Modeling transmembrane helical oligomers

Current Opinion in Structural Biology

Volumn 7, Issue 4, 1997, Pages 486-494

  Dieckmann, Gregg R ^a   Degrado, William F ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPHORIN; MEMBRANE PROTEIN; OLIGOMER; PHOSPHOLAMBAN; VIRUS PROTEIN;

ALPHA HELIX; INFLUENZA VIRUS A; MOLECULAR MODEL; PRIORITY JOURNAL; REVIEW;

INFLUENZA A VIRUS; INFLUENZA VIRUS;

EID: 0030846112     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80111-X     Document Type: Article

References (82)

1. Cohen C, Parry DAD. α-Helical coiled coils and bundles: how to design an α-helical protein. Proteins. 7:1990;1-15.
2. Bryson JW, Betz SV, Lu HS, Suich DJ, Zhou HX, O'Neil KT, DeGrado WF. Protein design, a heirarchic approach. Science. 270:1995;935-941.
3. Betz SF, DeGrado WF. Controlling topology and native-like behavior of de novo-designed peptides: design and characterization of antiparallel four-stranded coiled coils. Biochemistry. 35:1996;6955-6962.
4. Hodges RS. Unzipping the secrets of coiled coils. Curr Biol. 2:1992;122-124.
5. Lumb KJ, Kim PS. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry. 34:1995;8642-8648.
6. Lumb KJ, Kim PS. Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper. Science. 268:1995;436-439.
7. Kitakuni E, Kuorda Y, Oobatake M, Tanaka T, Nakamura H. Thermodynamic characterization of an artificially designed amphiphilic α-helical peptide containing periodic prolines: observation of high thermal stability and cold denaturation. Protein Sci. 3:1994;831-837.
8. Yu Y, Monera OD, Hodges RS, Privalov PL. Ion pairs significantly stabilize coiled-coils in the absence of electrolyte. J Mol Biol. 255:1996;367-372.
9. Sosnick TR, Jackson S, Wilk RR, Englander SW, DeGrado WF. The role of helix formation in the folding of a fully alpha-helical coiled coil. Proteins. 24:1996;427-432.
10. Wendt H, Berger C, Baici A, Thomas RM, Bosshard HR. Kinetics of folding of leucine zipper domains. Biochemistry. 34:1995;4097-4107.
11. Harbury PB, Zhang T, Kim PS, Alber T. A switch between two-, three-, and four-stranded coiled coils. Science. 262:1993;1401-1407.
12. Harbury PB, Kim PS, Alber T. Crystal structure of an isoleucine-zipper trimer. Nature. 371:1994;80-83.
13. Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D. Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science. 259:1993;1288-1293.
14. d: implications for engineering crystals and supramolecular assemblies. Protein Sci. 6:1997;78-86.
15. Montal M. Molecular mimicry in channel-protein structure. Curr Opin Struct Biol. 5:1995;501-506.
16. Koning F, Maloy WL, Coligan JE. The implications of subunit interactions for the structure of the T cell receptor - CD3 complex. Eur J Immunol. 20:1990;299-305.
17. Koning F. Lymphocyte antigen receptors: a common design? Immunol Today. 12:1991;100-101.
18. Manolios N, Bonifacino JS, Klausner RD. Transmembrane helical interactions and the assembly of the T cell receptor complex. Science. 249:1990;274-276.
19. Tan L, Turner J, Weiss A. Regions of the T cell receptor alpha and beta chains that are responsible for interactions with CD3. J Exp Med. 173:1991;1247-1256.
20. Cosson P, Bonifacino JS. Role of transmembrane domain interactions in the assembly of class II MHC molecules. Science. 258:1991;659-662.
21. Bargmann CI, Hung MC, Weinberg RA. Multiple independent activations of the neu oncogene by a point mutation altering the transmembrane domain of p185. Cell. 45:1986;649-657.
22. Bargmann CI, Weinberg RA. Increased tyrosine kinase activity associated with the protein encoded by the activated neu oncogene. Proc Natl Acad Sci USA. 85:1988;2371-2377.
23. Shai Y. Molecular recognition between membrane-spanning polypeptides. Trends Biochem Sci. 20:1995;460-464.
24. Cafiso DS. Alamethicin: a peptide model for voltage gating and protein - membrane interactions. Stroud RM. Annual Review of Biophysics and Biomolecular Structure. 1994;141-165 Annual Reviews Inc, Palo Alto, CA.
25. Sansom M. The biophysics of peptide models of ion channels. Prog Biophys Mol Biol. 55:1991;139-235.
26. Popot J-L, Engelman DM. Membrane protein folding and oligomerization: the two-stage model. Biochemistry. 29:1990;4031-4037.
27. Rees DC, DeAntonio L, Eisenberg D. Hydrophobic organization of membrane proteins. Science. 245:1989;510-513.
28. Donnelly D, Johnson MS, Blundell TL, Saunders J. An analysis of the periodicity of conserved residues in sequence alignments of G-protein coupled receptors. FEBS Lett. 251:1989;109-116.
29. Donnelly D, Overington JP, Ruffle SV, Nugent JHA, Blundell TL. Modeling alpha helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci. 2:1993;55-70.
30. Samatey FA, Xu C, Popot J-L. On the distribution of amino acid residues in transmembrane alpha helix bundles. Proc Natl Acad Sci USA. 92:1995;4577-4581.
31. 2 protein: a molecular modelling study of the ion channel. Protein Eng. 6:1993;65-74.
32. Lemmon MA, Engelman DM. Specificity and promiscuity in membrane helix interactions. Quart Rev Biophys. 27:1994;157-218.
33. Oh K, Zhan H, Cui C, Hideg K, Collier R, Hubbell W. Organization of diphtheria toxin T domain in bilayers: a site-directed spin labeling study. Science. 273:1996;810-812.
34. Lemmon MA, Flanagan JM, Treutlein HR, Zhang J, Engelman DM. Sequence specificity in the dimerization of transmembrane alpha helices. Biochemistry. 31:1992;12719-12725.
35. Dunker K, Zaleske DJ. Stereochemical considerations for constructing alpha-helical proteins with particular application to membrane proteins. Biochem J. 163:1977;45-57.
36. Crick FHC. The packing of alpha-helices: simple coiled-coils. Acta Cryst. 6:1953;689-697.
37. Adams PD, Brünger AT. Towards prediction of membrane structure. of outstanding interest von Heijne G. Membrane Protein Assembly. 1997;251-265 RG Landes Co, Austin, TX, This is an excellent review of work on the modeling of TM helical bundles.
38. Kerr ID, Sankararamakrishnan R, Smart O, Sansom M. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys J. 67:1994;1501-1515.
39. Adams PD, Engelman DM, Brünger AT. Improved prediction for the structure of the dimeric transmembrane domain of glycophorin obtained through global searching. of special interest Proteins. 26:1996;257-261 The refinement of earlier work on the modeling of the TM region of GP is presented.
40. Treutlein HR, Lemmon MA, Engelman DM, Brünger At. The glycophorin A transmembrane domain dimer: sequence-specific propensity for a right-handed supercoil of helices. Biochemistry. 31:1992;12726-12733.
41. Adams PD, Arkin IT, Engelman DM, Brünger AT. Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nat Struct Biol. 2:1995;154-162.
42. 2 proton channel of influenza A virus suggests a mechanism for its ion-selectivity. Proc Natl Acad Sci USA. 1997;. in press.
43. Dieckmann GR. Use of metal-binding de novo-designed α-helical peptides in the study of metalloprotein structures. PhD Thesis. 1995;University of Michigan, Michigan.
44. Harbury PB, Tidor B, Kim PS. Repacking protein cores with backbone freedom: structure prediction for coiled coils. Proc Natl Acad Sci USA. 92:1995;8408-8412.
45. Adair BD, Engelman DM. Glycophorin A helical transmembrane domains dimerize in phospholipid bilayers: a resonance energy transfer study. Biochemistry. 33:1994;5539-5544.
46. Bormann B-J, Knowles WJ, Marchesi VT. Synthetic peptides mimic the assembly of transmembrane glycoproteins. J Biol Chem. 264:1989;4033-4037.
47. Chothia C. Principals that determine the structure of proteins. Annu Rev Biochem. 53:1984;537-572.
48. Lemmon MA, Treutlein HR, Adams PD, Brünger AT, Engelman DM. A dimerization motif for transmembrane alpha helices. Nat Struct Biol. 1:1994;157-163.
49. Smith SO, Bormann BJ. Determination of helix - helix interactions in membranes by rotational resonance NMR. Proc Natl Acad Sci USA. 92:1995;488-491.
50. MacKenzie KR, Prestegard JH, Engelman DM. A transmembrane helix dimer: structure and implications. of outstanding interest Science. 276:1997;131-133 In the culmination of many years of work on this system, the authors describe the NMR structure of the TM region of GP.
51. Stowell MHB, Rees DC. Structure and stability of membrane proteins. Adv Prot Chem. 46:1995;279-311.
52. Arkin IT, Adams PD, MacKenzie KR, Lemmon MA, Brünger AT, Engelman DM. Structural organization of the pentameric transmembrane alpha-helices of phospholamban, a cardiac ion channel. EMBO J. 13:1994;4757-4764.
53. Arkin IT, Rothman M, Ludlam CFC, Aimoto S, Engelman DM, Rothschild KJ, Smith SO. Structural model of the phospholamban ion channel complex in phospholipid membranes. J Mol Biol. 248:1995;824-834.
54. Arkin IT, MacKenzie KR, Fisher L, Aimoto S, Engelman DM, Smith SO. Mapping the lipid-exposed surfaces of membrane proteins. Nat Struct Biol. 3:1996;240-243.
55. Simmerman HKB, Kobayashi, Yvonne M, Autry JM, Jones LR. A leucine zipper stabilizes the pentameric membrane domain of phospholamban and forms a coiled-coil pore structure. of outstanding interest J Biol Chem. 271:1996;5941-5946 An excellent application of scanning mutagenesis to determine the features defining the association of PL in membranes.
56. Malashkevich VN, Kammerer RA, Efimov VP, Schulthess T, Engel J. The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? Science. 274:1996;761-765.
57. Ludlam CFC, Arkin IT, Liu X-M, Rothman MS, Rath P, Aimoto S, Smith SO, Engelman DM, Rothschild KJ. Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban. Biophys J. 70:1996;1728-1736.
58. Tatulian SA, Jones LR, Reddy LG, Stokes DL, Tamm LK. Secondary structure and orientation of phospholamban reconstituted in supported bilayers from polarized attenuated total reflection RTIF spectroscopy. Biochemistry. 34:1995;4448-4456.
59. Maslennikov IV, Sobol AG, Anagli J, James P, Vorherr T, Arseniev AS, Carafoli E. The secondary structure of phospholamban: a two-dimensional NMR study. Biochem Biophys Res Commun. 217:1995;1200-1207.
60. 2 protein has ion channel activity. Cell. 69:1992;517-528.
61. Terwilliger EF, Cohen EA, Lu Y, Sodroski JG, Haseltine WA. Functional role of human immunodeficiency virus type 1 vpu. Proc Natl Acad Sci USA. 86:1989;5163-5167.
62. Hay AJ, Wolstenholme AJ, Skehel JJ, Smith MH. The molecular basis of the specific anti-influenza action of amantadine. EMBO J. 4:1985;3021-3024.
63. 2 protein: characterization of the amantadine block. J Virol. 67:1993;5585-5594.
64. 2 protein-dependent event in the replication cycle of avian influenza (H7) viruses. Arch Virol. 119:1991;265-273.
65. 2 protein and hemagglutinin conformation changes during intracellular-transport. Acta Virol. 39:1995;171-181.
66. 2 integral membrane protein is a homotetramer stabilized by formation of disulfide bonds. Virology. 183:1991;32-43.
67. 2 ion channel protein: a structure-function analysis. J Virol. 68:1994;1551-1563.
68. 2 protein. J Virol. 69:1995;1219-1225.
69. 2 ion channel of influenza virus. Biophys J. 70:1996;1335-1346.
70. 2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Biophys J. 69:1995;1363-1371.
71. 2 protein of influenza A viruses. Virology. 191:1992;541-549.
72. 2 ion channel in lipid bilayers. J Membrane Biol. 142:1994;117-126.
73. 2 protein forms amantadine-sensitive proton channels in planar lipid bilayers. Virology. 190:1992;485-489.
74. 2 transmembrane domain. A circular dichroism study. FEBS Lett. 311:1992;256-258.
75. 2 protein expressed by baculovirus: evidence for proton transfer activity. J Gen Virol. 75:1994;3477-3484.
76. 2 protein.
77. Deber CM, Khan AR, Li Z, Joensson C, Glibowicka M, Wang J. Val to Ala mutations selectively alter helix/helix packing in the transmembrane segment of phage M13 coat protein. Proc Natl Acad Sci USA. 90:1993;11648-11652.
78. Shon KJ, Kim Y, Colnago LA, Opella SJ. NMR studies of the structure and dynamics of membrane-bound bacteriophage Pf1 coat protein. Science. 252:1991;1303-1305.
79. Herzyk P, Hubbard RE. Automated method for modeling seven-helix transmembrane receptors from experimental data. Biophys J. 69:1995;2419-2442.
80. Tuffery P, Etchebest C, Popot J-L, Lavery R. Prediction of the positioning of the seven transmembrane α-helices of bacteriorhodopsin. J Mol Biol. 236:1994;1105-1122.
81. Eisenberg D, McLachlan AD. Solvation energy in protein folding and stability. Nature. 319:1986;199-203.
82. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst. 24:1991;946-950.