Promiscuous binding in a selective protein: The bacterial NA +/H + antiporter

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Alhadeff, Raphael ^a   Ganoth, Assaf ^a   Krugliak, Miriam ^a   Arkin, Isaiah T ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CESIUM ION; LITHIUM ION; POTASSIUM ION; RUBIDIUM ION; SODIUM ION; SODIUM PROTON EXCHANGE PROTEIN; CATION; ESCHERICHIA COLI PROTEIN; NHAA PROTEIN, E COLI;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; CYTOPLASM; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HISTOGRAM; HYDRATION; MICHAELIS MENTEN KINETICS; NONHUMAN; PROTEIN BINDING; PROTEIN TRANSPORT; RESPIRATORY CHAIN; FLUORESCENCE; METABOLISM; MOLECULAR DYNAMICS; THERMODYNAMICS;

BACTERIA (MICROORGANISMS);

CATIONS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLUORESCENCE; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; SODIUM-HYDROGEN ANTIPORTER; THERMODYNAMICS;

EID: 80053994565     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025182     Document Type: Article

References (49)

1. Corry B, (2006) Understanding ion channel selectivity and gating and their role in cellular signalling. Mol Biosyst 2: 527-35.
2. Gouaux E, Mackinnon R, (2005) Principles of selective ion transport in channels and pumps. Science 310: 1461-5.
3. Hachez C, Chaumont F, (2010) Aquaporins: a family of highly regulated multifunctional channels. Adv Exp Med Biol 679: 1-17.
4. Jensen ML, Schousboe A, Ahring PK, (2005) Charge selectivity of the cys-loop family of ligandgated ion channels. J Neurochem 92: 217-25.
5. Keramidas A, Moorhouse AJ, Schofield PR, Barry PH, (2004) Ligand-gated ion channels: mechanisms underlying ion selectivity. Prog Biophys Mol Biol 86: 161-204.
6. Miloshevsky GV, Jordan PC, (2004) Permeation in ion channels: the interplay of structure and theory. Trends Neurosci 27: 308-14.
7. Moomaw AS, Maguire ME, (2008) The unique nature of mg2+ channels. Physiology (Bethesda) 23: 275-85.
8. Noskov SY, Roux B, (2006) Ion selectivity in potassium channels. Biophys Chem 124: 279-91.
9. Owsianik G, Talavera K, Voets T, Nilius B, (2006) Permeation and selectivity of trp channels. Annu Rev Physiol 68: 685-717.
10. Roux B, (2005) Ion conduction and selectivity in k+ channels. Annual Review of Biophysics and Biomolecular Structure 34: 153-171.
11. Yamaoka K, Vogel SM, Seyama I, (2006) Na+ channel pharmacology and molecular mechanisms of gating. Curr Pharm Des 12: 429-42.
12. Zhou HX, McCammon JA, (2010) The gates of ion channels and enzymes. Trends Biochem Sci 35: 179-85.
13. West IC, Mitchell P, (1974) Proton/sodium ion antiport in Escherichia coli. Biochem J 144: 87-90.
14. Orlowski J, Grinstein S, (2004) Diversity of the mammalian sodium/proton exchanger SLC9 gene family. Pugers Arch 447: 549-65.
15. Karpel R, Olami Y, Taglicht D, Schuldiner S, Padan E, (1988) Sequencing of the gene ant which affects the Na+/H+ antiporter activity in Escherichia coli. J Biol Chem 263: 10408-14.
16. Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, et al. (2005) Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435: 1197-202.
17. Padan E, (2008) The enlightening encounter between structure and function in the NhaA Na+-H+ antiporter. Trends Biochem Sci 33: 435-43.
18. Inoue H, Noumi T, Tsuchiya T, Kanazawa H, (1995) Essential aspartic acid residues, Asp-133, Asp-163 and Asp-164, in the transmembrane helices of a Na+/H+ antiporter (NhaA) from Escherichia coli. FEBS Lett 363: 264-8.
19. Arkin IT, Xu H, Jensen MØ, Arbely E, Bennett ER, et al. (2007) Mechanism of Na+/H+ antiporting. Science 317: 799-803.
20. Taglicht D, Padan E, Schuldiner S, (1993) Proton-sodium stoichiometry of NhaA, an electrogenic antiporter from Escherichia coli. J Biol Chem 268: 5382-7.
21. Padan E, Tzubery T, Herz K, Kozachkov L, Rimon A, et al. (2004) NhaA of Escherichia coli, as a model of a pH-regulated Na+/H+ antiporter. Biochim Biophys Acta 1658: 2-13.
22. Inaba K, Kuroda T, Shimamoto T, Kayahara T, Tsuda M, et al. (1994) Lithium toxicity and Na+(Li+)-H+ antiporter in Escherichia coli. Biol Pharm Bull 17: 573-580.
23. Dickson A, Dinner AR, (2010) Enhanced sampling of nonequilibrium steady states. Annu Rev Phys Chem 61: 441-59.
24. Kumar S, Bouzida D, Swendsen R, Kollman P, Rosenberg J, (1992) The Weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 13: 1011-21.
25. Zuber D, Krause R, Venturi M, Padan E, Bamberg E, et al. (2005) Kinetics of charge translocation in the passive downhill uptake mode of the Na+/H+ antiporter NhaA of Escherichia coli. Biochim Biophys Acta 1709: 240-50.
26. Schuldiner S, Rottenberg H, Avron M, (1972) Determination of pH in chloroplasts. 2. Fluorescent amines as a probe for the determination of pH in chloroplasts. Eur J Biochem 25: 64-70.
27. Schuldiner S, Fishkes H, (1978) Sodium-proton antiport in isolated membrane vesicles of Escherichia coli. Biochemistry 17: 706-11.
28. Mullins LJ, (1959) The penetration of some cations into muscle. J Gen Physiol 42: 817-29.
29. Bezanilla F, Armstrong CM, (1972) Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons. J Gen Physiol 60: 588-608.
30. Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, et al. (1998) The structure of the potassium channel: molecular basis of k+ conduction and selectivity. Science 280: 69-77.
31. Toyoshima C, Nakasako M, Nomura H, Ogawa H, (2000) Crystal structure of the calcium pump ofsarcoplasmic reticulum at 2.6 Å resolution. Nature 405: 647-55.
32. Toyoshima C, Nomura H, (2002) Structural changes in the calcium pump accompanying the dissociation of calcium. Nature 418: 605-11.
33. Ohgaki R, Nakamura N, Mitsui K, Kanazawa H, (2005) Characterization of the ion transport activity of the budding yeast Na+/H+ antiporter, Nha1p, using isolated secretory vesicles. Biochim Biophys Acta 1712: 185-96.
34. Anderie I, Thévenod F, (1996) Evidence for involvement of a zymogen granule Na+/H+ exchanger in enzyme secretion from rat pancreatic acinar cells. J Membr Biol 152: 195-205.
35. Tieleman DP, Berendsen HJ, (1998) A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J 74: 2786-801.
36. Berendsen H, Postma J, van Gunsteren W, Hermans J, Pullman B, (1981) Intermolecular forces: Interaction models for water in relation to protein hydrationInteraction models for water in relation to protein hydration. pp. 331-342 Reidel, Dordrecht.
37. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: fast, exible, and free. J Comput Chem 26: 1701-18.
38. Berendsen H, van der Spoel D, vandrunen R, (1995) GROMACS- a message- passing parallel molecular-dynamics implementation. Comp Phys Comm 91: 43-56.
39. Siu SWI, Vácha R, Jungwirth P, Böckmann RA, (2008) Biomolecular simulations of membranes: physical properties from different force fields. J Chem Phys 128: 125103.
40. Hess B, Bekker H, Berendsen H, Fraaije J, (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463-72.
41. Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-92.
42. Torrie GM, Valleau JP, (1977) Nonphysical sampling distributions in Monte carlo free-energy estimation: umbrella sampling. J Comput Phys 23: 187-99.
43. Impey R, Sprik M, Klein M, (1987) Ionic solvation in nonaqueous solvents- The structure of Li+ and Cl- in methanol, ammonia, and methylamine. J Am Chem Soc 109: 5900-4.
44. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-8.
45. Nozaki K, Inaba K, Kuroda T, Tsuda M, Tsuchiya T, (1996) Cloning and sequencing of the gene for Na+/H+ antiporter of Vibrio parahaemolyticus. Biochem Biophys Res Commun 222: 774-9.
46. Rahav-Manor O, Carmel O, Karpel R, Taglicht D, Glaser G, et al. (1992) NhaR, a protein homologous to a family of bacterial regulatory proteins (LysR), regulates nhaA, the sodium proton antiporter gene in Escherichia coli. J Biol Chem 267: 10433-8.
47. Bertani G, (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62: 293-300.
48. Tsuchiya T, Rosen BP, (1975) Characterization of an active transport system for calcium in inverted membrane vesicles of Escherichia coli. J Biol Chem 250: 7687-92.
49. Michaelis L, Menten ML, (1913) Kinetics of Invertase Action. Biochem Z 49: 333-69.