Molecular dynamics simulation of WSK-3, a computationally designed, water-soluble variant of the integral membrane protein KcsA

Biophysical Journal

Volumn 90, Issue 4, 2006, Pages 1156-1163

  Bronson, Jonathan ^a   Lee, One Sun ^a   Saven, Jeffery G ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRAL MEMBRANE PROTEIN KCSA; MEMBRANE PROTEIN; UNCLASSIFIED DRUG; WATER; BACTERIAL PROTEIN; POTASSIUM CHANNEL; PROKARYOTIC POTASSIUM CHANNEL;

ANALYTIC METHOD; ARTICLE; HYDROPHILICITY; MATHEMATICAL COMPUTING; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR STABILITY; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTEIN VARIANT; SIMULATION; SOLUBILITY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; LIPID BILAYER; PROTEIN BINDING; PROTEIN CONFORMATION; STREPTOMYCES LIVIDANS;

BACTERIAL PROTEINS; COMPUTER SIMULATION; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; POTASSIUM CHANNELS; PROTEIN BINDING; PROTEIN CONFORMATION; STREPTOMYCES LIVIDANS; WATER;

EID: 33645778590     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.068965     Document Type: Article

References (38)

1. Drews, J. 2000. Drug discovery: a historical perspective. Science. 287:1960-1964.
2. MacKinnon, R. 2004. Potassium channels and the atomic basis of selective ion conduction (Nobel lecture). Angew. Chem. Int. Ed. Engl. 43:4265-4277.
3. Slovic, A. M., C. M. Summa, J. D. Lear, and W. F. DeGrado. 2003. Computational design of a water-soluble analog of phospholamban. Protein Sci. 12:337-348.
4. Slovic, A. M., H. Kono, J. D. Lear, J. G. Saven, and W. F. DeGrado. 2004. Computational design of water-soluble analogues of the potassium channel KcsA. Proc. Natl. Acad. Sci. USA. 101:1828-1833.
5. Saven, J. G., and P. G. Wolynes. 1997. Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules. J. Phys. Chem. B. 101:8375-8389.
6. Zou, J. M., and J. G. Saven. 2000. Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. J. Mol. Biol. 296:281-294.
7. Kono, H., and J. G. Saven. 2001. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J. Mol. Biol. 306:607-628.
8. Doyle, D. A., J. M. Cabral, R. A. Pfuetzner, A. L. Kuo, J. M. Gulbis, S. L. Cohen, B. T. Chait, and R. MacKinnon. 1998. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science. 280:69-77.
9. Zhou, Y. F., J. H. Morais-Cabral, A. Kaufman, and R. MacKinnon. 2001. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 angstrom resolution. Nature. 414:43-48.
10. Miller, C. 1988. Competition for block of a Ca-21-activated K+ channel by charybdotoxin and tetraethylammonium. Neuron. 1:1003-1006.
11. Cook, N. S., editor. 1990. Potassium Channels: Structure, Classification, Function, and Therapeutic Potential. Halsted Press, New York.
12. Trauner, D. 2003. Potassium channels: symmetric, selective, and sensitive. Angew. Chem. Int. Ed. Engl. 42:5671-5675.
13. MacKinnon, R., S. L. Cohen, A. L. Kuo, A. Lee, and B. T. Chait. 1998. Structural conservation in prokaryotic and eukaryotic potassium channels. Science. 280:106-109.
14. Aqvist, J., and V. Luzhkov. 2000. Ion permeation mechanism of the potassium channel. Nature. 404:881-884.
15. Domene, C., and M. S. P. Sansom. 2003. Potassium channel, ions, and water: simulation studies based on the high resolution x-ray structure of KcsA. Biophys. J. 85:2787-2800.
16. Shrivastava, I. H., and M. S. P. Sansom. 2000. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys. J. 78:557-570.
17. Berneche, S., and B. Roux. 2000. Molecular dynamics of the KcsA K+ channel in a bilayer membrane. Biophys. J. 78:2900-2917.
18. Guidoni, L., V. Torre, and P. Carloni. 1999. Potassium and sodium binding to the outer mouth of the K+ channel. Biochemistry. 38:8599-8604.
19. Shrivastava, I. H., and M. S. P. Sansom. 2002. Molecular dynamics simulations and KcsA channel gating. Eur. Biophys. J. 31:207-216.
20. Bek, S., and E. Jakobsson. 1994. Brownian dynamics study of a multiply occupied cation channel - application to understanding permeation in potassium channels. Biophys. J. 66:1028-1038.
21. Berneche, S., and B. Roux. 2002. The ionization state and the conformation of Glu-71 in the KcsA K+ channel. Biophys. J. 82:772-780.
22. Grubmuller, H. 1996. SOLVATE. Version 1.2. Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich.
23. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38.
24. MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
25. Jorgensen, W. L., J. Chandrasekhar, and J. D. Madura. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
26. Compoint, M., P. Carloni, C. Ramseyer, and C. Girardet. 2004. Molecular dynamics study of the KcsA channel at 2.0-angstrom resolution: stability and concerted motions within the pore. Biochim. Biophys. Acta. 1661:26-39.
27. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
28. Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant-pressure molecular-dynamics simulation - the Langevin piston method. J. Chem. Phys. 103:4613-4621.
29. Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant-pressure molecular-dynamics algorithms. J. Chem. Phys. 101:4177-4189.
30. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald - an N.Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
31. Stickle, D. F., L. G. Presta, K. A. Dill, and G. D. Rose. 1992. Hydrogen-bonding in globular-proteins. J. Mol. Biol. 226:1143-1159.
32. Roux, B., S. Berneche, and W. Im. 2000. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 39:13295-13306.
33. Allen, T. W., S. Kuyucak, and S. H. Chung. 1999. Molecular dynamics study of the KcsA potassium channel. Biophys. J. 77:2502-2516.
34. Allen, T. W., A. Bliznyuk, A. P. Rendell, S. Kuyucak, and S. H. Chung. 2000. The potassium channel: structure, selectivity and diffusion. J. Chem. Phys. 112:8191-8204.
35. Morais-Cabral, J. H., Y. F. Zhou, and R. MacKinnon. 2001. Energetic optimization of ion conduction rate by the K+ selectivity filter. Nature. 414:37-42.
36. Berneche, S., and B. Roux. 2001. Energetics of ion conduction through the K+ channel. Nature. 414:73-77.
37. Yu, K. Q., W. Fu, H. Liu, X. M. Luo, K. X. Chen, J. P. Ding, and J. H. Shen. 2004. Computational simulations of interactions of scorpion toxins with the voltage-gated potassium ion channel. Biophys. J. 86:3542-3555.
38. DeLano, W. L. 2002. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.