Studies of ligand diffusion pathways over a protein surface

Journal of Chemical Information and Computer Sciences

Volumn 43, Issue 1, 2003, Pages 255-258

  Kier, Lemont B ^a   Cheng, Cho Kung ^b   Testa, Bernard ^c  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b Virginia Commonwealth University   (United States)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; DIFFUSION; ISOMERS; SURFACES;

LIGAND DIFFUSION PATHWAYS; PROTEIN SURFACE; SOLUTE;

PROTEINS;

AMINO ACID; ANESTHETIC AGENT; LIGAND; PROTEIN; WATER;

ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; DIFFUSION; SURFACE PROPERTY;

AMINO ACIDS; ANESTHETICS; BINDING SITES; COMPUTER SIMULATION; DIFFUSION; LIGANDS; MODELS, CHEMICAL; PROTEINS; SURFACE PROPERTIES; WATER;

EID: 0037208310     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci020383f     Document Type: Article

References (21)

1. Adam, G.; Delbruk, M. Reduction of Dimensionality in Biological Diffusion Processes. In Structural Chemistry and Molecular Biology; Rich, A., Davidson, N., Eds.; Freeman: San Francisco, 1968; pp 198-215.
2. Eigen, M.; Diffusion Control in Biochemical Reactions. In Quantum Statistical Mechanics in the Natural Sciences: Mintz, S. L., Widemeyer, S. M. Eds.; Plenum Press: New York, 1974; pp 37-61.
3. Welch, G. R. On the Free Energy Cost of Transition in Intermediary Metabolic Processes and the Evolution of Cellular Infrastructures. J. Theor. Biol. 1977, 68, 267-279.
4. Chou, K.-C.; Zhou, G.-P. Role of the Protein Outside Active Site on the Diffusion-Controlled Reaction of Enzymes. J. Am. Chem. Soc. 1982, 104 4, 1409-1413.
5. Hasinoff, B. B. Kinetics of Acetylthiocholine Binding to Electric Eel Acetylcholine Esterase in Glycerol/Water Solvents of Increased Viscosity. Biochim. Biophys. Acta 1982, 704, 52-58.
6. Birch, G. C.; Latymer, Z. Intensity/Time Relationships in Sweetness: Evidence for a Queue Hypothesis in Taste Chemoreception. Chem. Senses 1980, 5, 63-78.
7. Kier, L. B.; Cheng, C.-K.; Testa, B. A Cellular Automata Model of Ligand Passage Over a Protein Hydrodynamic Landscape. J. Theor. Biol. 2002, 215, 415-426.
8. Knapp, E. W.; Muegge, I. Heterogeneous Diffusion of Water at Protein Surfaces: Application to BPTI. J. Phys. Chem. 1993, 97, 11339-11343.
9. Muegge, I.; Knapp, E. W. Residence Times and Lateral Diffusion of Water at Protein Surfaces: Application to BPTI. J. Phys. Chem. 1995, 99, 1371-1374.
10. Radic, Z.; Kirchoff, P. D.; Quinn, D. M.; McCammon, J. A.; Taylor, P.; Electro-static Influence on Kinetics of Ligand Binding to Acetylcholinesterase. J. Biol. Chem. 1997, 272, 23625-23277.
11. Brunori, M.; Cutruzzola, F.; Savino, C.; Travaglini-Allocatelli, C.; Vallone, B.; Gibson, Q. H. Structural Dynamics of Ligand Diffusion in the Protein Matrix: A Study on a New Myoglobin Mutant Y (B10)Q(E7)R(E10). Biophys. J. 1999, 76, 1259-1269.
12. Boyd, A.; Marnett, A. B.; Wong, L.; Taylor, P. Probing the Active Center Gorge of Acetylcholinesterase by Florophores Linked to Substituted Cysteines. J. Biol. Chem. 2000, 275, 22401-22408.
13. Kier, L. B.; Cheng, C.-K.; Testa, B. Cellular automata models of biochemical phenomena. Fut. Gen. Of Comp. Sys. 1999, 16, 273-289.
14. Kier, L. B.; Cheng, C.-K.; Seybold, P. G. Cellular automata models of chemical systems, SAR QSAR 2000, 11, 79-102.
15. Kier, L. B.; Cheng, C.-K.; Seybold, P. G. Cellular automata models of aqueous solution phenomena. Rev. Comp. Chem. 2001, 17, 205-254.
16. Von Neumann, J. In Theory of Self-Reproducing Automata; Burks, A., Ed.; University of Illinois Press: Urbana, IL, 1966.
17. Ermentrout, F. B.; Edelstein-Keshet, L.; Cellular Automata Approaches to Biological Modeling. J. Theor. Biol. 1993, 160, 97-133.
18. Chopard, B.; Droz, M. Cellular Automata Modeling of Physical Systems; Cambridge University Press: Cambridge, England. 1998.
19. Fidler, J.; Rodger, P. M.; Roger, A. Chiral Solvent Structure around Chiral Molecules: Experimental and Theoretical Studies. J. Am. Chem. Soc. 1994, 116, 7266-7273.
20. Testa, B.; Kier, L. B.; Cheng, C.-K. A Cellular Automata Model of Water Structuring by a Chiral Solute. J. Chem. Inf. Comput. Sci. 2002, 42, 712-716.
21. Zhang, X.; Zhu, Y.; Granick, S.; Hydrophobicity at a Janus Interface. Science 2002, 295, 663-666.