Chapter 14. Defining the Inefficiencies in the Chemical Mechanism of the Photosynthetic Enzyme Rubisco by Computational Simulation

  1. Dr. Anthony F. Collings2 and
  2. Prof. Christa Critchley3
  1. Jill E. Gready

Published Online: 9 MAY 2006

DOI: 10.1002/3527606742.ch14

Artificial Photosynthesis: From Basic Biology to Industrial Application

Artificial Photosynthesis: From Basic Biology to Industrial Application

How to Cite

Gready, J. E. (2005) Defining the Inefficiencies in the Chemical Mechanism of the Photosynthetic Enzyme Rubisco by Computational Simulation, in Artificial Photosynthesis: From Basic Biology to Industrial Application (eds A. F. Collings and C. Critchley), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527606742.ch14

Editor Information

  1. 2

    CSIRO Industrial Physics, PO Box 218, Lindfield, NSW 2070, Australia

  2. 3

    School of Integrative Biology, The University of Queensland, Brisbane, QLD 4072, Australia

Author Information

  1. Australian National University, John Curtin School of Medical Research, PO Box 334, Canberra, ACT 2601, Australia

Publication History

  1. Published Online: 9 MAY 2006
  2. Published Print: 5 AUG 2005

ISBN Information

Print ISBN: 9783527310906

Online ISBN: 9783527606740

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Keywords:

  • inefficiencies in the chemical mechanism of the photosynthetic enzyme rubisco;
  • computational simulation;
  • catalytic inefficiencies;
  • enzyme models;
  • active-site fragment complexes

Summary

This chapter contains sections titled:

  • Introduction

    • Catalytic Inefficiencies

    • Evolutionary Constraints?

    • Experimental Limitations

    • Goals of Simulations

    • Simulation Options

  • Computational Methods

    • Computational Programs

    • Enzyme Models

    • Active-site Fragment Complexes

    • QM/MM Simulations

  • Results and Discussion

    • Fragment-complex Calculations

      • Enolization Step

      • Carboxylation Step

      • Hydration Step

      • Sequential Addition of CO2 and H2O

      • Alternative Conformations of the Gem-diol

      • C2-C3 Bond Cleavage: Pathway I

      • C2-C3 Bond Cleavage: Pathway II

      • Protonation of C2

      • Dissociation of Products

    • Summary of Main Findings

    • QM/MM+MD Calculations

      • CO2 Addition: Early vs. Late Protonation of the Carboxylate

      • Hydration of the β-Keto Acid

      • His294 Protects Intermediates from Decarboxylation

      • The Tightly Coupled Active-site Environment

  • Conclusions

  • References