The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach

Giuliano Alagona; Caterina Ghio; Peter A. Kollman

doi:10.1002/jcc.10153

The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach

Journal of Computational Chemistry ◽

10.1002/jcc.10153 ◽

2002 ◽

Vol 24 (1) ◽

pp. 46-56 ◽

Cited By ~ 10

Author(s):

Giuliano Alagona ◽

Caterina Ghio ◽

Peter A. Kollman

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Intramolecular Mechanism

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Slow proton transfer from the hydrogen-labelled carboxylic acid side chain (Glu-165) of triosephosphate isomerase to imidazole buffer in D2O

Organic & Biomolecular Chemistry ◽

10.1039/b714304d ◽

2008 ◽

Vol 6 (2) ◽

pp. 391-396 ◽

Cited By ~ 9

Author(s):

AnnMarie C. O'Donoghue ◽

Tina L. Amyes ◽

John P. Richard

Keyword(s):

Carboxylic Acid ◽

Proton Transfer ◽

Triosephosphate Isomerase ◽

Side Chain

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Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: Proton transfer in triosephosphate isomerase

The Journal of Chemical Physics ◽

10.1063/1.2181145 ◽

2006 ◽

Vol 124 (12) ◽

pp. 124516 ◽

Cited By ~ 40

Author(s):

Mingliang Wang ◽

Zhenyu Lu ◽

Weitao Yang

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Reaction Path ◽

Quantum Effects ◽

Nuclear Quantum Effects

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A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM)

The Journal of Chemical Physics ◽

10.1063/1.472889 ◽

1996 ◽

Vol 105 (24) ◽

pp. 10812-10818 ◽

Cited By ~ 28

Author(s):

Eyal Neria ◽

Martin Karplus

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Friction Model ◽

Friction Regime

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Atomic resolution crystallography of a complex of triosephosphate isomerase with a reaction-intermediate analog: New insight in the proton transfer reaction mechanism

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.22701 ◽

2010 ◽

Vol 78 (8) ◽

pp. 1878-1888 ◽

Cited By ~ 14

Author(s):

Markus Alahuhta ◽

Rik K. Wierenga

Keyword(s):

Reaction Mechanism ◽

Proton Transfer ◽

Transfer Reaction ◽

Triosephosphate Isomerase ◽

Proton Transfer Reaction ◽

Atomic Resolution ◽

Reaction Intermediate

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Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

The Journal of Chemical Physics ◽

10.1063/1.1757437 ◽

2004 ◽

Vol 121 (1) ◽

pp. 101 ◽

Cited By ~ 13

Author(s):

Mingliang Wang ◽

Zhenyu Lu ◽

Weitao Yang

Keyword(s):

Proton Transfer ◽

Transmission Coefficient ◽

Triosephosphate Isomerase ◽

Reaction Path ◽

Potential Method

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A Paradigm for Enzyme-Catalyzed Proton Transfer at Carbon: Triosephosphate Isomerase

Biochemistry ◽

10.1021/bi300195b ◽

2012 ◽

Vol 51 (13) ◽

pp. 2652-2661 ◽

Cited By ~ 56

Author(s):

John P. Richard

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase

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Energetics of triosephosphate isomerase: the nature of the proton transfer between the catalytic base and solvent water

Biochemistry ◽

10.1021/bi00670a030 ◽

1976 ◽

Vol 15 (25) ◽

pp. 5621-5626 ◽

Cited By ~ 18

Author(s):

L. Mark Fisher ◽

W. John Albery ◽

Jeremy R. Knowles

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Solvent Water

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Enzymatic Catalysis of Proton Transfer at Carbon: Activation of Triosephosphate Isomerase by Phosphite Dianion†

Biochemistry ◽

10.1021/bi700409b ◽

2007 ◽

Vol 46 (19) ◽

pp. 5841-5854 ◽

Cited By ~ 61

Author(s):

Tina L. Amyes ◽

John P. Richard

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Enzymatic Catalysis

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Is the bias introduced in a FEP calculation by parameterizing a QM reaction acceptable? Comparison with Car–Parrinello MD/AMBER results for the second proton transfer in triosephosphate isomerase (TIM)

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2005.03.046 ◽

2005 ◽

Vol 729 (1-2) ◽

pp. 131-139 ◽

Cited By ~ 2

Author(s):

Giuliano Alagona ◽

Silvio Campanile ◽

Caterina Ghio ◽

Dafne Molin

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase

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Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0233793100 ◽

2002 ◽

Vol 100 (1) ◽

pp. 50-55 ◽

Cited By ~ 89

Author(s):

G. Jogl ◽

S. Rozovsky ◽

A. E. McDermott ◽

L. Tong

Keyword(s):

Proton Transfer ◽

Triosephosphate Isomerase ◽

Optimal Alignment ◽

Transfer Structure

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