Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban

Biophysical Journal

Volumn 74, Issue 3, 1998, Pages 1203-1214

  Herzyk, Pawel ^a   Hubbard, Roderick E ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ION CHANNEL; PHOSPHOLAMBAN;

ARTICLE; MOLECULAR MODEL; MUTAGENESIS; PROTEIN DOMAIN; PROTEIN LOCALIZATION; SIMULATION;

EID: 0031910468     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77835-X     Document Type: Article

References (30)

1. Adams, P. D., I. T. Arkin, D. M. Engelman, and A. T. Brünger. 1995. Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nature Struct. Biol. 2:154-162.
2. Adams, P. D., D. M. Engelman, and A. T. Brunger. 1996. Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching. Proteins Struct. Funct. Genet. 26:257-261.
3. Arkin, I. T., P. D. Adams, K. R. MacKenzie, M. A. Lemmon, A. T. Brünger, and D. M. Engelman. 1994. Structural organization of the pentameric transmembrane α-helices of phospholamban, a cardiac ion channel. EMBO J. 13:4757-4764.
4. Arkin, I. T., M. Rothman, C. F. C. Ludlam, S. Aimoto, D. M. Engelman, K. J. Rothschild, and S. O. Smith. 1995. Structural model of the phospholamban ion channel complex in phospholipid membranes. J. Mol. Biol. 248:824-834.
5. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Jr. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
6. Bormann, B. J., W. J. Knowles, and V. T. Marchesi. 1989. Synthetic peptides mimic the assembly of transmembrane glycoproteins. J. Biol. Chem. 264:4033-4037.
7. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
8. Brünger, A. T. 1992. X-PLOR: A System for X-ray Crystallography and NMR, version 3.1. Yale University Press, New Haven, CT.
9. Chothia, C., M. Levitt, and D. Richardson. 1981. Helix to helix packing in proteins. J. Mol. Biol. 145:215-250.
10. Herzyk, P., and R. E. Hubbard. 1993. A reduced representation of proteins for use in restraint satisfaction calculations. Proteins Struct. Funct. Genet. 17:310-324.
11. Herzyk, P., and R. E. Hubbard. 1995. An automated method for modelling seven-helix transmembrane receptors from experimental data. Biophys. J. 69:2419-2442.
12. Kerr, I. D., R. Sankararamakrishnan, O. S. Smart, and M. S. P. Sansom. 1994. Parallel helix bundles and ion channels: molecular modelling via simulated annealing and restrained molecular dynamics. Biophys. J. 67:1501-1515.
13. Kirchberger, M. A., M. Tada, and A. M. Katz. 1975. Phospholamban: a regulatory protein of the cardiac sarcoplasmic reticulum. Recent Adv. Stud. Cardiac Struct. Metab. 5:103-115.
14. Kirkpatrick, S., C. D. Gellat, Jr., and M. P. Vecchi. 1983. Optimization by simulated annealing. Science. 220:671-680.
15. 2+-selective channels in lipid bilayers. J. Biol. Chem. 263:18364-18368.
16. Lemmon, M. A., J. M. Flanagan, H. R. Treutlein, J. Zhang, and D. M. Engelman. 1992. Sequence specificity in the dimerization of transmembrane α-helices. Biochemistry. 31:12719-12725.
17. Ludlam, C. F. C., I. T. Arkin, X.-M. Liu, M. S. Rothman, P. Rath, S. Aimoto, S. O. Smith, D. M. Engelman, and K. J. Rothschild. 1996. Fourier transform infrared spectroscopy and site-directed isotope label-ling as a probe of local secondary structure in the transmembrane domain of phospholamban. Biophys. J. 70:1728-1736.
18. MacKenzie, K. R., J. H. Prestegard, and D. M. Engelman. 1997. A transmembrane helix dimer: structure and implications. Science. 276: 131-133.
19. Malashkevich, V. N., R. A. Kammerer, V. P. Efimov, T. Schulthess, and J. Engel. 1996. The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? Science. 274:761-765.
20. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculation by fast computing machines. J. Chem. Phys. 21:1087-1092.
21. Neria, E., S. Fisher, and M. Karplus. 1996. Simulation of activation free-energies in molecular systems. J. Chem. Phys. 105:1902-1921.
22. Nilges, M., and A. T. Brünger. 1991. Automated modeling of coiled coils: application to the GCN4 dimerization region. Protein Eng. 4:649-659.
23. Oldfield, T. J. 1992. SQUID: a program for the analysis and display of data from crystallography and molecular dynamics. J. Mol. Graph. 10: 247-252.
24. O'Shea, E. K., J. D. Klemm, P. S. Kim, and T. Alber. 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 245:539-544.
25. 2+-ATPaSe. J. Biol. Chem. 270: 9390-9397.
26. Simmerman, H. K. B., Y. M. Kobayashi, J. M. Autry, and L. R. Jones. 1996. A leucine zipper stabilizes the pentamer membrane domain of phospholamban and forms a coiled-coil pore structure. J. Biol. Chem. 271:5941-5946.
27. Simmerman, H. K. B., D. E. Lovelace, and L. R. Jones. 1989. Secondary structure of detergent-solubilized phospholamban, a phosphorylatable, oligomeric protein of cardiac sarcoplasmic reticulum. Biochim. Biophys. Acta. 997:322-329.
28. Smith, S. O., and B. J. Bormann. 1995. Determination of helix-helix interactions in membranes by rational resonance NMR. Proc. Natl. Acad. Sci. USA. 92:488-491.
29. 2+-pump ATPase by cAMP-dependent phosphorylation of phospholamban. BioEssays. 10: 157-163.
30. Treutlein, H. R., M. A. Lemmon, D. M. Engelman, and A. T. Brünger. 1992. The glycophorin A transmembrane domain dimer: sequence-specific propensity for a right-handed supercoil of helices. Biochemistry. 31:12726-12733.