Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

Journal of Molecular Graphics and Modelling

Volumn 27, Issue 8, 2009, Pages 944-950

  Hall, Spencer E ^a   Roberts, Kyle ^a   Vaidehi, Nagarajan ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

Dynamics; GPCR structure; Helical kinks; Transmembrane helices

Indexed keywords

[CARBONYL; COMPUTATIONAL PREDICTIONS; FUNCTIONAL DIVERSITY; GPCR STRUCTURE; HELICAL KINKS; MAIN CHAINS; MD SIMULATION; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; PROLINE KINKS; ROTATIONAL ORIENTATION; SIDE CHAINS; STRUCTURAL FEATURE; STRUCTURAL MODELS; STRUCTURE PREDICTION; TRANSMEMBRANE HELICES; TRANSMEMBRANE PROTEINS;

AMINES; AMINO ACIDS; BINDING SITES; CELL MEMBRANES; DYNAMICS; HYDROGEN; HYDROGEN BONDS; LIPID BILAYERS; MEMBRANES; MODEL STRUCTURES; MOLECULAR DYNAMICS; ORGANIC ACIDS;

PROTEINS;

AMINO ACID; CARBONYL DERIVATIVE; MEMBRANE PROTEIN; PROLINE;

ARTICLE; CRYSTAL STRUCTURE; DATA BASE; HYDROGEN BOND; LIPID BILAYER; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MEMBRANE PROTEINS; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 67349266230     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.02.004     Document Type: Article

References (26)

1. Yohannan S., Faham S., Yang D., Whitelegge J.P., and Bowie J.U. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. U.S.A. 101 4 (2004) 959-963
2. Constantini S., Colonna G., and Facchiano A.M. Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem. Biophys. Res. Commun. 342 (2006) 441-451
3. Kyngas J., and Valjakka J. Unreliability of the Chou-Fasman parameters in predicting protein secondary structure. Protein Eng. 11 5 (1998) 345-348
4. Zhang J., and Madden T.L. PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7 6 (1997) 649-656
5. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucl. Acids Res. 31 13 (2003) 3497-3500
6. Jayasinghe S., Hristova K., and White S.H. MPtopo: a database of membrane protein topology. Protein Sci. 10 2 (2001) 455-458
7. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 12 (1983) 2577-2637
8. Visiers I., Braunheim B.B., and Weinstein H. ProKink: a protocol for numerical evaluation of helix distortions by proline. Protein Eng. 13 9 (2000) 603-606
9. M. Mezei, Simulaid: simulation setup utilities [cited 2007; available from: http://inka.mssm.edu/∼mezei/simulaid].
10. Mayo S.L., Olafson B.D., and Goddard III W.A. DRIEDING-a generic force field for molecular simulations. J. Phys. Chem. 94 (1990) 8897-8909
11. MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., and Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
12. Vaidehi N., Floriano W.B., Trabanino R., Hall S., Freddolino P., Choi E.J., Zamanakos G., and Goddard III W.A. Prediction of structure and function of G protein-coupled receptors. Proc. Natl. Acad. Sci. U.S.A. 99 20 (2002) 12622-12627
13. Rappe A.K., and Goddard III W.A. Charge equilibration for molecular-dynamics simulations. J. Phys. Chem. 95 (1991) 3358-3363
14. Ghosh A., Rapp C.S., and Friesner R.A. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B 102 (1998) 10983-10990
15. Ding H.Q., Karasawa N., and Goddard III W.A. Atomic level simulations on a million particles-the cell multipole method for Coulomb and London nonbond interactions. Chem. Phys. Lett. 97 (1992) 4309-4315
16. Lim K.-T., Brunett S., Iotov M., McClurg R.B., Vaidehi N., Dasgupta S., Taylor S., and Goddard III W.A. Molecular dynamics for very large systems on massively parallel computers: the MPSim program. J. Comput. Chem. 18 (1997) 501-521
17. BIOGRAF/POLYGRAF, Molecular Simulations Inc., 1992.
18. Deupi X., Olivella M., Govaerts C., Ballesteros J.A., Campillo M., and Pardo L. Ser and Thr residues modulate the conformation of pro-kinked transmembrane alpha-helices. Biophys. J. 86 (2004) 105-115
19. Chou P.Y., and Fasman G.D.E. Prediction of Protein Structure and the Principles of Protein Conformation (1989), Plenum Press, New York pp. 549-586
20. Russ W.P., and Engelman D.M. The GxxxG motif: a framework for transmembrane helix-helix association. J. Mol. Biol. 296 3 (2000) 911-919
21. Walters R.F., and DeGrado W.F. Helix-packing motifs in membrane proteins. Proc. Natl. Acad. Sci. U.S.A. 103 37 (2006) 13658-13663
22. Senes A., Gerstein M., and Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol. 296 3 (2000) 921-936
23. Schlyer S., and Horuk R. I want a new drug: G-protein-coupled receptors in drug development. Drug Discov. Today 11 11-12 (2006) 481-493
24. Trabanino R.J., Hall S.E., Vaidehi N., Floriano W.B., Kam V.W., and Goddard W.A. First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin. Biophys. J. 86 (2004) 1904-1921
25. Bhattacharya S., Hall S.E., and Vaidehi N. Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors. J. Mol. Biol. 382 (2008) 539-555
26. Canutescu A.A., Shelenkov A.A., and Dunbrack Jr. R.L. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12 9 (2003) 2001-2014