Barrier passage and protein dynamics in enzymatically catalyzed reactions

European Journal of Biochemistry

Volumn 269, Issue 13, 2002, Pages 3103-3112

  Antoniou, Dimitri ^a   Caratzoulas, Stavros ^a,c   Kalyanaraman, C ^a   Mincer, Joshuas S ^a   Schwartz, Steven D ^a,b  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b Princeton University ^*  (United States)

^c Princeton University   (United States)

Author keywords

Enzyme catalysis; Promoting mode; Promoting vibration; Protein dynamics; Tunneling

Indexed keywords

ALCOHOL DEHYDROGENASE; ENZYME; PROTEIN;

CATALYSIS; CHEMICAL REACTION; ENZYME ACTIVITY; LABORATORY; MATHEMATICAL ANALYSIS; MOTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; SHORT SURVEY; VIBRATION;

CATALYSIS; ENZYMES; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEIN FOLDING; VIBRATION;

EID: 0036305753     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.03021.x     Document Type: Short Survey

References (67)

1. Chemical basis for enzyme catalysis
2. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites
3. The low barrier hydrogen bond in enzymatic catalysis
4. Nature of forces between large molecules of biological interest
5. Enzymatic transition state analysis and transition-state analogues
6. Binding energy, specificity and enzymatic catalysis, the circle effect
7. Electrostatic stress in catalysis, structure and mechanism of the enzyme orotidine monophosphate decarboxylase
8. Energetics of enzyme catalysis
9. Solvation, reorganization energy and biological catalysis
10. The mechanism of phosphodiester hydrolysis: Near in-line attack conformations in the hammerhead ribozyme
11. Chemical and electrochemical electron transfer theory
12. Dynamics of hydrogen atom and proton transfer reactions: Symmetric case
13. The importance of correlated motions in forming highly reactive near attack conformations in catechol O-methyltransferase
14. + in the active site of formate dehydrogenase
15. Computational characterization of substrate binding and catalysis in, S-adenosylhomocysteine hydrolase
16. A molecular dynamics quantum kramers study of proton transfer in solution
17. Quantum proton transfer with spatially dependent friction: Phenol-amine in methyl chloride
18. Molecular dynamics study of an isomerizing diatomic in a lennard-jones fluid
19. Nonequilibrium solvation effects on reaction rates for model SN2 reactions in water
20. On the generalized langevin equation: Classical and quantum mechanical
21. The nonlinear generalized langevin equation
22. Accurate quantum mechanics from high order resumed operator expansions
23. Vibrational energy transfer from resumed evolution operators
24. Vibrational energy transfer in linear hydrocarbon chains: New quantum results
25. The interaction representation and non-adiabatic corrections to adiabatic evolution operators
26. Nonadiabatic effects in a method that combines classical and quantum mechanics
27. The interaction representation and non-adiabatic corrections to adiabatic evolution operators II: Nonlinear quantum systems
28. Nonequilibrium solvation, and the quantum kramers problem: Proton transfer in aqueous glycine
29. Curve crossing formulation for proton transfer reactions in solution
30. Large kinetic isotope effects in enzymatic proton transfer, and the role of substrate oscillations
31. Dynamics of double proton transfer reactions in the excited state model of hydrogen bonded base pairs
32. The correlation between hydrogen bond tunneling dynamics, and the structure of benzoic acid dimers
33. Structure, and dynamics of intramolecular hydrogen bonds in carboxylic acid dimers: A solid state NMR study
34. Hydrogen bond dynamics in isotopically substituted benzoic acid dimers
35. Proton tunneling in benzoic acid crystals at intermediate temperatures: Nuclear magnetic resonance and neutron scattering studies
36. Activated chemistry in the presence of a strongly symmetrically coupled vibration
37. Proton transfer in benzoic acid crystals: Another look using quantum operator theory
38. Tunneling splittings in model, 2D potentials I
39. Tunneling splittings in model, 2D potentials III. Generalization to N dimensional case
40. Low-temperature chemical reactions. Effect of symmetrically coupled vibrations in collinear exchange reactions
41. Reaction coordinate tunneling in hydride-transfer reactions
42. Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase
43. Enzyme dynamics and hydrogen tunneling in a thermophilic alcohol dehydrogenase
44. Hydrogen tunneling in enzyme reactions
45. Evidence that both protium and deuterium undergo significant tunneling in the reaction catalyzed by bovine serum amine oxidase
46. Enzyme catalysis: Beyond classical paradigms
47. Hydrogen tunneling in enzyme catalysis
48. Role of internal thermodynamics in determining hydrogen tunneling in enzyme-catalyzed hydrogen transfer reactions
49. Protein flexibility correlates with degree of hydrogen tunneling in thermophilic, and mesophilic alcohol dehydrogenases
50. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins
51. A link between protein structure, A. and enzyme catalyzed hydrogen tunneling
52. Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis
53. 2OH on the distance between reactants when catalyzed by horse liver alcohol dehydrogenase and 203 single point mutants
54. Probes of Hydrogen tunneling with horse liver alcohol dehydrogenase at subzero temperatures
55. Importance of barrier shape in enzyme catalyzed reactions
56. Enzymatic H-transfer requires vibration driven extreme tunneling
57. Internal enzyme motions as a source of catalytic activity: Rate promoting vibrations and hydrogen tunneling
58. Three pulse stimulated photon echo experiments as a probe of polar solvation dynamics: Utility of harmonic bath modes
59. A computational method to discover the existence of promoting vibrations for chemical reactions in condensed phases
60. Identification of a protein promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase
61. + and substituted benzyl alcohols
62. CHARMM, a program for macromolecular energy, minimization, dynamics calculations
63. Comparison of simple potential functions for simulating liquid water
64. A molecular mechanics force field for NAD+ NADH and the pyrophosphate groups of nucleotides