Channeling by proximity: The catalytic advantages of active site colocalization using brownian dynamics

Journal of Physical Chemistry Letters

Volumn 1, Issue 9, 2010, Pages 1332-1335

  Bauler, Patricia ^a,b   Huber, Gary ^a,b   Leyh, Thomas ^c   McCammon, J Andrew ^a,b  

^a Department of Chemistry and Biochemistry ^*  (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Biophysical Chemistry

Indexed keywords

ACTIVE SITE; BIOPHYSICAL CHEMISTRY; BROWNIAN DYNAMICS; CATALYTIC EFFICIENCIES; COLOCALIZATION; EFFECTIVE CONCENTRATION; METABOLIC PATHWAYS; REACTION PATHWAYS; SUBSTRATE PARTICLES; TWO-STEP REACTIONS;

BROWNIAN MOVEMENT;

ENZYMES;

EID: 77952050895     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz1002007     Document Type: Article

References (19)

1. Charles, I. G.; Keyte, J. W.; Brammar, W. J.; Smith, M.; Hawkins, A. R. The Isolation and Nucleotide Sequence of the Complex AROM Locus of Aspergillus nidulans Nucleic Acids Res. 1986, 14, 2201-2213
2. Dunn, M. F.; Niks, D.; Ngo, H.; Barends, T. R. M.; Schlichting, I. Tryptophan Synthase: The Workings of a Channeling Nanomachine Trends Biochem. Sci. 2008, 33, 254-264
3. Sun, M.; Andreassi, J. L., II; Liu, S.; Pinto, R.; Triccas, J. A.; Leyh, T. S. The Trifunctional Sulfate-Activating Complex (SAC) of Mycobacterium tuberculosis J. Biol. Chem. 2005, 280, 7861-7866
4. Schmeing, T. M.; Ramakrishnan, V. What Recent Ribosome Structures Have Revealed about the Mechanism of Translation Nature 2009, 461, 1234-1242
5. Leibundgut, M.; Maier, T.; Jenni, S.; Ban, N. The Multienzyme Architecture of Eukaryotic Fatty Acid Synthases Curr. Opin. Struct. Biol. 2008, 18, 714-725
6. Jorgensen, K.; Rasmussen, A. V.; Morant, M.; Nielsen, A. H.; Bjarnholt, N.; Zagrobelny, M.; Bak, S.; Moller, B. L. Metabolon Formation and Metabolic Channeling in the Biosynthesis of Plant Natural Products Curr. Opin. Plant Biol. 2005, 8, 280-291
7. Shaw-Reid, C. A.; Kelleher, N. L.; Losey, H. C.; Gehring, A. M.; Berg, C.; Walsh, C. T. Assembly Line Enzymology by Multimodular Nonribosomal Peptide Synthetases: The Thioesterase Domain of E. coli EntF Catalyzes Both Elongation and Cyclolactonization Chem. Biol. 1999, 6, 385-400
8. Miles, E. W.; Rhee, S.; Davies, D. R. The Molecular Basis of Substrate Channeling J. Biol. Chem. 1999, 274, 12193-12196
9. Elcock, A. H.; Potter, M. J.; Matthews, D. A.; Knighton, D. R.; McCammon, J. A. Electrostatic Channeling in the Bifunctional Enzyme Dihydrofolate Reductase-Thymidylate Synthase J. Mol. Biol. 1996, 262, 370-374
10. Elcock, A. H.; McCammon, J. A. Evidence for Electrostatic Channeling in a Fusion Protein of Malate Dehydrogenase and Citrate Synthase Biochemistry 1996, 35, 12652-12658
11. Elcock, A. H.; Huber, G. A.; McCammon, J. A. Electrostatic Channeling of Substrates between Enzyme Active Sites: Comparison of Simulation and Experiment Biochemistry 1997, 36, 16049-16058
12. Cheng, Y.; Chang, C. A.; Yu, Z.; Zhang, Y.; Sun, M.; Leyh, T. S.; Holst, M. J.; McCammon, J. A. Diffusional Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-Grained Brownian Dynamics Studies Biophys. J. 2008, 95, 4659-4667
13. Conrado, R. J.; Varner, J. D.; DeLisa, M. P. Engineering the Spatial Organization of Metabolic Enzymes: Mimicking Nature's Synergy Curr. Opin. Biotechnol. 2008, 19, 492-499
14. Erban, R.; Chapman, S. J. Stochastic Modeling of Reaction-Diffusion Processes: Algorithms for Bimolecular Reactions Phys. Biol. 2009, 6, 46001
15. Ermak, D. L.; McCammon, J. A. Brownian Dynamics with Hydrodynamic Interactions J. Chem. Phys. 1978, 69, 1352-1360
16. Northrup, S. H.; Allison, S. A.; McCammon, J. A. Brownian Dynamics Simulation of Diffusion-Influenced Bimolecular Reactions J. Chem. Phys. 1984, 80, 1517-1524
17. Zhou, H.-X. On the Calculation of Diffusive Reaction Rates Using Brownian Dynamics Simulations J. Chem. Phys. 1990, 92, 3092-3095
18. Luty, B. A.; McCammon, J. A.; Zhou, H.-X. Diffusive Reaction Rates from Brownian Dynamics Simulations: Replacing the Outer Cutoff Surface by an Analytical Treatment J. Chem. Phys. 1992, 97, 5682-5686
19. Huber, G. A. BrownDye: Brownian Dynamics of Biological Molecules. http://browndye.ucsd.edu/ (accessed March 18, 2010).