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J Biol Phys. 2017 Mar;43(1):69-86. doi: 10.1007/s10867-016-9434-3. Epub 2017 Jan 3.

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

Author information

1
Faculty of Science, University of Split, Ruđera Boškovića 33, 21000, Split, Croatia.
2
Medical High School, Šibenik, Ante Šupuka bb, 22000, Šibenik, Croatia.
3
Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000, Split, Croatia. davor.juretic@gmail.com.

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.

KEYWORDS:

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

PMID:
28050739
PMCID:
PMC5323346
DOI:
10.1007/s10867-016-9434-3
[Indexed for MEDLINE]
Free PMC Article

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