Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins

Journal of Theoretical Biology

Volumn 269, Issue 1, 2011, Pages 88-95

  Zhang, Jiapu ^a  

^a UNIVERSITY OF BALLARAT   (Australia)

Author keywords

Immunity; Molecular dynamics; Prion diseases; Rabbit prion protein

Indexed keywords

PRION PROTEIN;

IMMUNITY; MOLECULAR ECOLOGY; PROTEIN; SMALL MAMMAL;

ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; CONTROLLED STUDY; HYDROGEN BOND; IMMUNITY; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; SCRAPIE;

ANIMALS; HUMANS; HYDROGEN-ION CONCENTRATION; MICE; PRIONS; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; RABBITS;

ANIMALIA; MAMMALIA; MAMMALIAN PRION; ORYCTOLAGUS CUNICULUS;

EID: 77958611177     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.10.020     Document Type: Article

References (52)

1. Aguzzi A., Heikenwalder M. Pathogenesis of prion diseases: current status and future outlook. Nat. Rev. Microbiol. 2006, 4:765-775.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 2000, 28:242-253.
3. Cappaia R., Collinsa S.J. Structural biology of prions. Prions. A Challenge for Science Medicine and the Public Health System. Contributions to Microbiology 2004, vol. 11:14-32. Basel, Karger.
4. Case D.A., Pearlman J.W., Caldwell T.E., Cheatham III., Wang J., Ross W.S., Simmerling C.L., Darden T.A., Merz K.M., Stanton R.V., Cheng A.L., Vincent J.J., Crowley M., Tsui V., Gohlke H., Radmer R.J., Duan Y., Pitera J., Massova I., Seibel G.L., Singh U.C., Weiner P.K., Kollman P.A. AMBER 7 2002, University of California, San Francisco.
5. Case D.A., Darden T.A., Caldwell T.E., Cheatham III., Simmerling C.L., Wang J., Duke R.E., Luo R., Merz K.M., Pearlman D.A., Crowley M., Walker R.C., Zhang W., Wang B., Hayik S., Roitberg A., Seabra G., Wong K.F., Paesani F., Wu X., Brozell S., Tsui V., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Beroza P., Mathews D.H., Schafmeister C., Ross W.S., Kollman P.A. AMBER 9 2006, University of California, San Francisco.
6. Chou K.C. The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophys. J. 1984, 45:881-890.
7. Chou K.C. The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition. Biophys. Chem. 1984, 20:61-71.
8. Chou K.C. The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers 1987, 26:285-295.
9. Chou K.C. Review: low-frequency collective motion in biomacromolecules and its biological functions. Biophys. Chem. 1988, 30:3-48.
10. Chou K.C. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem. Sci. 1989, 14:212.
11. Chou K.C., Mao B. Collective motion in DNA and its role in drug intercalation. Biopolymers 1988, 27:1795-1815.
12. Chou K.C., Zhang C.T., Maggiora G.M. Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers 1994, 34:143-153.
13. Daude N. Prion diseases and the spleen. Viral Immunol. 2004, 17:334-349.
14. Dima R.I., Thirumalai D. Exploring the propensities of helices in PrPC to form Β sheet using NMR structures and sequence alignments. Biophys. J. 2002, 83:1268-1280.
15. Dima R.I., Thirumalai D. Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc. Natl. Acad. Sci. USA 2004, 101:15335-15340.
16. El-Bastawissy E., Knaggs M.H., Gilbert I.H. Molecular dynamics simulations of wild-type and point mutation human prion protein at normal and elevated temperature. J. Mol. Graph. Model. 2001, 20:145-154.
17. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
18. Liemann S., Glockshuber R. Influence of amino acid substitutions related to inherited human prion diseases on the thermodynamic stability of the cellular prion protein. Biochem. 1999, 38:3258-3267.
19. Mills, N.L., Surewicz, K., Surewicz, W.K., Sonnichsen F.D., 2009. Residue 129 polymorphism and conformational dynamics of familial prion diseases associated with the human prion protein variant D178N. doi:10.2210/pdb2k1d/pdb http://www.rcsb.org/pdb/explore/explore.do?structureId=2K1D.
20. Nisbet R.M., Harrison C.F., Lawson V.A., Masters C.L., Cappai R., Hill A.F., 2010. Residues surrounding the GPI anchor attachment site of PrP modulate prion infection: insight from the resistance of rabbits to prion diseases. J. Virol. 84 (13), 6678-86.
21. Ogayar A., Snchez-Prez M. Prions: an evolutionary perspective. Int. Microbiol. 1998, 1:183-190.
22. Pan K.M., Baldwin M., Nguyen J. Conversion of α-helices into Β-sheets features in the formation of the scrapie prion proteins. Proc. Natl. Acad. Sci. USA 1993, 90:10962-10966.
23. Prusiner S.B. Prions. Proc. Natl. Acad. Sci. USA 1998, 95:13363-13383.
24. Reilly C.E. Nonpathogenic prion protein (PrPC) acts as a cell-surface signal transducer. J. Neurol. 2000, 247:819-820.
25. Riek R., Hornemann S., Wider G., Billeter M., Glockshuber R., Wuthrich K. NMR structure of the mouse prion protein domain PrP(121-231). Nature 1996, 382:180-182.
26. Sekijima M., Motono C., Yamasaki S., Kaneko K., Akiyama Y. Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties. Biophys. J. 2003, 85:1176-1185.
27. Shamsir M.S., Dalby A.R. One gene two diseases and three conformations: molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures. PROTEINS: Struct. Funct. Bioinf. 2005, 59:275-290.
28. Sweeting, B., Brown, E., Chakrabartty, A., Pai, E.F., 2009. The structure of rabbit prion PrPC: clues into species barrier and prion disease susceptibility. Canada Light Source 28: http://www.lightsource.ca/science/pdf/activity_report_2009/28.pdf.
29. Vorberg I., Martin H.G., Eberhard P., Suzette A.P. Multiple amino acid residues within the rabbit prion protein inhibit formation of its abnormal isoform. J. Virol. 2003, 77:2003-2009.
30. Wang J.F., Chou K.C. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem. Biophys. Res. Commun. 2009, 390:608-612.
31. Wang J.F., Wei D.Q. Role of structural bioinformatics and traditional Chinese medicine databases in pharmacogenomics. Pharmacogenomics 2009, 10:1213-1215.
32. Wang J.F., Wei D.Q., Li L., Zheng S.Y., Li Y.X., Chou K.C. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem. Biophys. Res. Commun. 2007, 355:513-519.
33. Wang J.F., Wei D.Q., Lin Y., Wang Y.H., Du H.L., Li Y.X., Chou K.C. Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun. 2007, 359:323-329.
34. Wang J.F., Wei D.Q., Chen C., Li Y., Chou K.C. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Protein Pept. Lett. 2008, 15:27-32.
35. Wang J.F., Wei D.Q., Chou K.C. Pharmacogenomics and personalized use of drugs. Curr. Top. Med. Chem. 2008, 8:1573-1579.
36. Wang J.F., Wei D.Q., Chou K.C. Drug candidates from traditional Chinese medicines. Curr. Top. Med. Chem. 2008, 8:1656-1665.
37. Wang J.F., Gong K., Wei D.Q., Li Y.X., Chou K.C. Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. Protein Eng. Des. Sel. 2009, 22:349-355.
38. Wang J.F., Wei D.Q., Chou K.C. Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem. Biophys. Res. Commun. 2009, 388:413-417.
39. Wang J.F., Yan J.Y., Wei D.Q., Chou K.C. Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism. Med. Chem. 2009, 5:263-270.
40. Wang J.F., Zhang C.C., Chou K.C., Wei D.Q. Structure of cytochrome p450s and personalized drug. Curr. Med. Chem. 2009, 16:232-244.
41. Wang Y., Wei D.Q., Wang J.F. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J. Chem. Inf. Model. 2010, 50:875-878.
42. Weissmann C. The state of the prion. Nat. Rev. Microbiol. 2004, 2:861-871.
43. Wen, Y., Li, J., Yao, W.M., Xiong, M.Q., Hong, J., Peng, Y., Xiao, G.F., Lin1, D.H., 2010a. Unique structural characteristics of the rabbit prion protein. J. Biol. Chem. 285 (41), 31682-93. http://www.jbc.org/cgi/doi/10.1074/jbc.M110.118844.
44. Wen, Y., Li, J., Xiong, M.Q., Peng, Y., Yao, W.M., Hong, J., Lin, D.H., 2010b. Solution structure and dynamics of the I214V mutant of the rabbit prion protein. PloS One 5(10), e13272.
45. Yang S.C., Levine H., Onuchic J.N., Cox D.L. Structure of infectious prions: stabilization by domain swapping. FASEB J. 2005, 19:1778-1782.
46. Zahn R., Liu A.Z., Luhrs T., Riek R., Schroetter C.V., Garcia F.L., Billeter M., Calzolai L., Wider G., Wuthrich K. NMR solution structure of the human prion protein. Proc. Natl. Acad. Sci. USA 2000, 97:145-150.
47. Zhang J.P. Studies on the structural stability of rabbit prion probed by molecular dynamics simulations. J. Biomol. Struct. Dyn. 2009, 27:159-162.
48. Zhang J.P. Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants. J. Theor. Biol. 2010, 264:119-122.
49. Zhang, J.P., 2010b. Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing. J. Mol. Model. doi:. http://www.springerlink.com/content/l5kk5k208u4853g8/.
50. Zhang, J.P., Sun, J., 2010c. Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils probed by hybrid local and global optimization searches. In: Proceedings of the International Conference on Optimization and Control 2010, pp. 91-112. http://sci.gzu.edu.cn/icoco/ICOCO-Proceedings.pdf.
51. Zhang, J.P., Varghese, J.N., Epa, V.C., 2006. Studies on the conformational stability of the rabbit prion protein. CSIRO Preventative Health National Research Flagship Science Retreat, Aitken Hill, Melbourne, 12-15 September 2006, Poster in Excellence. http://sites.google.com/site/jiapuzhang/.
52. Zhong L.H. Exposure of hydrophobic core in human prion protein pathogenic mutant H187R. J. Biomol. Struct. Dyn. 2010, 28(3):355-361.