Bridging the Micro-Macro Gap between Single-Molecular Behavior and Bulk Hydrolysis Properties of Cellulase

Takahiro Ezaki (Corresponding Author), Katsuhiro Nishinari, Masahiro Samejima, Kiyohiko Igarashi (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

Abstract

The microscopic kinetics of enzymes at the single-molecule level often deviate considerably from those expected from bulk biochemical experiments. Here, we propose a coarse-grained-model approach to bridge this gap, focusing on the unexpectedly slow bulk hydrolysis of crystalline cellulose by cellulase, which constitutes a major obstacle to mass production of biofuels and biochemicals. Building on our previous success in tracking the movements of single molecules of cellulase on crystalline cellulose, we develop a mathematical description of the collective motion and function of enzyme molecules hydrolyzing the surface of cellulose. Model simulations robustly explained the experimental findings at both the microscopic and macroscopic levels and revealed a hitherto-unknown mechanism causing a considerable slowdown of the reaction, which we call the crowding-out effect. The size of the cellulase molecule impacted significantly on the collective dynamics, whereas the rate of molecular motion on the surface did not.

Original languageEnglish
Article number098102
Number of pages5
JournalPhysical Review Letters
Volume122
Issue number9
DOIs
Publication statusPublished - 7 Mar 2019
MoE publication typeNot Eligible

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hydrolysis
cellulose
enzymes
molecules
crowding
kinetics
simulation

Keywords

  • Biochemistry
  • Biomolecular processes
  • Chemical kinetics

Cite this

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abstract = "The microscopic kinetics of enzymes at the single-molecule level often deviate considerably from those expected from bulk biochemical experiments. Here, we propose a coarse-grained-model approach to bridge this gap, focusing on the unexpectedly slow bulk hydrolysis of crystalline cellulose by cellulase, which constitutes a major obstacle to mass production of biofuels and biochemicals. Building on our previous success in tracking the movements of single molecules of cellulase on crystalline cellulose, we develop a mathematical description of the collective motion and function of enzyme molecules hydrolyzing the surface of cellulose. Model simulations robustly explained the experimental findings at both the microscopic and macroscopic levels and revealed a hitherto-unknown mechanism causing a considerable slowdown of the reaction, which we call the crowding-out effect. The size of the cellulase molecule impacted significantly on the collective dynamics, whereas the rate of molecular motion on the surface did not.",
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Bridging the Micro-Macro Gap between Single-Molecular Behavior and Bulk Hydrolysis Properties of Cellulase. / Ezaki, Takahiro (Corresponding Author); Nishinari, Katsuhiro; Samejima, Masahiro; Igarashi, Kiyohiko (Corresponding Author).

In: Physical Review Letters, Vol. 122, No. 9, 098102, 07.03.2019.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Bridging the Micro-Macro Gap between Single-Molecular Behavior and Bulk Hydrolysis Properties of Cellulase

AU - Ezaki, Takahiro

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AU - Igarashi, Kiyohiko

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AB - The microscopic kinetics of enzymes at the single-molecule level often deviate considerably from those expected from bulk biochemical experiments. Here, we propose a coarse-grained-model approach to bridge this gap, focusing on the unexpectedly slow bulk hydrolysis of crystalline cellulose by cellulase, which constitutes a major obstacle to mass production of biofuels and biochemicals. Building on our previous success in tracking the movements of single molecules of cellulase on crystalline cellulose, we develop a mathematical description of the collective motion and function of enzyme molecules hydrolyzing the surface of cellulose. Model simulations robustly explained the experimental findings at both the microscopic and macroscopic levels and revealed a hitherto-unknown mechanism causing a considerable slowdown of the reaction, which we call the crowding-out effect. The size of the cellulase molecule impacted significantly on the collective dynamics, whereas the rate of molecular motion on the surface did not.

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