Transmembrane α-helices in the gap junction membrane channel: Systematic search of packing models based on the pair potential function

Microscopy Research and Technique

Volumn 52, Issue 3, 2001, Pages 344-351

  Nunn, Rashmi S ^a   Macke, Thomas J ^a   Olson, Arthur J ^a   Yeager, Mark ^a,b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b SCRIPPS CLINIC   (United States)

Author keywords

Connexins; Electron cryo microscopy; Gap junctions; Protein modeling; helix

Indexed keywords

ACTIVATION ANALYSIS; AMINO ACIDS; CONFORMATIONS; ELECTRONS; FUNCTION EVALUATION; PROTEINS;

CONNEXIN; ELECTRON CRYO MICROSCOPIES; GAP-JUNCTIONS; MEMBRANE CHANNELS; PACKING MODELS; PAIR POTENTIAL FUNCTION; PROTEIN MODELS; THREE-DIMENSIONAL MAPS; TRANSMEMBRANE Α HELICES; Α-HELIX;

BIOLOGICAL MEMBRANES;

GAP JUNCTION PROTEIN;

ALPHA HELIX; ARTICLE; ELECTRON MICROSCOPY; GAP JUNCTION; MEMBRANE CHANNEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE;

EID: 0035253804     PISSN: 1059910X     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0029(20010201)52:3<344::AID-JEMT1018>3.0.CO;2-4     Document Type: Article

References (42)

1. Abola EE, Sussman JL, Prilusky J, Manning NO. 1997. Protein data bank archives of three-dimensional macromolecular structures. Methods Enzmol 277:566-571.
2. Beyer EC, Paul DL, Goodenough DA. 1990. Connexin family of gap junction proteins. J Membr Biol 116:187-194.
3. Beyer EC, Veenstra RD. 1994. Molecular biology and electrophysiology of cardiac gap junctions. In: Handbook of membrane channels: Molecular and cellular physiology, Chapter 25. C. Peracchia, editor. San Diego: Academic Press, Inc., p 379-401.
4. Bowie JU. 1997. Helix packing in membrane proteins. J Mol Biol 272:780-789.
5. Canady MA, Tihova M, Hanslik TN, Johnson JE, Yeager M. 2000. Large conformational changes in the maturation of a simple RNA virus, Nudaurelia capensis ω Virus (NωV). J Mol Biol 299: 573-584.
6. Crowther RA, Henderson R, Smith JM. 1996. MRC image processing programs. J Struct Biol 116:9-16.
7. Deisenhofer J, Epp O, Miki K, Huber R, Michel H. 1984. X-ray structure analysis of a membrane protein complex. Electron density map at 3 Å resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. J Mol Biol 180:385-398.
8. Dorset DL. 1995. Direct structure analysis in protein electron crystallography: crystallographic phases for halorhodopsin to 6-Å resolution. Proc Natl Acad Sci USA 92:10074-10078.
9. Engelman DM, Steitz TA, Goldman A. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 15:321-353.
10. Finkelstein AV, Badretdinov AY, Gutin AM. 1995. Why do protein architectures have Boltzmann-like statistics? Proteins 23:142-150.
11. Gilmore CJ, Nicholson WV, Dorset DL. 1996. Direct methods in protein electron crystallography: the ab initio structure determination of two membrane protein structures in projection using maximum entropy and likelihood. Acta Cryst A52:937-946.
12. Jones TA, Zou J-Y, Cowan SW, Kjeldgaard M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst A47:110-119.
13. Karplus K, Sjölander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. 1997. Predicting protein structure using hidden Markov models. Proteins(Suppl 1):134-139.
14. Kumar NM, Gilula NB. 1992. Molecular biology and genetics of gap junction channels. Seminars in Cell Biol 3:3-16.
15. Loewenstein WR. 1981. Junctional intercellular communication: the cell-to-cell membrane channel. Physiol Rev 61:829-913.
16. Macke TJ, Duncan BS, Goodsell DS, Olson AJ. 1998. Interactive modeling of supramolecular assemblies. J Mol Graph Model 16: 115-120.
17. McRee DE. 1999. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125:156-165.
18. Milks LC, Kumar NM, Houghton R, Unwin N, Gilula NB. 1988. Topology of the 32-kd liver gap junction protein determined by site-directed antibody localizations. EMBO J 7:2967-2975.
19. Orengo CA, Todd AE, Thornton JM. 1999. From protein structure to function. Curr Opin Struct Biol 9:374-382.
20. +-channel activation gating. Science 285:73-78.
21. Perrakis A, Morris R, Lamzin VS. 1999. Automated protein model building combined with iterative structure refinement. Nature Struct Biol 6:458-463.
22. Ramón F, Rivera A. 1986. Gap junction channel modulation: a physiological viewpoint. Prog Biophys Mol Biol 48:127-153.
23. Rayment I, Holden HM, Whittaker M, Yohn CB, Lorenz M, Holmes KC, Milligan RA. 1993. Structure of the actin-myosin complex and its implications for muscle contraction. Science 261:58-65.
24. Reva BA, Finkelstein AV, Sanner MF, Olson AJ. 1997. Residue-residue mean-force potentials for protein structure recognition. Prot Eng 10:865-876.
25. Reva BA, Skolnick J, Finkelstein AV. 1999. Averaging interaction energies over homologs improves protein fold recognition in gapless threading. Proteins 35:353-359.
26. Rost B, Fariselli P, Casadio R. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Prot Sci 5:1704-1718.
27. Rost B, Schneider R, Sander C. 1997. Protein fold recognition by prediction-based threading. J Mol Biol 270:471-480.
28. Sheehan B, Fuller SD, Pique ME, Yeager M. 1996. AVS software for visualization in molecular microscopy. J Struct Biol 116:99-106.
29. Spray DC, Burt JM. 1990. Structure-activity relations of the cardiac gap junction channel. Am J Physiol 258:C195-C205.
30. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
31. Unger VM, Kumar NM, Gilula NB, Yeager M. 1997. Projection structure of a gap junction channel at 7Å resolution. Nature Struct Biol 4:39-43.
32. Unger VM, Kumar NM, Gilula NB, Yeager M. 1999a. Expression, two-dimensional crystallization, and electron cryo-crystallography of recombinant gap junction membrane channels. J Struct Biol128: 98-105.
33. Unger VM, Kumar NM, Gilula NB, Yeager M. 1999b. Three-dimensional structure of a recombinant gap junction membrane channel. Science 283:1176-1180.
34. Unwin PNT, Ennis PD. 1984. Two configurations of a channel-forming membrane protein. Nature 307:609-613.
35. Upson C, Faulhaber JT, Kamins D, Laidlaw D, Schlegel D, Vroom J, Gurwitz R, van Dam A. 1989. The application visualization system: a computational environment for scientific visualization. IEEE Computer Graphics Applications 9:30-42.
36. Weiss MS, Wacker T, Weckesser J, Weite W, Schulz GE. 1990. The three-dimensional structure of porin from Rhodobacter capsulatus at 3 Å resolution. FEBS Lett 267:268-272.
37. Willecke K, Hennemann H, Dahl E, Jungbluth S, Heynkes R. 1991. The diversity of connexin genes encoding gap junction proteins. Eur J Cell Biol 56:1-7.
38. Yancey SB (I), John SA (II), Lal R (III), Austin BJ, Revel J-P. 1989. The 43-kD polypeptide of heart gap junctions: Immunolocalization (I), topology (II), and functional domains (III). J Cell Biol 108:2241-2254.
39. Yeager M, Gilula NB. 1992. Membrane topology and quaternary structure of cardiac gap junction ion channels. J Mol Biol 223:929-948.
40. Yeager M, Nicholson BJ. 1996. Structure of gap junction intercellular channels. Curr Opin Struct Biol 6:183-192.
41. Yeager M, Nicholson BJ. 2000. Structure and biochemistry of gap junctions. In: Hertzberg E, editor. Gap junctions, advances in molecular and cell biology. New York: JAI Press, Advances in Molecular and Cell Biology, Vol. 30, p 31-98.
42. Zhou X-W, Pfahnl A, Werner R, Hudder A, Llanes A, Luebke A, Dahl G. 1997. Identification of a pore lining segment in gap junction hemichannels. Biophys J 72:1946-1953.