Salt bridges in the miniature viral channel Kcv are important for function

European Biophysics Journal

Volumn 39, Issue 7, 2010, Pages 1057-1068

  Hertel, Brigitte ^a   Tayefeh, Sascha ^a   Kloss, Thomas ^a   Hewing, Jennifer ^a   Gebhardt, Manuela ^a   Baumeister, Dirk ^a   Moroni, Anna ^b   Thiel, Gerhard ^a   Kast, Stefan M ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

Channel gating; K+ channel; Kcv channel; MD simulation; Salt bridge

Indexed keywords

POTASSIUM CHANNEL; VIRUS PROTEIN;

AMINO ACID SEQUENCE; CELL LINE; CELL MEMBRANE POTENTIAL; CHEMISTRY; CONFERENCE PAPER; CONFOCAL MICROSCOPY; GENETIC TRANSFECTION; GENETICS; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PATCH CLAMP; PHYSIOLOGY; POINT MUTATION; PROTEIN SECONDARY STRUCTURE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; CELL LINE; HUMANS; MEMBRANE POTENTIALS; MICROSCOPY, CONFOCAL; MOLECULAR DYNAMICS SIMULATION; PATCH-CLAMP TECHNIQUES; POINT MUTATION; POTASSIUM CHANNELS; PROTEIN STRUCTURE, SECONDARY; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID; TRANSFECTION; VIRAL PROTEINS;

EID: 77955658127     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-009-0451-z     Document Type: Conference Paper

References (41)

1. Alam A, Jiang Y (2009) High-resolution structure of the open NaK channel. Nat Struct Mol Biol 16:30-34. doi:10.1038/nsmb.1531
2. Anderson JA, Huprikar SS, Kochian LV, Lucas WJ, Gaber RF (1992) Functional expression of a probable Arabidopsis thaliana potassium channel in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 89:3736-3740. doi:10.1073/pnas.89.9.3736
3. + channels is a signal for mitochondria targeting. Proc Natl Acad Sci USA 105:12313-12318. doi:10.1073/pnas.0805709105
4. Beckstein O, Biggin PC, Bond P, Bright JN, Domen C, Grottesi A, Holyoake J, Sansom MSP (2003) Ion channel gating: insight via molecular simulations. FEBS 555:85-90. doi:10.1016/S0014- 5793(03)01151-7
5. Beglov D, Roux B (1997) An integral equation to describe the solvation of polar molecules in liquid water. J Phys Chem B 101:7821-7826. doi:10.1021/jp971083h
6. Bolte S, Cordelières FP (2007) A guided tour into subcellular colocalization analysis in light microscopy. J Microsc 224:213-232. doi:10.1111/j.1365-2818.2006.01706.x
7. Brickmann J, Goetze T, Heiden W, Moeckel G, Reiling S, Vollhardt H, Zachmann C-D (1995) Interactive visualization of molecular scenarios with MOLCAD/SYBYL. In: Bowie JE (ed) Data visualisation in molecular science: tools for insight and innovation. Addison-Wesley, Reading, pp 83-97
8. Cordero-Morales JF, Jogini V, Lewis A, Vásquez V, Cortes DM, Roux B, Perozo E (2007) Molecular driving forces determining potassium channel slow inactivation. Nat Struct Mol Biol 14:1062-1069. doi:10.1038/nsmb1309
9. Cortes DM, Cuello LG, Perozo E (2001) Molecular architecture of full-length KcsA: role of cytoplasmic domains in ion permeation and activation gating. J Gen Physiol 117:165-180. doi:10.1085/ jgp.117.2.165
10. Craven K, Zagotta WN (2004) Salt bridges and gating in the COOHterminal region of HCN2 and CNGA1 channels. J Gen Physiol 124:663-677. doi:10.1085/jgp.200409178
11. Domene C, Bond PJ, Sansom MSP (2003) Membrane protein simulations: ion channels and bacterial outer membrane proteins. Adv Protein Chem 66:159-193. doi:10.1016/S0065-3233(03)66005-5
12. + conduction and selectivity. Science 280:69-76. doi:10.1126/science.280.5360.69
13. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593. doi:10.1063/1.470117
14. + channel Kcv. J Membr Biol 187:15-25. doi:10.1007/s00232-001-0147-5
15. Gazzarrini S, Kang M, Van Etten JL, Tayefeh S, Kast SM, DiFrancesco D, Thiel G, Moroni A (2004) Long-distance interactions within the potassium channel pore are revealed by molecular diversity of viral proteins. J Biol Chem 279:28443-28449. doi:10.1074/ jbc.M401184200
16. Hamill OP, Marty A, Neher E, Sakmann B, Sigworth FJ (1981) Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches. PXugers Arch 391:85-100. doi:10.1007/BF00656997
17. + channel Kcv. J Membr Biol 210:21-29. doi:10.1007/s00232-005-7026-4
18. Hille B (1992) Ionic channels of excitable membranes. Sinauer, Sunderland
19. Hong H, Szabo G, Tamm LK (2006) Electrostatic couplings in OmpA ion-channel gating suggests mechanism for pore opening. Nat Chem Biol 2:627-635. doi:10.1038/nchembio827
20. Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33-38. doi:10.1016/0263-7855(96) 00018-5
21. Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (2002) The open pore conformation of potassium channels. Nature 417:523-526. doi:10.1038/417523a
22. Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 151:283-312. doi:10.1006/jcph.1999. 6201
23. Khalili-Araghi F, Tajkhorshid E, Schulten K (2006) Dynamics of K + ion conductance through Kv1.2. Biophys J 91:72-74. doi:10.1529/biophysj.106.091926
24. Kovalenko A, Hirata F (1998) Three-dimensional density proWles of water in contact with a solute of arbitrary shape: a RISM approach. Chem Phys Lett 290:237-244. doi:10.1016/S0009- 2614(98)00471-0
25. Kuo A, Gulbis JM, AntcliV JF, Rahman T, Lowe ED, Zimmer J, Cuthbertson J, Ashcroft FM, Ezaki T, Doyle DA (2003) Crystal structure of the potassium channel KirBac1.1 in the closed state. Science 300:1922-1926. doi:10.1126/science.1085028
26. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK F, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modelling and dynamics. Studies of proteins. J Phys Chem B 102:3586-3616. doi:10.1021/jp973084f
27. MacKinnon R (2003) Potassium channels. FEBS Lett 555:62-65. doi:10.1016/S0014-5793(03)01104-9
28. Marti-Renom MA, Stuart A, Fiser A, Sánchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325. doi:10.1146/annurev. biophys.29.1.291
29. Moroni A, Thiel G (2006) Flip-Xopping salt bridges gate an ion channel. Nat Chem Biol 2:572-573. doi:10.1038/nchembio1106-572
30. + channel Kcv. FEBS Lett 530:65-69. doi:10.1016/S0014-5793(02)03397- 5
31. Nishida M, Cadene M, Chait BT, MacKinnon R (2007) Crystal structure of a Kir3.1-prokaryotic Kir channel chimera. EMBO J 26:4005-4015. doi:10.1038/sj.emboj.7601828
32. + channel. Biochem 46:1079-1090. doi:10.1021/bi061530w
33. Plugge B, Gazzarrini S, Nelson M, Cerana R, Van Etten JL, Derst C, DiFrancesco D, Moroni A, Thiel G (2000) A potassium channel protein encoded by chlorella virus PBCV-1. Science 287:1641-1644. doi:10.1126/science.287.5458.1641
34. Rapedius M, Fowler PW, Shang L, Sansom MSP, Tucker SJ, Baukrowitz T (2007a) H Bonding at the helix-bundle crossing controls gating in Kir. Neurone 16:602-614. doi:10.1016/j.neuron.2007.07.026
35. 2 gating in heteromeric Kir4.1/ Kir5.1 channels by H-bonding at the helix bundle crossing. Channels 1:327-330
36. Roux B, Schulten K (2004) Computational studies of membrane channels. Structure 12:1343-1351. doi:10.1016/j.str.2004.06.013
37. Roux B, Allen T, Bernéche S, Im W (2004) Theoretical and computational models of biological ion channels. Q Rev Biophys 37:15-103. doi:10.1017/S0033583504003968
38. Schlenkrich M, Brickmann J, MacKerell AD Jr, Karplus M (1996) An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In: Merz KM, Roux B (eds) Biological membranes: a molecular perspective from computation and experiment. Birkhäuser, Boston, pp 31-81
39. +-conducting channel. Nature 440:570-574. doi:10.1038/nature04508
40. Tayefeh S, Kloss T, Thiel G, Hertel B, Moroni A, Kast SM (2007) Molecular dynamics simulation study of the cytosolic mouth in Kcv-type potassium channels. Biochem 46:4826-4839. doi:10.1021/bi602468r
41. Tayefeh S, Kloss T, Kreim M, Gebhardt M, Baumeister D, Hertel B, Richter C, Schwalbe H, Moroni A, Thiel G, Kast SM (2009) Model development for the viral potassium channel. Biophys J 96:485-498. doi:10.1016/j.bpj.2008.09.050