Multipass membrane protein structure prediction using Rosetta

Proteins: Structure, Function and Genetics

Volumn 62, Issue 4, 2006, Pages 1010-1025

  Yarov Yarovoy, Vladimir ^a   Schonbrun, Jack ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Fragment assembly; Knowledge based scoring function; Molecular modeling; Rosetta method

Indexed keywords

ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); AQUAPORIN; CYTOCHROME C OXIDASE; FUMARATE REDUCTASE; LACTOSE PERMEASE; MEMBRANE PROTEIN; NICOTINIC RECEPTOR; PERMEASE; ROSETTA SOLUBLE PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; ARTICLE; COMPUTER PREDICTION; ENVIRONMENTAL FACTOR; EVALUATION; HYDROPHOBICITY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ENZYMES; MEMBRANE PROTEINS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SOLUBILITY; SOLUTIONS; SUCCINATE DEHYDROGENASE; WATER;

EID: 33644842630     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20817     Document Type: Article

References (72)

1. Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov 2002;1(9):727-730.
2. Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7(4):1029-1038.
3. Arkin IT, Brunger AT, Engelman DM. Are there dominant membrane protein families with a given number of helices? Proteins 1997;28(4):465-466.
4. Liu J, Rost B. Comparing function and structure between entire proteomes. Protein Sci 2001;10(10):1970-1979.
5. White SH. http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html.
6. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000;28(1):235-242.
7. Bradley P, Chivian D, Meiler J, et al. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 2003;53(Suppl 6):457-468.
8. Bradley P, Malmstrom L, Qian B, et al. Free modeling with Rosetta in CASP6. Proteins (in press).
9. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309(5742):1868-1871.
10. Rees DC, DeAntonio L, Eisenberg D. Hydrophobic organization of membrane proteins. Science 1989;245(4917):510-513.
11. Ulmschneider MB, Sansom MS, Di Nola A. Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 2005;59(2):252-265.
12. Pilpel Y, Ben-Tal N, Lancet D. kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. J Mol Biol 1999;294(4):921-935.
13. Adamian L, Nanda V, Degrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins 2005;59(3):496-509.
14. Eilers M, Patel AB, Liu W, Smith SO. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys J 2002;82(5):2720-2736.
15. Javadpour MM, Eilers M, Groesbeek M, Smith SO. Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J 1999;77(3):1609-1618.
16. Jiang S, Vakser IA. Side chains in transmembrane helices are shorter at helix-helix interfaces. Proteins 2000;40(3):429-435.
17. Jiang S, Vakser IA. Shorter side chains optimize helix-helix packing. Protein Sci 2004;13(5):1426-1429.
18. Adamian L, Liang J. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol 2001;311(4):891-907.
19. Adamian L, Liang J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins 2002;47(2):209-218.
20. Choma C, Gratkowski H, Lear JD, DeGrado WP. Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 2000;7(2):161-166.
21. Gratkowski H, Lear JD, DeGrado WF. Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA 2001;98(3):880-885.
22. Zhou FX, Cocco MJ, Russ WP, Brunger AT, Engelman DM. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol 2000;7(2):154-160.
23. Zhou FX, Merianos HJ, Brunger AT, Engelman DM. Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 2001;98(5):2250-2255.
24. Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004;383:66-93.
25. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268(1):209-225.
26. Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34(1):82-95.
27. White SH, Wimley WC. Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 1999;28:319-365.
28. Karplus K, Karchin R, Barrett C, et al. What is the value added by human intervention in protein structure prediction? Proteins 2001;Suppl 5:86-91.
29. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292(2):195-202.
30. Meiler J. JUFO3D: Secondary structure prediction for proteins from low resolution tertiary structure. http://www.jens-meiler.de/. 2003.
31. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305(3):567-580.
32. Sonnhammer EL, von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 1998;6:175-182.
33. Hofmann K, Stoffel W. TMbase - a database of membrane spanning proteins segments. Biol Chem Hoppe Seyler 1993;374:166.
34. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16(4):404-405.
35. Tusnady GE, Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 1998;283(2):489-506.
36. Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics 2001;17(9):849-850.
37. Tusnady GE, Dosztanyi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 2004;20(17):2964-2972.
38. Ulmschneider MB, Sansom MS. Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta 2001;1512(1):1-14.
39. Yau WM, Wimley WC, Gawrisch K, White SH. The preference of tryptophan for membrane interfaces. Biochemistry 1998;37(42):14713-14718.
40. Schiffer M, Chang CH, Stevens FJ. The functions of tryptophan residues in membrane proteins. Protein Eng 1992;5(3):213-214.
41. Eilers M, Shekar SC, Shieh T, Smith SO, Fleming PJ. Internal packing of helical membrane proteins. Proc Natl Acad Sci USA 2000;97(11):5796-5801.
42. Liu W, Eilers M, Patel AB, Smith SO. Helix packing moments reveal diversity and conservation in membrane protein structure. J Mol Biol 2004;337(3):713-729.
43. Gimpelev M, Forrest LR, Murray D, Honig B. Helical packing patterns in membrane and soluble proteins. Biophys J 2004;87(6):4075-4086.
44. Jones DT. Do transmembrane protein superfolds exist? FEBS Lett 1998;423(3):281-285.
45. Jones DT, Taylor WR, Thornton JM. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 1994;33(10):3038-3049.
46. Bonneau R, Strauss CE, Rohl CA, et al. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322(1):65-78.
47. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31(13):3370-3374.
48. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 1997;277(5332):1676-1681.
49. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14(10):846-856.
50. Park J, Karplus K, Barrett C, et al. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 1998;284(4):1201-1210.
51. Van den Berg B, Clemons WM Jr, Collinson I, et al. X-ray structure of a protein-conducting channel. Nature 2004;427(6969):36-44.
52. Higy M, Junne T, Spiess M. Topogenesis of membrane proteins at the endoplasmic reticulum. Biochemistry 2004;43(40):12716-12722.
53. Popot JL, Engelman DM. Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 2000;69:881-922.
54. Marti T. Refolding of bacteriorhodopsin from expressed polypeptide fragments. J Biol Chem 1998;273(15):9312-9322.
55. Taylor WR, Jones DT, Green NM. A method for alpha-helical integral membrane protein fold prediction. Proteins 1994;18(3):281-294.
56. Briggs JA, Torres J, Arkin IT. A new method to model membrane protein structure based on silent amino acid substitutions. Proteins 2001;44(3):370-375.
57. Dobbs H, Orlandini E, Bonaccini R, Seno F. Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins 2002;49(3):342-349.
58. Fleishman SJ, Ben-Tal N. A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices. J Mol Biol 2002;321(2):363-378.
59. Kim S, Chamberlain AK, Bowie JU. A simple method for modeling transmembrane helix oligomers. J Mol Biol 2003;329(4):831-840.
60. Pellegrini-Calace M, Carotti A, Jones DT. Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures. Proteins 2003;50(4):537-545.
61. Pappu RV, Marshall GR, Ponder JW. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat Struct Biol 1999;6(1):50-55.
62. Shacham S, Marantz Y, Bar-Haim S, et al. PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins 2004;57(1):51-86.
63. Shacham S, Topf M, Avisar N, et al. Modeling the 3D structure of GPCRs from sequence. Med Res Rev 2001;21(5):472-483.
64. Park Y, Elsner M, Staritzbichler R, Helms V. Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices. Proteins 2004;57(3):577-585.
65. Jones DT. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins 1997;Suppl 1:185-191.
66. Jones DT. Predicting novel protein folds by using FRAGFOLD. Proteins 2001;Suppl 5:127-132.
67. Baldwin JM, Schertler GF, Unger VM. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 1997;272(1):144-164.
68. Sorgen PL, Hu Y, Guan L, Kaback HR, Girvin ME. An approach to membrane protein structure without crystals. Proc Natl Acad Sci USA 2002;99(22):14037- 14040.
69. Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J 2004;87(5):3448-3459.
70. Beuming T, Weinstein H. Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT. Protein Eng Des Sel 2005;18(3):119-125.
71. Bourne HR, Meng EC. Structure: rhodopsin sees the light. Science 2000;289(5480):733-734.
72. Palczewski K, Kumasaka T, Hori T, et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 2000;289(5480):739-745.