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The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants

Frontiers in plant science, 2021-09, Vol.12, p.662425-662425

Cummins, Peter L.

2021

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Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Frontiers in plant science, 2018-03, Vol.9, p.183-183

2018

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Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Frontiers in plant science, 2019-11, Vol.10, p.1426-1426

2019

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Kohn–Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

The journal of physical chemistry. B, 2020-04, Vol.124 (15), p.3015-3026

2020

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Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Journal of computational chemistry, 2018-08, Vol.39 (21), p.1656-1665

2018

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Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism

The journal of physical chemistry. B, 2019-03, Vol.123 (12), p.2679-2686

2019

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Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn–Sham Density Functional Calculations

The journal of physical chemistry. B, 2019-04, Vol.123 (13), p.2833-2843

2019

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Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

Biophysical journal, 2004-04, Vol.86 (4), p.2467-2483

2004

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Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues

The journal of physical chemistry. B, 2009-11, Vol.113 (44), p.14787-14796

2009

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Energetically Most Likely Substrate and Active-Site Protonation Sites and Pathways in the Catalytic Mechanism of Dihydrofolate Reductase

Journal of the American Chemical Society, 2001-04, Vol.123 (15), p.3418-3428

2001

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Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

Journal of chemical theory and computation, 2007-05, Vol.3 (3), p.1203-1211

2007

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Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation

Journal of computational chemistry, 2005-04, Vol.26 (6), p.561-568

2005

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QM/MM and SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond

Journal of molecular graphics & modelling, 2000-02, Vol.18 (1), p.42-49

2000

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Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase

The journal of physical chemistry. B, 2002-09, Vol.106 (38), p.9934-9944

2002

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Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase

The journal of physical chemistry. B, 2000-05, Vol.104 (18), p.4503-4510

2000

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Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

Journal of computational chemistry, 2002-11, Vol.23 (14), p.1314-1322

2002

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Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase

Journal of computer-aided molecular design, 2005-03, Vol.19 (3), p.165-187

2005

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Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions

Chemical physics letters, 2000-03, Vol.320 (1), p.169-176

2000

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Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules

Chemical physics letters, 2002-01, Vol.352 (3), p.245-251

2002

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Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase

Journal of the American Chemical Society, 1991-10, Vol.113 (22), p.8247-8256

1991

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Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

Journal of computational chemistry, 1999-07, Vol.20 (10), p.1028-1038

1999

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Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

Journal of computational chemistry, 1997-09, Vol.18 (12), p.1496-1512

1997

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Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

Journal of computational chemistry, 1998-06, Vol.19 (8), p.977-988

1998

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Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase

Journal of computational chemistry, 1996-11, Vol.17 (14), p.1598-1611

1996

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Prediction of Relative Binding Constants of Cofactors and Designed Ligands to Dihydrofolate Reductase by Computer Simulation

Pteridines, 1991-02, Vol.3 (1-2), p.137-139

1991

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The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants

Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

Kohn–Sham Density Functional Calculations Reveal Proton Wires in the Enolization and Carboxylase Reactions Catalyzed by Rubisco

Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism

Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn–Sham Density Functional Calculations

Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues

Energetically Most Likely Substrate and Active-Site Protonation Sites and Pathways in the Catalytic Mechanism of Dihydrofolate Reductase

Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation

QM/MM and SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond

Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase

Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions

Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules

Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase

Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase

Prediction of Relative Binding Constants of Cofactors and Designed Ligands to Dihydrofolate Reductase by Computer Simulation

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