 99%

Section: Two Conformations On the Pathway For The Enzyme-catalysed Re...mentioning

confidence: 99%

Section: Very High Resolution Structure Of Apo-s536r That Favours The...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Walker

Hamill

Crean

et al. 2023

Preprint

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“…2) il est employé, en manière d'hyperbole, pour des êtres ou des objets excellents, supérieurs aux autres ; 3) il est souvent l'équivalent d'ἐ νθεος, au sens d'inspiré, de possédé par le dieu 15 .…”

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Theios Homèros : du poète inspiré au poète divinisé ?

Kimmel-Clauzet¹

2020

mythos

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R. W. Marriott, Astronomer

Cited by 2 publications

References 1 publication

Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Cooperative conformational transitions and the temperature dependence of enzyme catalysis

Theios Homèros : du poète inspiré au poète divinisé ?

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