Assigning transmembrane segments to helices in intermediate-resolution structures

Bioinformatics

Volumn 20, Issue SUPPL. 1, 2004, Pages

  Enosh, Angela ^a   Fleishman, Sarel J ^a   Ben Tal, Nir ^a   Halperin, Dan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; LACTOSE PERMEASE; MEMBRANE PROTEIN;

ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; CONFERENCE PAPER; CRYOELECTRON MICROSCOPY; FEASIBILITY STUDY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SCORING SYSTEM; STRUCTURE ANALYSIS;

EID: 16344394956     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth939     Document Type: Conference Paper

References (21)

1. Adams, P.D., Arkin, I.T., Engelman, D.M. and Brunger, A.T. (1995) Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nat. Struct. Biol., 2, 154-162.
2. de Berg, M., van Kreveld, M., Overmars, M. and Schwarzkopf, O. (2000) Computational Geometry: Algorithms and Applications, 2nd edition. Springer-Verlag, Berlin.
3. Canutescu, A.A. and Dunbrack, R.L. (2003) Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci., 12, 963-972.
4. Chen, C.P., Kernytsky, A. and Rost, B. (2002) Transmembrane helix predictions revisited. Protein Sci., 11, 2774-2791.
5. Choma, C., Gratkowski, H., Lear, J.D. and DeGrado, W.F. (2000) Asparagine-mediated self-association of a model transmembrane helix. Nat. Struct. Biol., 7, 161-166.
6. Creighton, T.E. (1993) Poteins, Structures and Molecular Properties. Freeman, New York.
7. Eilers, M., Shekar, S.C., Shieh, T., Smith, S.O. and Fleming, P.J. (2000) Internal packing of helical membrane proteins. Proc. Natl Acad. Sci., USA, 97, 5796-5801.
8. Fleishman, S.J. and Ben-Tal, N. (2002) A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices. J. Mol. Biol., 321, 363-378.
9. Holm, P.J., Morgenstern, R. and Hebert, H. (2002) The 3-D structure of microsomal glutathione transferase 1 at 6 A resolution as determined by electron crystallography of p22(1)2(1) crystals. Biochim. Biophys. Acta, 1594, 276-285.
10. Jakobsson, P.J., Morgenstern, R., Mancini, J., Ford-Hutchinson, A. and Persson, B. (1999) Common structural features of MAPEG-a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism. Protein Sci., 8, 689-692.
11. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonding and geometrical features, http://www.cmbi.kun.nl/gv/dssp/. Biopolymers, 22, 2577-2637.
12. Kim, S., Chamberlain, A.K. and Bowie, J.U. (2003) A simple method for modeling transmembrane helix oligomers. J. Mol. Biol., 329, 831-840.
13. MacKenzie, K.R. and Engelman, D.M. (1998) Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization. Proc. Natl Acad. Sci., USA, 95, 3583-3590.
14. Manocha, D. and Zhu, Y. (1994) Kinematic manipulation of molecular chains subject to rigid constraints. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 285-293.
15. Pellegrini-Calace, M., Carotti, A. and Jones, D.T. (2003) Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures. Proteins, 50, 537-545.
16. Russ, W.P. and Engelman, D.M. (2000) The GxxxG motif: a framework for transmembrane helix-helix association. J. Mol. Biol., 296, 911-919.
17. Schmidt-Krey, I., Mitsuoka, K., Hirai, T., Murata, K., Cheng, Y., Fujiyoshi, Y., Morgenstern, R. and Hebert, H. (2000) The three-dimensional map of microsomal glutathione transferase 1 at 6 A resolution. EMBO J, 19, 6311-6316.
18. Unger, V.M. (2001) Electron cryomicroscopy methods. Curr. Opin. Struct. Biol., 11, 548-554.
19. Wedemeyer, W.J. and Scheraga, H.A. (1999) Exact analytical loop closure in proteins using polynomial equations. J. Comp. Chem., 20, 819-844.
20. Wojcik, J., Mornon, J.P. and Chomilier, J. (1999) New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J. Mol. Biol., 289, 1469-1490.
21. Xiang, Z., Soto, C.S. and Honig, B. (2002) Evaluating conformational free energies: The colony energy and its application to the problem of protein loop prediction. Proc. Natl Acad. Sci., USA, 99, 7432-7437.