Structure prediction of helical transmembrane proteins at two length scales

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 2, 2006, Pages 317-333

  Chen, Zhong ^a   Xu, Ying ^a  

^a University of Georgia ^*  (United States)

Author keywords

Local energy minima; Multi scale modeling; Statistical potential; Structure prediction; Transmembrane helix packing; Wang Landau algorithm

Indexed keywords

HELIX LOOP HELIX PROTEIN; MEMBRANE PROTEIN;

ALGORITHM; ATOM; CONFERENCE PAPER; CONTROLLED STUDY; FEASIBILITY STUDY; MATHEMATICAL COMPUTING; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; RANDOMIZATION; SIMULATION; STATISTICAL MODEL;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; MEMBRANE PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE ANALYSIS, PROTEIN;

EID: 33745726575     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006001965     Document Type: Conference Paper

References (39)

1. Fleming KG, Riding the wave: Structural and energetic principles of helical membrane proteins, Curr Opin Biotechnol 11:67-71, 2000.
2. Berman HM, Westbrook J, Feng Z, et al., The protein data bank, Nucleic Acids Res 28:235-242, 2000.
3. Wallin E, von Heijne G, Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms, Protein Sci 7:1029-1038, 1998.
4. Adams PD, Engelman DM, Brunger AT, Improved prediction for the structure of the dimeric transmembrane domain of glycophorin a obtained through global searching, Proteins Struct Funct Genet 26:257-261, 1996.
5. Fleming KG, Engelman DM, Computation and mutagenesis suggest a right-handed structure for the synaptobrevin transmembrane dimer, Proteins Struct Funct Genet 45:313-317, 2001.
6. Torres J, Briggs JAG, Arkin IT, Contribution of energy values to the analysis of global searching molecular dynamics simulations of transmembrane helical bundles, Biophys J 82:3063-3071, 2002.
7. Pappu RV, Marshall GR, Ponder JW, A potential smoothing algorithm accurately predicts transmembrane helix packing, Nat Struct Biol 6:50-55, 1999.
8. Piela L, Kostrowicki J, Scheraga HA, On the multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method, J Phys Chem 93:3339-3346, 1989.
9. Orlandini E, Seno F, Banavar JR, Laio A, Maritan A, Deciphering the folding kietics of transmembrane helical proteins, Proc Natl Acad Sci USA 97:14229-14234, 2000.
10. Chen C-M, Chen C-C, Computer simulations of membrane protein folding: Structure and dynamics, Biophys J 84:1902-1908, 2003.
11. Nikiforovich GV, Galaktionov S, Balodis J, Marshall GR, Novel approach to computer modeling of seven-helical transmembrane proteins: Current progress in the test case of bacteriorhodopsin, Acta Biochim Pol 48:53-64, 2001.
12. Vaidehi N, Floriano WB, Trabanino R, et al., Prediction of structure and function of g protein-coupled receptors, Proc Natl Acad Sci USA 99:12622-12627, 2002.
13. 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 50:537-545, 2003.
14. Kim S, Chamberlain AK, Bowie JU, A simple method for modeling transmembrane helix oligomers, J Mol Biol 329:831-840, 2003.
15. Kokubo H, Okamoto Y, Prediction of membrane protein structures by replica-exchange monte carlo simulations: Case of two helices, J Chem Phys 120:10837-10847, 2004.
16. Kokubo H, Okamoto Y, Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange monte carlo simulation, Chem Phys Lett 392:168-175, 2004.
17. Popot JL, Engelman DM, Membrane protein folding and oligomerization: The two-stage model, Biochemistry 29:4031-4037, 1990.
18. Chen CP, Kernytsky A, Rost B, Transmembrane helix predictions revisited, Protein Sci 11:2774-2791, 2002.
19. Kall L, Krogh A, Sonnhammer ELL, A combined transmembrane topology and signal peptide prediction method, J Mol Biol 338:1027-1036, 2004.
20. Zhou HY, Zhang C, Liu S, Zhou YQ, Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations, Nucleic Acids Res 33:W193-W197, 2005.
21. Wang F, Landau DP, Efficient, multiple-range random walk algorithm to calculate the density of states, Phys Rev Lett 86:2050-2053, 2001.
22. Wang F, Landau DP, Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram, Phys Rev E Stat Nonlin Soft Matter Phys 64:056101, 2001.
23. Rathore N, Knotts TA, de Pablo JJ, Density of states simulations of proteins, J Chem Phys 118:4285-4290, 2003.
24. Chen Z, Xu Y, Energetics and stability of transmembrane helix packing: A replica-exchange simulation with a knowledge-based membrane potential, Proteins Struct Funct Bioinformatics 62:539-552, 2006.
25. Bormann BJ, Engelman DM, Intramembrane helix-helix association in oligomerization and transmembrane signaling, Ann Rev Biophy Biomol Struct 21:223-242, 1992.
26. Cramer WA, Engelman DM, Vonheijne G, Rees DC, Forces involved in the assembly and stabilization of membrane-proteins, Faseb J 6:3397-3402, 1992.
27. Lemmon MA, Engelman DM, Specificity and promiscuity in membrane helix interactions, Quarterly Reviews of Biophysics 27:157-218, 1994.
28. White SH, Wimley WC, Membrane protein folding and stability: Physical principles, Annu Rev Biophys Biomol Struct 28:319-365, 1999.
29. Zhou H, Zhou Y, Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction, Protein Sci 11:2714-2726, 2002.
30. Zhang C, Liu S, Zhou HY, Zhou YQ, An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state, Protein Sci 13:400-411, 2004.
31. MacKenzie KR, Prestegard JH, Engelman DM, A transmembrane helix dimer: structure and implications, Science 276:131-133, 1997.
32. Kahn TW, Sturtevant JM, Engelman DM, Thermodynamic measurements of the contributions of helix-connecting loops and of retinal to the stability of bacteriorhodopsin, Biochemistry 31:8829-8839, 1992.
33. Belrhali H, Nollert P, Royant A, et al., Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 a resolution, Struct Fold Des 7:909-917, 1999.
34. Neria E, Fischer S, Karplus M, Simulation of activation free energies in molecular systems, J Chem Phys 105:1902-1921, 1996.
35. von Heijne G, The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology, EMBO J 5:3021-3027, 1986.
36. von Heijne G, Membrane proteins: From sequence to structure, Annu Rev Biophys Biomol Struct 23:167-192, 1994.
37. Zhou H, Zhou Y, Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-markov-model-based method, Protein Sci 12:1547-1555, 2003.
38. Bowie JU, Helix packing in membrane proteins, J Mol Biol 272:780-789, 1997.
39. Ichiye T, Karplus M, Collective motions in proteins - a covariance analysis of atomic fluctuations in molecular-dynamics and normal mode simulations, Proteins Struct Funct Genet 11:205-217, 1991.