Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

Jilai Li; Maryam Farrokhnia; Lubomír Rulíšek; Ulf Ryde

doi:10.1021/acs.jpcb.5b02864

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.5b02864 ◽

2015 ◽

Vol 119 (26) ◽

pp. 8268-8284 ◽

Cited By ~ 17

Author(s):

Jilai Li ◽

Maryam Farrokhnia ◽

Lubomír Rulíšek ◽

Ulf Ryde

Keyword(s):

Free Energy ◽

Perturbation Methods ◽

Catalytic Cycle ◽

Free Energy Perturbation ◽

Multicopper Oxidases ◽

Energy Perturbation

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A theoretical examination of solvatochromism and solute-solvent structuring in simple alkyl carbonyl compounds. Simulations using statistical mechanical free energy perturbation methods

Journal of the American Chemical Society ◽

10.1021/ja00177a010 ◽

1990 ◽

Vol 112 (21) ◽

pp. 7515-7524 ◽

Cited By ~ 75

Author(s):

Stephen E. DeBolt ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Carbonyl Compounds ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Theoretical Examination ◽

Statistical Mechanical ◽

Energy Perturbation

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A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy-perturbation methods

Journal of the American Chemical Society ◽

10.1021/ja00255a010 ◽

1987 ◽

Vol 109 (21) ◽

pp. 6283-6289 ◽

Cited By ~ 109

Author(s):

Piotr Cieplak ◽

Paul Bash ◽

U. Chandra Singh ◽

Peter A. Kollman

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Quantum Mechanics ◽

Gas Phase ◽

Perturbation Methods ◽

Theoretical Study ◽

State Of The Art ◽

Free Energy Perturbation ◽

Combined Use ◽

Energy Perturbation

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems ii: Co and dioxygen binding to myoglobin

Protein Science ◽

10.1002/pro.5560021119 ◽

1993 ◽

Vol 2 (11) ◽

pp. 1975-1986 ◽

Cited By ~ 18

Author(s):

Marco A. Lopez ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. I. Carbon monoxide and dioxygen binding to four heme systems

Journal of the American Chemical Society ◽

10.1021/ja00198a036 ◽

1989 ◽

Vol 111 (16) ◽

pp. 6212-6222 ◽

Cited By ~ 19

Author(s):

Marco A. Lopez ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Carbon Monoxide ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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Mayer Sampling: Calculation of Cluster Integrals using Free-Energy Perturbation Methods

Physical Review Letters ◽

10.1103/physrevlett.92.220601 ◽

2004 ◽

Vol 92 (22) ◽

Cited By ~ 120

Author(s):

Jayant K. Singh ◽

David A. Kofke

Keyword(s):

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Cluster Integrals ◽

Energy Perturbation

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Application of the quantum mechanics and free energy perturbation methods to study molecular processes

International Journal of Quantum Chemistry ◽

10.1002/qua.560320811 ◽

1987 ◽

Vol 32 (S14) ◽

pp. 65-74 ◽

Cited By ~ 11

Author(s):

Piotr Cieplak ◽

U. Chandra Singh ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Molecular Processes ◽

Energy Perturbation

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Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods

Reviews in Computational Chemistry ◽

10.1002/9780470125786.ch8 ◽

2007 ◽

pp. 295-320 ◽

Cited By ~ 19

Author(s):

Terry P. Lybrand

Keyword(s):

Molecular Dynamics ◽

Computer Simulation ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Biomolecular Systems ◽

Energy Perturbation

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Free-Energy Perturbation Methods to Study Structure and Energetics of DNA Adducts: Results for the Major N2-dG Adduct of Benzo[a]pyrene in Two Conformations and Different Sequence Contexts

Chemical Research in Toxicology ◽

10.1021/tx049646l ◽

2005 ◽

Vol 18 (7) ◽

pp. 1108-1123 ◽

Cited By ~ 6

Author(s):

Sushil Chandani ◽

Chiu Hong Lee ◽

Edward L. Loechler

Keyword(s):

Free Energy ◽

Dna Adducts ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(19980901)32:4<438::aid-prot4>3.0.co;2-c ◽

1998 ◽

Vol 32 (4) ◽

pp. 438-458 ◽

Cited By ~ 17

Author(s):

Lu Wang ◽

David L. Veenstra ◽

Randall J. Radmer ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Protein Stability ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

T4 Lysozyme ◽

Energy Derivatives ◽

Energy Perturbation ◽

Do So

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Studies on the binding of pepstatin and its derivatives to Rhizopus pepsin by quantum mechanics, molecular mechanics, and free energy perturbation methods

Journal of the American Chemical Society ◽

10.1021/ja00018a004 ◽

1991 ◽

Vol 113 (18) ◽

pp. 6735-6750 ◽

Cited By ~ 11

Author(s):

B. G. Rao ◽

U. Chandra Singh

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Molecular Mechanics ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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