Statistical sequence analyses of G-protein-coupled receptors: Structural and functional characteristics viewed with periodicities of entropy, hydrophobicity, and volume

Proteins: Structure, Function and Genetics

Volumn 56, Issue 4, 2004, Pages 650-660

  Imai, Takashi ^a   Fujita, Norihisa ^a  

^a RITSUMEIKAN UNIVERSITY   (Japan)

Author keywords

Accessibility; GPCR; Ligand binding; Lipid; Signal transduction; Structural packing; Transmembrane helix

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND; MEMBRANE PROTEIN; PHOSPHOLIPID;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CONSENSUS SEQUENCE; DRUG DESIGN; ENTROPY; HUMAN; HYDROPHOBICITY; LIGAND BINDING; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SHANNON ENTROPY; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; STATISTICAL SEQUENCE ANALYSIS; STRUCTURAL PACKING; THREE DIMENSIONAL PROTEIN STRUCTURE; TRANSMEMBRANE HELIX; UNINDEXED SEQUENCE; VOLUMETRY;

ENTROPY; HYDROPHOBICITY; RECEPTORS, G-PROTEIN-COUPLED; SEQUENCE ANALYSIS, PROTEIN;

EID: 4043121012     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20068     Document Type: Article

References (31)

1. Takeda S, Kadowaki S, Haga T, Takaesu H, Mitaku S. Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Lett 2002;520:97-101.
2. Drews J. Drug discovery: a historical perspective. Science 2000;287:1960-1964.
3. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 2000;289:739-745.
4. Ballesteros JA, Shi L, Javitch JA. Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol Pharmacol 2001;60:1-19.
5. Archer E, Maigret B, Escrieut C, Pradayrol L, Fourmy D. Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol Sci 2003;24:36-40.
6. Ballesteros J, Palczewski K. G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr Opin Drug Discovery Dev 2001;4:561-574.
7. Klabunde T, Hessler G. Drug design strategies for targeting G-protein-coupled receptors. ChemBioChem 2002;3:928-944.
8. Baldwin JM. The probable arrangement of the helices in G protein-coupled receptors. EMBO J 1993;12:1693-1703.
9. Baldwin JM, Schertler GFX, Unger VM. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 1997;272:144-164.
10. Mirzadegan T, Benko G, Filipek S, Palczewski K. Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin. Biochemistry 2003;42:2759-2767.
11. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
12. Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 1986;15:321-353.
13. Ballesteros JA, Weinstein H. Integrated methods for the construction of three dimensional models and computational probing of structure-function relations in G-protein coupled receptors. Methods Neurosci 1995;25:366-428.
14. 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 1989;51:109-116.
15. Donnelly D, Overington JP, Ruffle SV, Nugent JHA, Blundell TL. Modeling α-helical transmembrane domains: The calculation and use of substitution tables for lipid-facing residues. Protein Sci 1993;2:55-70.
16. Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci USA 1984;81:140-144.
17. Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structure in proteins. J Mol Biol 1987;195:659-685.
18. Donnelly D, Findlay JBC, Blundell TL. The evolution and structure of aminergic G protein-coupled receptors. Receptors Channels 1994;2:61-78.
19. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 2003;31:294-297.
20. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 1987;84:4355-4358.
21. Mount DW. Bioinformatics: sequence and genome analysis. New York: Cold Spring Harbor Laboratory Press; 2001.
22. Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998;14:378-379.
23. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-580.
24. Henikoff S, Henikoff JG. Position-based sequence weights. J Mol Biol 1994;243:574-578.
25. Edelsbrunner H, Facello M, Fu P, Liang J. Measuring proteins and voids in proteins. In: Proceedings of the 28th annual Hawaii international conference on system sciences. Los Alamitos: IEEE Computer Society Press; 1995. p 256-264.
26. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
27. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
28. Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y. Functional role of internal water molecules in rhodopsin revealed by x-ray crystallography. Proc Natl Acad Sci USA 2002;99:5982-5987.
29. Oliveira L, Paiva ACM, Vriend G. A common motif in G-protein-coupled seven transmembrane helix receptors. J Comput-Aided Mol Des 1993;7:649-658.
30. Cronet P, Sander C, Vriend G. Modeling of transmembrane seven helix bundles. Protein Eng 1993;6:59-64.
31. Donnelly D, Cogdell RJ. Predicting the point at which transmembrane helices protrude from the bilayer: a model of the antenna complexes from photosynthetic bacteria. Protein Eng 1993;6:629-635.