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Is the catalytic activity of triosephosphate isomerase fully optimized? An investigation based on maximization of entropy production

Abstract

Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states. The maximal entropy production (MaxEP) requirement for any of the first three transitions between TIM functional states leads to decreased total entropy production. Only the MaxEP requirement for the product (R-glyceraldehyde-3-phosphate) release step led to a 30% increase in enzyme activity, specificity constant kcat/KM, and overall entropy production. The product release step, due to the TIM molecular machine working in the physiological direction of glycolysis, has not been identified before as the rate-limiting step by using irreversible thermodynamics. Together with structural studies, our results open the possibility for finding amino acid substitutions leading to an increased frequency of loop six opening and product release.

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Abbreviations

TIM:

Triosephosphate isomerase

DHAP:

Dihydroxyacetone phosphate

GAP:

d-glyceraldehyde 3-phosphate

MaxEP:

Maximum entropy production

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Acknowledgments

The present work was supported by the Croatian Science Foundation, project number 8481. We thank Prof. Alessandro Tossi for improvements in presentation and to anonymous reviewer for careful reading of our manuscript and insightful suggestions.

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Correspondence to Davor Juretić.

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Bonačić Lošić, Ž., Donđivić, T. & Juretić, D. Is the catalytic activity of triosephosphate isomerase fully optimized? An investigation based on maximization of entropy production. J Biol Phys 43, 69–86 (2017). https://doi.org/10.1007/s10867-016-9434-3

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Keywords

  • Enzyme kinetic scheme
  • Triosephosphate isomerase
  • Maximum entropy production
  • Kinetic constants