Computational study of the Na +/H + antiporter from Vibrio parahaemolyticus

Journal of Molecular Modeling

Volumn 17, Issue 8, 2011, Pages 1877-1890

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

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Antiporting; Membrane proteins

Indexed keywords

LITHIUM ION; SODIUM ION; SODIUM PROTON EXCHANGE PROTEIN;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; ION TRANSPORT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; VIBRIO PARAHAEMOLYTICUS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; ELECTROPHYSIOLOGY; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN STABILITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SODIUM-HYDROGEN ANTIPORTER; VIBRIO PARAHAEMOLYTICUS;

ESCHERICHIA COLI; NEGIBACTERIA; VIBRIO PARAHAEMOLYTICUS;

EID: 80051798670     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0883-5     Document Type: Article

References (67)

1. IC West P Mitchell 1974 Proton/sodium ion antiport in Escherichia coli Biochem J 144 1 87 90 1:CAS:528:DyaE2MXpsFWgtg%3D%3D
2. J Orlowski S Grinstein 2004 Diversity of the mammalian sodium/proton exchanger SLC9 gene family Pflugers Arch 447 5 549 565 10.1007/s00424-003-1110-3 1:CAS:528:DC%2BD2cXhtVygsbc%3D (Pubitemid 38241440)
3. + antiporters Biochim Biophys Acta 1505 1 144 157 10.1016/S0005-2728(00)00284-X 1:CAS:528:DC%2BD3MXhvVagtrs%3D (Pubitemid 32204466)
4. + antiporter gene of Escherichia coli Proc Natl Acad Sci U S A 84 9 2615 2619 10.1073/pnas.84.9.2615 1:CAS:528:DyaL2sXktVWksLc%3D (Pubitemid 17064703)
5. + antiporter of Vibrio parahaemolyticus J Biochem 116 5 1030 1038 1:CAS:528:DyaK2MXislCjtrY%3D (Pubitemid 24354652)
6. + antiporter gene J Biol Chem 266 34 23483 23489 1:CAS:528:DyaK38Xlt1GmsLk%3D (Pubitemid 21908820)
7. M Waser D Hess-Bienz K Davies M Solioz 1992 Cloning and disruption of a putative NaH-antiporter gene of Enterococcus hirae J Biol Chem 267 8 5396 5400 1:CAS:528:DyaK3sXhvVKjsbc%3D
8. + antiporter in Escherichia coli J Biol Chem 267 16 11064 11068 1:CAS:528:DyaK3sXit1Kru7o%3D
9. + antiporter Trends Biochem Sci 33 9 435 443 10.1016/j.tibs.2008.06.007 1:CAS:528:DC%2BD1cXhtVyktLfL
10. + antiporter and insights into mechanism of action and regulation by pH Nature 435 7046 1197 1202 10.1038/nature03692 1:CAS:528:DC%2BD2MXls1OntbY%3D (Pubitemid 40943079)
11. + antiporter coded by NhaA (ant) from Escherichia coli J Biol Chem 266 17 11289 11294 1:CAS:528:DyaK3MXlsFajt7g%3D (Pubitemid 21906945)
12. J Lacroix M Pöet C Maehrel L Counillon 2004 A mechanism for the activation of the Na/H exchanger NHE-1 by cytoplasmic acidification and mitogens EMBO Rep 5 1 91 96 10.1038/sj.embor.7400035 1:CAS:528:DC%2BD2cXhtFKrtw%3D%3D (Pubitemid 38228534)
13. E Padan E Bibi M Ito TA Krulwich 2005 Alkaline pH homeostasis in bacteria: new insights Biochim Biophys Acta 1717 2 67 88 10.1016/j.bbamem.2005. 09.010 1:CAS:528:DC%2BD2MXht1OltLrP (Pubitemid 41682429)
14. E Olkhova L Kozachkov E Padan H Michel 2009 Combined computational and biochemical study reveals the importance of electrostatic interactions between the "pH sensor" and the cation binding site of the sodium/proton antiporter NhaA of Escherichia coli Proteins 76 3 548 559 10.1002/prot.22368 1:CAS:528:DC%2BD1MXns1ertrk%3D
15. + antiporter genes in Escherichia coli Mol Microbiol 59 2 651 663 10.1111/j.1365-2958.2005.04966.x 1:CAS:528:DC%2BD28XhsFersb0%3D
16. + antiporter of Escherichia coli, at physiological pH Biochemistry 46 9 2419 2430 10.1021/bi602393s 1:CAS:528:DC%2BD2sXhtlGlsLc%3D (Pubitemid 46362416)
17. E Olkhova E Padan H Michel 2007 The influence of protonation states on the dynamics of the NhaA antiporter from Escherichia coli Biophys J 92 11 3784 3791 10.1529/biophysj.106.098269 1:CAS:528:DC%2BD2sXls1ygu7s%3D (Pubitemid 46910566)
18. + antiporter J Biol Chem 284 10 6337 6347 10.1074/jbc.M807720200 1:CAS:528: DC%2BD1MXisVSku78%3D
19. + antiporter of Escherichia coli in the membrane and its functional and structural consequences Biochemistry 40 11 3403 3412 10.1021/bi002669o 1:CAS:528:DC%2BD3MXhtFynt74%3D (Pubitemid 32221644)
20. + antiporter of E. coli Biophys J 89 2 1328 1338 10.1529/biophysj.105.062232 1:CAS:528:DC%2BD2MXnvVSrsbs%3D (Pubitemid 41099014)
21. KA Williams U Geldmacher-Kaufer E Padan S Schuldiner W Kühlbrandt 1999 Projection structure of NhaA, a secondary transporter from Escherichia coli, at 4.0 Å resolution EMBO J 18 13 3558 3563 10.1093/emboj/18.13.3558 1:CAS:528:DyaK1MXksFKlsbg%3D (Pubitemid 29308836)
22. + antiporter dimer obtained by pulsed electron paramagnetic resonance distance measurements Biophys J 93 10 3675 3683 10.1529/biophysj.107.109769 1:CAS:528:DC%2BD2sXht12js7%2FP (Pubitemid 350190829)
23. + antiporter (NhaA) from Escherichia coli FEBS Lett 363 3 264 268 10.1016/0014-5793(95)00331-3 1:CAS:528:DyaK2MXlsFCmsLY%3D
24. + antiporting Science 317 5839 799 803 10.1126/science.1142824 1:CAS:528:DC%2BD2sXptVWjt7o%3D (Pubitemid 47257916)
25. MT Kelly EM Stroh 1988 Temporal relationship of Vibrio parahaemolyticus in patients and the environment J Clin Microbiol 26 9 1754 1756 1:STN:280:DyaL1M%2FjsVOksg%3D%3D
26. L McCarter 1999 The multiple identities of Vibrio parahaemolyticus J Mol Microbiol Biotechnol 1 1 51 57 1:CAS:528:DyaK1MXls12ru7s%3D (Pubitemid 129491924)
27. YC Su C Liu 2007 Vibrio parahaemolyticus: a concern of seafood safety Food Microbiol 24 6 549 558 10.1016/j.fm.2007.01.005 (Pubitemid 46517975)
28. + antiporter emrE Eur J Biochem 267 12 3422 3431 10.1046/j.1432-1327.2000.01324.x 1:CAS:528:DC%2BD3cXksVKgsbc%3D (Pubitemid 30423001)
29. A Ivetac MSP Sansom 2008 Molecular dynamics simulations and membrane protein structure quality Eur Biophys J 37 4 403 409 10.1007/s00249-007-0225-4 1:CAS:528:DC%2BD1cXjsF2gu7c%3D (Pubitemid 351423115)
30. RD Finn J Mistry J Tate P Coggill A Heger JE Pollington OL Gavin P Gunasekaran G Ceric K Forslund L Holm ELL Sonnhammer SR Eddy A Bateman 2010 The Pfam protein families database Nucleic Acids Res 38 Database issue D211 222 10.1093/nar/gkp985 1:CAS:528:DC%2BC3cXktlyhsA%3D%3D
31. Brenner DJ, Krieg NR, Staley JR, Garrity G (eds.) (2001) The Bergey's Manual of Systematic Bacteriology, vol. 2, 2nd edn. Springer
32. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. version 2.72. URL http://mesquiteproject.org/mesquite/mesquite.html
33. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 3 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D
34. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and psi-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 17 3389 3402 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D (Pubitemid 27359211)
35. A Sali TL Blundell 1993 Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 234 3 779 815 10.1006/jmbi.1993.1626 1:CAS:528:DyaK2cXnt1ylug%3D%3D (Pubitemid 24007801)
36. AL Morris MW MacArthur EG Hutchinson JM Thornton 1992 Stereochemical quality of protein structure coordinates Proteins 12 4 345 364 10.1002/prot.340120407 1:CAS:528:DyaK38XisFWls7o%3D
37. R Laskowski M Macarthur D Moss J Thornton 1993 PROCHECK: a program to check the stereochemical quality of protein structures Journal of Applied Crystallography 26 283 291 10.1107/S0021889892009944 1:CAS:528: DyaK3sXit12lurY%3D
38. MJ Sippl 1993 Recognition of errors in three-dimensional structures of proteins Proteins 17 4 355 362 10.1002/prot.340170404 1:CAS:528: DyaK2cXis1Ghsbk%3D (Pubitemid 23358545)
39. M Wiederstein MJ Sippl 2007 ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res 35 W407 W410 10.1093/nar/gkm290
40. R Lüthy JU Bowie D Eisenberg 1992 Assessment of protein models with three-dimensional profiles Nature 356 6364 83 85 10.1038/356083a0
41. S Henikoff JG Henikoff 1992 Amino acid substitution matrices from protein blocks Proc Natl Acad Sci U S A 89 22 10915 10919 10.1073/pnas.89.22.10915 1:CAS:528:DyaK3sXjsFCgsQ%3D%3D
42. DP Tieleman HJ Berendsen 1998 A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer Biophys J 74 6 2786 2801 10.1016/S0006-3495(98)77986-X 1:CAS:528:DyaK1cXjs12ltLY%3D (Pubitemid 28268103)
43. Berendsen H, Postma J, van Gunsteren W, Hermans J, Pullman B (1981) Intermolecular forces: interaction models for water in relation to protein hydration. Reidel, Dordrecht
44. D Van Der Spoel E Lindahl B Hess G Groenhof AE Mark HJC Berendsen 2005 GROMACS: fast, flexible, and free J Comput Chem 26 16 1701 1718 10.1002/jcc.20291 (Pubitemid 43076182)
45. H Berendsen D van der Spoel R van Drunen 1995 GROMACS - a message - passing parallel molecular dynamics implementation Computer Physics Communications 91 1-3 43 56 10.1016/0010-4655(95)00042-E 1:CAS:528: DyaK2MXps1Wrtr0%3D
46. SWI Siu R Vacha P Jungwirth RA Bockmann 2008 Biomolecular simulations of membranes: physical properties from different force fields J Chem Phys 128 12 125103 10.1063/1.2897760 (Pubitemid 351474132)
47. B Hess H Bekker H Berendsen J Fraaije 1997 LINCS: a linear constraint solver for molecular simulations J Comput Chem 18 12 1463 1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H 1:CAS:528:DyaK2sXlvV2nu7g%3D (Pubitemid 127637344)
48. T Darden D York L Pedersen 1993 Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems Journal of Chemical Physics 98 12 10089 10092 10.1063/1.464397 1:CAS:528:DyaK3sXks1Ohsr0%3D
49. A Amadei AB Linssen HJ Berendsen 1993 Essential dynamics of proteins Proteins 17 4 412 425 10.1002/prot.340170408 1:CAS:528:DyaK2cXis1Ghsbc%3D (Pubitemid 23358549)
50. GJ Kleywegt TA Jones 1994 Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallogr D Biol Crystallogr 50 Pt 2 178 185 10.1107/S0907444993011333 1:STN:280:DC%2BD2czpsVynug%3D%3D (Pubitemid 2054290)
51. Rossmann MG, Arnold E (eds.) (2001) International tables for crystallography, Vol. F. Crystallography of Biological Macromolecules, chap. Around O, pp. 353-356, 366-367. Kluwer, Dordrecht
52. NA Baker D Sept S Joseph MJ Holst JA McCammon 2001 Electrostatics of nanosystems: application to microtubules and the ribosome Proc Natl Acad Sci U S A 98 18 10037 10041 10.1073/pnas.181342398 1:CAS:528:DC%2BD3MXmvFWisbc%3D (Pubitemid 32802969)
53. + antiporter of Escherichia coli with functional implications Proc Natl Acad Sci U S A 103 8 2629 2634 10.1073/pnas.0510914103 1:CAS:528:DC%2BD28XksF2rsb0%3D
54. W Humphrey A Dalke K Schulten 1996 VMD: visual molecular dynamics J Mol Graph 14 1 33 38 10.1016/0263-7855(96)00018-5 1:CAS:528:DyaK28Xis12nsrg%3D (Pubitemid 26152973)
55. + J Biol Chem 282 37 26810 26821 10.1074/jbc.M704469200 1:CAS:528:DC%2BD2sXhtVWjsLvM (Pubitemid 47501951)
56. LR Forrest CL Tang B Honig 2006 On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins Biophys J 91 2 508 517 10.1529/biophysj.106.082313 1:CAS:528:DC%2BD28XmvVags7w%3D
57. D Donnelly JP Overington SV Ruffle JH Nugent TL Blundell 1993 Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues Protein Sci 2 1 55 70 1:CAS:528: DyaK3sXit12ltrg%3D (Pubitemid 23029009)
58. TJ Stevens IT Arkin 2001 Substitution rates in alpha-helical transmembrane proteins Protein Sci 10 12 2507 2517 10.1110/ps.ps.10501 1:CAS:528:DC%2BD3MXovVyru7w%3D (Pubitemid 33091574)
59. J Torres JAG Briggs IT Arkin 2002 Convergence of experimental, computational and evolutionary approaches predicts the presence of a tetrameric form for CD3-zeta J Mol Biol 316 2 375 384 10.1006/jmbi.2001.5268 1:CAS:528:DC%2BD38Xht1Kitb4%3D (Pubitemid 34722151)
60. CE Capener IH Shrivastava KM Ranatunga LR Forrest GR Smith MS Sansom 2000 Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel Biophys J 78 6 2929 2942 10.1016/S0006-3495(00) 76833-0 1:CAS:528:DC%2BD3cXjvFOhu7o%3D (Pubitemid 30396925)
61. + antiporter lines the cation passage, and Asp65 is critical for pH activation of the antiporter J Biol Chem 285 3 2211 2220 10.1074/jbc.M109.047134 1:CAS:528:DC%2BC3cXjsVWjsQ%3D%3D
62. H Gv 1986 The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology EMBO J 5 11 3021 3027
63. T Shimamura S Weyand O Beckstein NG Rutherford JM Hadden D Sharples MSP Sansom S Iwata PJF Henderson AD Cameron 2010 Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1 Science 328 5977 470 473 10.1126/science.1186303 1:CAS:528:DC%2BC3cXkvFegsrw%3D
64. F Kiefer K Arnold M Künzli L Bordoli T Schwede 2009 The SWISS-MODEL repository and associated resources Nucleic Acids Res 37 Database issue D387 392 10.1093/nar/gkn750 1:CAS:528:DC%2BD1cXhsFejtb7P
65. TM Pan CS Chiou SY Hsu HC Huang TK Wang SI Chiu HL Yea CL Lee 1996 Food-borne disease outbreaks in Taiwan, 1994 J Formos Med Assoc 95 5 417 420 1:STN:280:DyaK283otVentw%3D%3D
66. M Ansaruzzaman A Chowdhury NA Bhuiyan M Sultana A Safa M Lucas L von Seidlein A Barreto CL Chaignat DA Sack JD Clemens GB Nair SY Choi YS Jeon JH Lee HR Lee J Chun DW Kim 2008 Characteristics of a pandemic clone of O3:K6 and O4: K68 Vibrio parahaemolyticus isolated in Beira, Mozambique J Med Microbiol 57 Pt 12 1502 1507 10.1099/jmm.0.2008/004275-0 1:CAS:528:DC%2BD1MXhtVWqsr8%3D
67. E Harth L Matsuda C Hernandez ML Rioseco J Romero N Gonzalez-Escalona J Martínez-Urtaza RT Espejo 2009 Epidemiology of Vibrio parahaemolyticus outbreaks, southern Chile Emerg Infect Dis 15 2 163 168 10.3201/eid1502.071269 1:CAS:528:DC%2BD1MXjt1ertrk%3D