Proton transport pathway in the ClC Cl-/H+ antiporter

Biophysical Journal

Volumn 97, Issue 1, 2009, Pages 121-131

  Wang, Dong ^a,b   Voth, Gregory A ^a  

^a UNIVERSITY OF UTAH   (United States)

^b BEIJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIPORTER; CHLORIDE ION; GLUTAMINE; PROTEIN CIC CI; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; CHLORIDE TRANSPORT; CRYSTAL STRUCTURE; DISSOCIATION; HYDROGEN BOND; MATHEMATICAL COMPUTING; PROTON TRANSPORT;

AMINO ACID SEQUENCE; ANTIPORTERS; BIOLOGICAL TRANSPORT; COMPUTER SIMULATION; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MUTATION; PROTONS; WATER;

EID: 68949143576     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.04.038     Document Type: Article

References (52)

1. - channels. Nature. 427:803-807.
2. Jentsch, T. J., L. Neagoe, and O. Scheel. 2005. ClC chloride channels and transporters. Curr. Opin. Neurobiol. 15:319-325.
3. Picollo, A., and M. Pusch. 2005. Chloride/proton antiporter activity of mammalian ClC proteins ClC-4 and ClC-5. Nature. 436:420-423.
4. Scheel, O., A. A. Zdebik, S. Lourdel, and T. J. Jentsch. 2005. Voltage-dependent electrogenic chloride/proton exchange by endosomal ClC proteins. Nature. 436:424-427.
5. Iyer, R., T. M. Iverson, A. Accardi, and C. Miller. 2002. A biological role for prokaryotic ClC chloride channels. Nature. 419:715-718.
6. Dutzler, R., E. B. Campbell, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. X-ray structure of a ClC chloride channel at 3.0 Angstrom reveals the molecular basis of anion selectivity. Nature. 415:287-294.
7. Chen, M. F., and T. Y. Chen. 2003. Side-chain charge effects and conductance determinants in the pore of ClC-0 chloride channels. J. Gen. Physiol. 122:133-145.
8. Traverso, S., L. Elia, and M. Pusch. 2003. Gating competence of constitutively open ClC-0 mutants revealed by the interaction with a small organic inhibitor. J. Gen. Physiol. 122:295-306.
9. Estevez, R., B. C. Schroeder, A. Accardi, T. J. Jentsch, and M. Pusch. 2003. Conservation of chloride channel structure revealed by an inhibitor binding site in ClC-1. Neuron. 38:47-59.
10. Dutzler, R., E. B. Campbell, and R. MacKinnon. 2003. Gating the selectivity filter in ClC chloride channels. Science. 300:108-112.
11. + exchanger. J. Gen. Physiol. 126:563-570.
12. Accardi, A., S. Lobet, C. Williams, C. Miller, and R. Dutzler. 2006. Synergism between Halide binding and proton transport in a ClC-type exchanger. J. Mol. Biol. 362:691-699.
13. + exchange transporter by polyatomic anions. J. Mol. Biol. 362:682-690.
14. Miller, C. 2006. ClC chloride channels viewed through a transporter lens. Nature. 440:484-489.
15. + exchange transporter. J. Gen. Physiol. 129:317-329.
16. Faraldo-Gomez, J. D., and B. Roux. 2004. Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. J. Mol. Biol. 339:981-1000.
17. - pores: electrostatic effects of charged residues. Biophys. J. 86:825-835.
18. Miloshevsky, G. V., and P. C. Jordan. 2005. Permeation and gating in proteins: kinetic Monte Carlo reaction path following. J. Chem. Phys. 122:214901.
19. Cohen, J., and K. Schulten. 2004. Mechanism of anionic conduction across ClC. Biophys. J. 86:836-845.
20. Gervasio, F. L., M. Parrinello, M. Ceccarelli, and M. L. Klein. 2006. Exploring the gating mechanism in the ClC chloride channel via metadynamics. J. Mol. Biol. 361:390-398.
21. Bostick, D. L., and M. L. Berkowitz. 2004. Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the ClC chloride channel. Biophys. J. 87:1686-1696.
22. Jian, Y., Z. F. Kuang, U. Mahankali, and T. L. Beck. 2004. Ion transit pathways and gating in ClC chloride channels. Proteins. 57:414-421.
23. - stoichiometry in bacterial chloride transporters. Proteins. 68:26-33.
24. Voth, G. A. 2006. Computer simulation of proton solvation and transport in aqueous and biomolecular systems. Acc. Chem. Res. 39:143-150.
25. Swanson, J. M. J., C. M. Maupin, H. N. Chen, M. K. Petersen, J. C. Xu, et al. 2007. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J. Phys. Chem. B. 111:4300-4314.
26. Schmitt, U. W., and G. A. Voth. 1998. Multistate empirical valence bond model for proton transport in water. J. Phys. Chem. B. 102:5547-5551.
27. Schmitt, U. W., and G. A. Voth. 1999. The computer simulation of proton transport in water. J. Chem. Phys. 111:9361-9381.
28. Day, T. J. F., A. V. Soudackov, M. Cuma, U. W. Schmitt, and G. A. Voth. 2002. A second generation multistate empirical valence bond model for proton transport in aqueous systems. J. Chem. Phys. 117:5839-5849.
29. + exchanger. J. Gen. Physiol. 133:131-138.
30. Wu, Y., H. Chen, F. Wang, F. Paesani, and G. A. Voth. 2008. An improved multistate empirical valence bond model for aqueous proton solvation and transport. J. Phys. Chem. B. 112:467-482.
31. Cuma, M., U. W. Schmitt, and G. A. Voth. 2001. A multi-state empirical valence bond model for weak acid dissociation in aqueous solution. J. Phys. Chem. A. 105:2814-2823.
32. Kumar, S., J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman. 1995. Multidimensional free-energy calculations using the weighted histogram analysis method. J. Comput. Chem. 16:1339-1350.
33. Roux, B. 1995. The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun. 91:275-282.
34. Agmon, N. 1995. The Grotthuss mechanism. Chem. Phys. Lett. 244:456-462.
35. Decoursey, T. E. 2003. Voltage-gated proton channels and other proton transfer pathways. Physiol. Rev. 83:475-579.
36. Wraight, C. A. 2006. Chance and design-proton transfer in water, channels and bioenergetic proteins. Biochim. Biophys. Acta. 1757:886-912.
37. Cukierman, S. 2006. Et tu, Grotthuss! And other unfinished stories. Biochim. Biophys. Acta. 1757:876-885.
38. Yin, H., G. Hummer, and J. C. Rasaiah. 2007. Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J. Am. Chem. Soc. 129:7369-7377.
39. Rasaiah, J. C., S. Garde, and G. Hummer. 2008. Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu. Rev. Phys. Chem. 59:713-740.
40. Kaila, V. R. I., M. I. Verkhovsky, G. Hummer, and M. Wikström. 2008. Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc. Natl. Acad. Sci. USA. 105:6255-6259.
41. Tuukkanen, A., V. R. I. Kaila, L. Laakkonen, G. Hummer, and M. Wikström. 2007. Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochim. Biophys. Acta. 1767:1102-1106.
42. Wikström, M., M. I. Verkhovsky, and G. Hummer. 2003. Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim. Biophys. Acta. 1604:61-65.
43. Xu, J., and G. A. Voth. 2008. Redox-coupled proton pumping in cytrochrome c oxidase: further insights from computer simulation. Biochim. Biophys. Acta. 1777:196-201.
44. Zhang, L., and J. Hermans. 1996. Hydrophilicity of cavities in proteins. Proteins. 24:433-438.
45. Hummer, G., J. C. Rasaiah, and J. P. Noworyta. 2001. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 414:188-190.
46. Abramson, J., S. Iwata, and H. R. Kaback. 2004. Lactose permease as a paradigm for membrane transport proteins (review). Mol. Membr. Biol. 21:227-236.
47. + antiporter and insights into mechanism of action and regulation by pH. Nature. 435:1197-1202.
48. Knauf, P. A., F. Y. Law, T. W. V. Leung, A. U. Gehret, and M. L. Perez. 2002. Substrate-dependent reversal of anion transport site orientation in the human red blood cell anion-exchange protein, Ae1. Proc. Natl. Acad. Sci. USA. 99:10861-10864.
49. Lemieux, M. J., Y. F. Huang, and D. N. Wang. 2004. The structural basis of substrate translocation by the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Curr. Opin. Struct. Biol. 14:405-412.
50. Riistama, S., G. Hummer, A. Puustinen, R. B. Dyer, W. H. Woodruff, et al. 1997. Bound water in the proton translocation mechanism of the haem-copper oxidases. FEBS Lett. 414:275-280.
51. Zdebik, A. A., G. Zifarelli, E. Y. Bergsdorf, P. Soliani, O. Scheel, et al. 2008. Determinants of anion-proton coupling in mammalian endosomal ClC proteins. J. Biol. Chem. 283:4219-4227.
52. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD:visual molecular dynamics. J. Mol. Graph. 14:33-38.