Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, III: Molecular dynamics simulation incorporating a cyanophenylalanine spectroscopic probe

Biophysical Journal

Volumn 96, Issue 10, 2009, Pages 4188-4199

  Zou, Hongling ^a   Liu, Jing ^a   Blasie, J Kent ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYANOPHENYLALANINE; FLUORINE DERIVATIVE; HALOTHANE; HYDROGEN; ION CHANNEL; MEMBRANE PROTEIN; NITRILE; PHENYLALANINE DERIVATIVE; UNCLASSIFIED DRUG; ALANINE; ANESTHETIC AGENT; DRUG DERIVATIVE; FLUORESCENT DYE; P CYANOPHENYLALANINE; P-CYANOPHENYLALANINE;

ANALYSIS; ARTICLE; ATOM; DECOMPOSITION; ELECTRICITY; ENVIRONMENT; EXPERIMENTAL STUDY; FORCE; INFRARED RADIATION; INTROSPECTION; MODEL; MOLECULAR DYNAMICS; MOTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; SPECTROSCOPY; VIBRATION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; INFRARED SPECTROPHOTOMETRY; METABOLISM; MOVEMENT (PHYSIOLOGY); MUTATION; PROTEIN BINDING;

ALANINE; ANESTHETICS, GENERAL; FLUORESCENT DYES; HALOTHANE; HYDROGEN; ION CHANNELS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOVEMENT; MUTATION; NITRILES; PROTEIN BINDING; SPECTROPHOTOMETRY, INFRARED; VIBRATION;

EID: 68049133058     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.01.054     Document Type: Article

References (33)

1. Johansson, J. S. 2003. Noninactivating tandem pore domain potassium channels as attractive targets for general anesthetics. Anesth. Analg. 96:1248-1250.
2. Chiara, D. C., L. J. Dangott, R. G. Eckenhoff, and J. B.Cohen. 2003. Identification of nicotinic acetylcholine receptor amino acids photolabeled by the volatile anesthetic halothane. Biochemistry. 42:13457-13467.
3. Ye, S. X., J. Strzalka, I. Y. Churbanova, S. Y. Zheng, J. S. Johansson, et al. 2004. A model membrane protein for binding volatile anesthetics. Biophys. J. 87:4065-4074.
4. Churbanova, I. Y., A. Tronin, J. Strzalka, T. Gog, I. Kuzmenko, et al. 2006. Monolayers of a model anesthetic-binding membrane protein: Formation, characterization, and halothane-binding affinity. Biophys. J. 90:3255-3266.
5. Strzalka, J., J. Liu, A. Tronin, J. S. Johansson, and J. K. Blasie. 2009. Mechanism of interaction between the general anesthetic halothane and a synthetic protein model ion channel, I: structural investigations via x-ray reflectivity from Langmuir monolayers. Biophys. J. 96:4164-4175.
6. Johansson, J. S., B. R. Gibney, F. Rabanal, K. S. Reddy, and P. L. Dutton. 1998. A designed cavity in the hydrophobic core of a four-alpha-helix bundle improves volatile anesthetic binding affinity. Biochemistry. 37:1421-1429.
7. Katz, B. A., B. S. Liu, and R. Cass. 1996. Structure-based design tools: structural and thermodynamic comparison with biotin of a small molecule that binds to streptavidin with micromolar affinity. J. Am. Chem. Soc. 118:7914-7920.
8. Getahun, Z., C. Y. Huang, T. Wang, B. De Leon, W. F. DeGrado, et al. 2003. Using nitrile-derivatized amino acids as infrared probes of local environment. J. Am. Chem. Soc. 125:405-411.
9. Yoshikawa, S., D. H. Okeeffe, and W. S. Caughey. 1985. Investigations of cyanide as an infrared probe of hemeprotein ligand-binding sites. J. Biol. Chem. 260:3518-3528.
10. Liu, J., J. Strzalka, A. Tronin, J. S. Johansson, and J. K. Blasie. 2009. Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, II: fluorescence and vibrational spectroscopy using a cyanophenylalanine probe. Biophys. J. 96:4176-4187.
11. Tuckerman, M. E., and G. J. Martyna. 2000. Understanding modern molecular dynamics: techniques and applications. J. Phys. Chem. B. 104:159-178.
12. Hansson, T., C. Oostenbrink, and W. F. van Gunsteren. 2002. Molecular dynamics simulations. Curr. Opin. Struct. Biol. 12:190-196.
13. Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure. 12:1343-1351.
14. Adcock, S. A., and J. A. McCammon. 2006. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106:1589-1615.
15. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, et al. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
16. MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
17. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
18. Yin, D. 1997. Parameterization for empirical force field calculations and a theoretical study of membrane permeability of pyridine derivative. PhD thesis. Department of Pharmaceutical Sciences. University of Maryland, College Park, MD.
19. Liu, Z. W., Y. Xu, A. C. Saladino, T. Wymore, and P. Tang. 2004. Parametrization of 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) and hexafluoroethane for nonbonded interactions. J. Phys. Chem. A. 108:781-786.
20. Zou, H. L., J. Strzalka, T. Xu, A. Tronin, and J. K. Blasie. 2007. Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations. J. Phys. Chem. B. 111:1823-1833.
21. Rey, R., and J. T. Hynes. 1998. Vibrational phase and energy relaxation of CN- in water. J. Chem. Phys. 108:142-153.
22. Hutchinson, E. J., and D. Ben-Amotz. 1998. Molecular force measurement in liquids and solids using vibrational spectroscopy. J. Phys. Chem. B. 102:3354-3362.
23. Suydam, I. T., C. D. Snow, V. S. Pande, and S. G. Boxer. 2006. Electric fields at the active site of an enzyme: Direct comparison of experiment with theory. Science. 313:200-204.
24. Andrews, S. S., and S. G. Boxer. 2002. Vibrational Stark effects of nitriles II. Physical origins of stark effects from experiment and perturbation models. J. Phys. Chem. A. 106:469-477.
25. Andrews, S. S., and S. G. Boxer. 2000. Vibrational stark effects of nitriles I. Methods and experimental results. J. Phys. Chem. A. 104:11853-11863.
26. Mukherjee, S., P. Chowdhury, W. F. DeGrado, and F. Gai. 2007. Site-specific hydration status of an amphipathic peptide in AOT reverse micelles. Langmuir. 23:11174-11179.
27. Zou, H. L., M. J. Therien, and J. K. Blasie. 2008. Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation. J. Phys. Chem. B. 112:1350-1357.
28. Dipaolo, T., and C. Sandorfy. 1974. Hydrogen-bond breaking potency of fluorocarbon anesthetics. J. Med. Chem. 17:809-814.
29. Tang, P., and Y. Xu. 2002. Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: The implication of molecular mechanisms of general anesthesia. Proc. Natl. Acad. Sci. USA. 99:16035-16040.
30. Davies, L. A., M. L. Klein, and D. Scharf. 1999. Molecular dynamics simulation of a synthetic four-alpha-helix bundle that binds the anesthetic halothane. FEBS Lett. 455:332-338.
31. Cui, T. X., V. Bondarenko, D. J. Ma, C. Canlas, N. R. Brandon, et al. 2008. Four-alpha-helix bundle with designed anesthetic binding pockets. Part II: halothane effects on structure and dynamics. Biophys. J. 94:4464-4472.
32. Domene, C., S. Vemparala, S. Furini, K. Sharp, and M. L. Klein. 2008. The role of conformation in ion permeation in a K+ channel. J. Am. Chem. Soc. 130:3389-3398.
33. Ma, D. J., N. R. Brandon, T. X. Cui, V. Bondarenko, C. Canlas, et al. 2008. Four-alpha-helix bundle with designed anesthetic binding pockets; Part I: structural and dynamical analyses. Biophys. J. 94:4454-4463.