Role of methyl-induced polarization in ion binding

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 32, 2013, Pages 12978-12983

  Rossi, Mariana ^a   Tkatchenko, Alexandre ^a   Rempe, Susan B ^b   Varma, Sameer ^b,c  

^a FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

Density functional theory; Dispersion; Ion channels; Methylation; Quantum chemistry

Indexed keywords

BARIUM ION; MEGESTROL ACETATE; METHYL GROUP; POTASSIUM CHANNEL; SERINE; SODIUM CHLORIDE; THREONINE;

ARTICLE; CHEMICAL BINDING; ELECTRON; ION TRANSPORT; POLARIZATION; PRIORITY JOURNAL; QUANTUM MECHANICS;

DENSITY-FUNCTIONAL THEORY; DISPERSION; ION CHANNELS; METHYLATION; QUANTUM CHEMISTRY;

ALGORITHMS; AMINO ACID SUBSTITUTION; BARIUM; BINDING SITES; ION CHANNEL GATING; ION TRANSPORT; MODELS, CHEMICAL; MODELS, MOLECULAR; POTASSIUM; POTASSIUM CHANNELS; PROTEIN STRUCTURE, TERTIARY; SERINE; THERMODYNAMICS; THREONINE;

EID: 84881453126     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1302757110     Document Type: Article

References (61)

1. Paik WK, Paik DC, Kim S (2007) Historical review: The field of protein methylation. Trends Biochem Sci 32(3):146-152.
2. Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6(8): 597-610.
3. Lide DR (2008) CRC Handbook of Chemistry and Physics (Taylor and Francis, Boca Raton, FL).
4. Sowers LC, Shaw BR, Sedwick WD (1987) Base stacking and molecular polarizability: Effect of a methyl group in the 5-position of pyrimidines. Biochem Biophys Res Commun 148(2):790-794.
5. Wang S, Kool ET (1995) Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2′-hydroxyl effects. Biochemistry 34(12):4125-4132.
6. Hille B (2001) Ionic Channels of Excitable Membranes (Sinauer, Sunderland, MA).
7. + channel-Fab complex at 2.0 A resolution. Nature 414(6859):43-48.
8. Armstrong CM, Taylor SR (1980) Interaction of barium ions with potassium channels in squid giant axons. Biophys J 30(3):473-488.
9. Eaton DC, Brodwick MS (1980) Effects of barium on the potassium conductance of squid axon. J Gen Physiol 75(6):727-750.
10. + channel. J Gen Physiol 92(5): 569-586.
11. Jiang Y, MacKinnon R (2000) The barium site in a potassium channel by x-ray crystallography. J Gen Physiol 115(3):269-272.
12. 2+ blockade. J Gen Physiol 75:727-750.
13. + channel: Differential contribution by two discrete residues. J Physiol 534(Pt 2):381-393.
14. Proks P, Antcliff JF, Ashcroft FM (2003) The ligand-sensitive gate of a potassium channel lies close to the selectivity filter. EMBO Rep 4(1):70-75.
15. Chatelain FC, et al. (2005) The pore helix dipole has a minor role in inward rectifier channel function. Neuron 47(6):833-843.
16. Chatelain FC, et al. (2009) Selection of inhibitor-resistant viral potassium channels identifies a selectivity filter site that affects barium and amantadine block. PLoS ONE 4(10):e7496.
17. + selectivity in membrane transport. J Gen Physiol 137(6):479-488.
18. Kim I, Allen TW (2011) On the selective ion binding hypothesis for potassium channels. Proc Natl Acad Sci USA 108(44):17963-17968.
19. +-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophys J 84(5):2929-2942.
20. + inward rectifier channel associated with motoneurons of cranial nerve nuclei. J Neurosci 18(11):4096-4105.
21. Hibino H, et al. (2010) Inwardly rectifying potassium channels: Their structure, function, and physiological roles. Physiol Rev 90(1):291-366.
22. Wimley WC, White SH (1996) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 3(10):842-848.
23. Varma S, Rempe SB (2010) Multibody effects in ion binding and selectivity. Biophys J 99(10):3394-3401.
24. + and Na+ in simple polarizable ion-ligating systems. J Am Chem Soc 132(38):13185-13187.
25. Tkatchenko A, Rossi M, Blum V, Ireta J, Scheffler M (2011) Unraveling the stability of polypeptide helices: Critical role of van der Waals interactions. Phys Rev Lett 106(11): 118102-118106.
26. Perdew JP, Burke K, Ernzerhof M (1996) Generalized Gradient Approximation Made Simple. Phys Rev Lett 77(18):3865-3868.
27. Ernzerhof M, Scuseria GE (1999) Assessment of the Perdew-Burke-Ernzerhof exchange-correlation functional. J Chem Phys 110(11):5029-5036.
28. Adamo C, Barone V (1999) Toward reliable density functional methods without adjustable parameters: The PBE0 model. J Chem Phys 110(13):6158-6170.
29. Marom N, Tkatchenko A, Scheffler M, Kronik L (2010) Describing both dispersion interactions and electronic structure using density functional theory: The case of metal-phthalocyanine dimers. J Chem Theory Comput 6(1):81-90.
30. Tkatchenko A, Scheffler M (2009) Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys Rev Lett 102(7): 073005.
31. Marom N, et al. (2011) Dispersion interactions within density functional theory: Benchmarking semi-empirical and pair-wise corrected density functionals. J Chem Theory Comput 7(12):3944-3951.
32. Nelson RD, Lide DR, Maryott AA (1967) National Standard Reference Data Series - National Bureau of Standards 10: Selected Values of Electric Dipole Moments for Molecules in the Gas Phase (U.S. Government Printing Office, Washington). Available at http://www.nist.gov/data/nsrds/NSRDS-NBS-10.pdf.
33. Tissandier MD, et al. (1998) The proton's absolute aqueous enthalpy and Gibbs free energy of solvation from cluster-ion solvation data. J Phys Chem A 102:7787-7794.
34. 2+ from gas-phase ion-water molecule equilibria determinations. J Phys Chem A 102:9978-9985.
35. Nielsen SB, Masella M, Kebarle P (1999) Competitive gas-phase solvation of alkali metal ions by water and methanol. J Phys Chem A 103:9891-9898.
36. Dahlke EE, Truhlar DJ (2006) Assessment of the pairwise additive approximation and evaluation of many-body terms for water clusters. J Phys Chem B 110(22): 10595-10601.
37. Krekeler C, Delle Site L (2007) Solvation of positive ions in water: The dominant role of water-water interaction. J Phys Condens Matter 19:192101-192107.
38. Pauling L (1935) The structure and entropy of ice and of other crystals with some randomness of atomic arrangement. J Am Chem Soc 57:2680-2684.
39. DiStasio RA, Jr., von Lilienfeld OA, Tkatchenko A (2012) Collective many-body van der Waals interactions in molecular systems. Proc Natl Acad Sci USA 109(37):14791-14795.
40. Varma S, Rempe SB (2007) Tuning ion coordination architectures to enable selective partitioning. Biophys J 93(4):1093-1099.
41. Varma S, Rempe SB (2008) Structural transitions in ion coordination driven by changes in competition for ligand binding. J Am Chem Soc 130(46):15405-15419.
42. + channel. J Gen Physiol 126(3):271-283.
43. + channel tetramer: Cation interactions and the conserved threonine residue at the innermost site (S4) of the KcsA selectivity filter. Biochemistry 47(19):5354-5367.
44. Wang S, Alimi Y, Tong A, Nichols CG, Enkvetchakul D (2009) Differential roles of blocking ions in KirBac1.1 tetramer stability. J Biol Chem 284(5):2854-2860.
45. Hodgkin AL, Keynes RD (1955) The potassium permeability of a giant nerve fibre. J Physiol 128(1):61-88.
46. Shrivastava IH, Sansom MS (2000) Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer. Biophys J 78(2): 557-570.
47. Aqvist J, Luzhkov V (2000) Ion permeation mechanism of the potassium channel. Nature 404(6780):881-884.
48. + channel. Nature 414(6859):73-77.
49. Mashl RJ, Tang Y, Schnitzer J, Jakobsson E (2001) Hierarchical approach to predicting permeation in ion channels. Biophys J 81(5):2473-2483.
50. Furini S, Domene C (2009) Atypical mechanism of conduction in potassium channels. Proc Natl Acad Sci USA 106(38):16074-16077.
51. + channels. Proc Natl Acad Sci USA 107(13):5833-5838.
52. Iwamoto M, Oiki S (2011) Counting ion and water molecules in a streaming file through the open-filter structure of the K channel. J Neurosci 31(34):12180-12188.
53. Noskov SY, Bernèche S, Roux B (2004) Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431(7010): 830-834.
54. Derebe MG, et al. (2011) Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. Proc Natl Acad Sci USA 108(2): 598-602.
55. + channels is due to topological control of the permeant ion's coordinated state. Proc Natl Acad Sci USA 104(22): 9260-9265.
56. ThomasM, Jayatilaka D, Corry B (2007) The predominant role of coordination number in potassium channel selectivity. Biophys J 93(8):2635-2643.
57. Blum V, et al. (2009) Ab initio molecular simulations with numeric atom-centered orbitals. Comput Phys Commun 180(11):2175-2196.
58. Havu V, Blum V, Havu P, Scheffler M (2009) Efficient o(n) integration for all-electron electronic structure calculation using numeric basis functions. J Comput Phys 228(22): 8367-8379.
59. Jurecka P, Sponer J, Cerný J, Hobza P (2006) Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys 8(17):1985-1993.
60. van Lenthe E, Baerends EJ, Snijders JG (1993) Relativistic regular two-component Hamiltonians. J Chem Phys 99(6):4597-4610.
61. Cohen A, Mori-Sánchez P, Yang W (2008) Insights into current limitations of density functional theory. Science 321(5890):792-794.