Literature DB >> 26183776

Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose.

Trine Holst Sørensen1, Nicolaj Cruys-Bagger1, Kim Borch2, Peter Westh3.   

Abstract

Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association.
© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Entities:  

Keywords:  Hypocrea jecorina; Rasamsonia emersonii; carbohydrate-binding protein; cellulase; enzyme kinetics; enzyme mechanism; thermodynamics

Mesh:

Substances:

Year:  2015        PMID: 26183776      PMCID: PMC4571971          DOI: 10.1074/jbc.M115.659656

Source DB:  PubMed          Journal:  J Biol Chem        ISSN: 0021-9258            Impact factor:   5.157


  59 in total

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Review 2.  Industrial enzyme applications.

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Journal:  Curr Opin Biotechnol       Date:  2002-08       Impact factor: 9.740

Review 3.  Processive and nonprocessive cellulases for biofuel production--lessons from bacterial genomes and structural analysis.

Authors:  David B Wilson
Journal:  Appl Microbiol Biotechnol       Date:  2011-11-24       Impact factor: 4.813

4.  Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis.

Authors:  Jürgen Jalak; Priit Väljamäe
Journal:  Biotechnol Bioeng       Date:  2010-08-15       Impact factor: 4.530

5.  Transition-state mimicry by glycosidase inhibitors: a critical kinetic analysis.

Authors:  Jacqueline Wicki; Spencer J Williams; Stephen G Withers
Journal:  J Am Chem Soc       Date:  2007-03-27       Impact factor: 15.419

6.  Loss of translational entropy in binding, folding, and catalysis.

Authors:  L M Amzel
Journal:  Proteins       Date:  1997-06

7.  Glycosidic-bond hydrolysis mechanism catalyzed by cellulase Cel7A from Trichoderma reesei: a comprehensive theoretical study by performing MD, QM, and QM/MM calculations.

Authors:  Jinghua Li; Likai Du; Lushan Wang
Journal:  J Phys Chem B       Date:  2010-10-28       Impact factor: 2.991

8.  A quantitative approach to the evaluation of 2-acetamide substituent effects on the hydrolysis by Taka-N-acetyl-beta-D-glucosaminidase. Role of the substrate 2-acetamide group in the N-acyl specificity of the enzyme.

Authors:  K Yamamoto
Journal:  J Biochem       Date:  1974-08       Impact factor: 3.387

9.  Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

Authors:  Brandon C Knott; Michael F Crowley; Michael E Himmel; Jerry Ståhlberg; Gregg T Beckham
Journal:  J Am Chem Soc       Date:  2014-06-06       Impact factor: 15.419

10.  Implications of cellobiohydrolase glycosylation for use in biomass conversion.

Authors:  Tina Jeoh; William Michener; Michael E Himmel; Stephen R Decker; William S Adney
Journal:  Biotechnol Biofuels       Date:  2008-05-01       Impact factor: 6.040

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  7 in total

1.  Temperature Effects on Kinetic Parameters and Substrate Affinity of Cel7A Cellobiohydrolases.

Authors:  Trine Holst Sørensen; Nicolaj Cruys-Bagger; Michael Skovbo Windahl; Silke Flindt Badino; Kim Borch; Peter Westh
Journal:  J Biol Chem       Date:  2015-07-16       Impact factor: 5.157

2.  Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues.

Authors:  Nanna Røjel; Jeppe Kari; Trine Holst Sørensen; Silke F Badino; J Preben Morth; Kay Schaller; Ana Mafalda Cavaleiro; Kim Borch; Peter Westh
Journal:  J Biol Chem       Date:  2019-12-17       Impact factor: 5.157

3.  The dissociation mechanism of processive cellulases.

Authors:  Josh V Vermaas; Riin Kont; Gregg T Beckham; Michael F Crowley; Mikael Gudmundsson; Mats Sandgren; Jerry Ståhlberg; Priit Väljamäe; Brandon C Knott
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-30       Impact factor: 11.205

4.  Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution.

Authors:  Manuel Eibinger; Thomas Zahel; Thomas Ganner; Harald Plank; Bernd Nidetzky
Journal:  Biotechnol Biofuels       Date:  2016-03-08       Impact factor: 6.040

5.  Engineering enhanced cellobiohydrolase activity.

Authors:  Larry E Taylor; Brandon C Knott; John O Baker; P Markus Alahuhta; Sarah E Hobdey; Jeffrey G Linger; Vladimir V Lunin; Antonella Amore; Venkataramanan Subramanian; Kara Podkaminer; Qi Xu; Todd A VanderWall; Logan A Schuster; Yogesh B Chaudhari; William S Adney; Michael F Crowley; Michael E Himmel; Stephen R Decker; Gregg T Beckham
Journal:  Nat Commun       Date:  2018-03-22       Impact factor: 14.919

6.  Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach.

Authors:  Kay S Schaller; Jeppe Kari; Gustavo A Molina; Kasper D Tidemand; Kim Borch; Günther H J Peters; Peter Westh
Journal:  ACS Omega       Date:  2021-01-06

Review 7.  Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives.

Authors:  Heidi Østby; Line Degn Hansen; Svein J Horn; Vincent G H Eijsink; Anikó Várnai
Journal:  J Ind Microbiol Biotechnol       Date:  2020-08-25       Impact factor: 3.346

  7 in total

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