Simulations of human lysozyme: Probing the conformations triggering amyloidosis

Biophysical Journal

Volumn 84, Issue 4, 2003, Pages 2149-2158

  Moraitakis, George ^a   Goodfellow, Julia M ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; LYSOZYME;

AMYLOIDOSIS; ARTICLE; HYDROPHOBICITY; MOLECULAR DYNAMICS; NORMAL DISTRIBUTION; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; SIMULATION; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE;

EID: 0037381819     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75021-8     Document Type: Article

References (43)

1. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulations of Liquids. Clarendon, Oxford.
2. Alonso, D. O. V., and V. Daggett. 2000. Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. Biophysics. 97:133-138.
3. Artymiuk, P. J., and C. C. F. Blake. 1981. Refinement of human lysozyme at 1.5 Å resolution. Analysis of non-bonded and hydrogen-bond interactions. J. Mol. Biol. 152:737-762.
4. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for waters in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. D. Reidel, Dordrecht, The Netherlands. 331-342.
5. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gusteren, A. Di Nola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
6. Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91:43-56.
7. Booth, D. R., M. Sund, V. Bellotti, C. V. Robinson, W. L. Hutchinson, P. E. Fraser, P. N. Hawkins, C. M. Dobson, S. E. Radford, C. C. F. Blake, and M. B. Pepys. 1997. Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature. 385:787-793.
8. Brooks, C. L., 3rd. 1998. Simulations of protein folding and unfolding. Curr. Op. Struct. Biol. 8:222-226.
9. Canet, D., A. M. Last, P. Tito, M. Sunde, A. Spencer, D. B. Archer, C. Redfield, C. V. Robinson, and C. M. Dobson. 2002. Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme. Nat. Struct. Biol. 9:308-315.
10. Canet, D., M. Sunde, A. M. Last, A. Miranker, A. Spencer, C. V. Robinson, and C. M. Dobson. 1999. Mechanistic studies of the folding of human lysozyme and the origin of amyloidogenic behavior in its disease-related variants. Biochemistry. 38:6419-6427.
11. Chipman, D. M., and N. Sharon. 1969. Mechanism of lysozyme action. Science. 165:454-465.
12. Daggett, V. 2000. Long timescale simulations. Curr. Op. Struct. Biol. 10: 160-164.
13. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: A N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
14. Dyson, H. J., J. R. Sayre, G. Merutka, H. C. Shin, R. A. Lerner, and P. E. Wright. 1992. Folding of peptide fragments comprising the complete sequence of proteins models for initiation of protein folding. II. Plastocyanin. J. Mol. Biol. 226:819-835.
15. Everitt, B. S. 1993. Cluster Analysis. John Wiley & Sons, New York.
16. Gilquin, B., C. Guilbert, and D. Perahia. 2000. Unfolding of hen egg lysozyme by molecular dynamics simulations at 300K: insight into the role of the interdomain interface. Proteins. 41:58-74.
17. Hess, B., H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18:1463-1472.
18. Hunenberger, P. H., A. E. Mark, and W. F. van Gunsteren. 1995. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Nature: Struct. Funct. Genet. 21:196-213.
19. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
20. Karplus, M., and A. Sali. 1995. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73.
21. Kazmirski, S. L., and V. Daggett. 1998. Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme. J. Mol. Biol. 284:793-806.
22. Kazmirski, S. L., A. Li, and V. Daggett. 1999. Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J. Mol. Biol. 290: 283-304.
23. Kelly, J. W. 1998. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. Curr. Opin. Struct. Biol. 8:101-106.
24. Li, A., and V. Daggett. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA. 91:10430-10434.
25. Li, A., and V. Daggett. 1998. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275:677-694.
26. Mahalanobis, P. C. 1930. On tests and measures of groups divergence I. Journal of the Asiatic Society of Bengal. 26:541.
27. Mark, A. E., and W. F. van Gunsteren. 1992. Simulation of the thermal denaturation of HEW-lysozyme: trapping the molten globule state. Biochemistry. 31:7745-7748.
28. Miranker, A., S. E. Radford, M. Karplus, and C. M. Dobson. 1991. Demonstration by NMR of folding domains in lysozyme. Nature. 349:633-636.
29. Miranker, A., C. V. Robinson, S. E. Radford, R. T. Alpin, and C. M. Dobson. 1993. Detection of transient protein folding populations by mass spectroscopy. Science. 262:896-900.
30. Morozova-Roche, L. A., J. Zurdo, A. Spencer, W. Noppe, V. Receveur, D. B. Archer, M. Joniau, and C. M. Dobson. 2000. Amyloid fibril formation and seeding by wild-type human lysozyme and its disease-related mutational variants. J. Struct. Biol. 130:339-351.
31. Otto, M. 1998. Chemometrics: Statistics and Computer Application in Analytical Chemistry. Weinheim, Cambridge.
32. Pepys, M. B., P. N. Hawkins, D. R. Booth, D. M. Viguishin, G. A. Tennent, A. K. Soutar, N. Totty, O. Nguyen, C. C. F. Blake, C. J. Terry, T. G. Feest, A. M. Zalin, and J. J. Hsuan. 1993. Human lysozyme gene mutations cause hereditary systemic amyloidosis. Nature. 206:553-557.
33. Pepys, M. B. 1996. Amyloidosis. In The Oxford Textbook of Medicine, Vol. 2. D. J. Weatherall, J. G. G. Ledingham, and D. A. Warell, editors. Oxford University Press, Oxford.
34. Schormann, N., J. R. Murrell, and M. D. Benson. 1998. Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation. Amyloid. 5:175-187.
35. Skolnick, J., and A. Kolinski. 1991. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J. Mol. Biol. 221:499-531.
36. Späth, H. 1980. Cluster Analysis Algorithms for Data Reduction and Classification of Objects. Ellis Horwood, Chichester, UK.
37. Tobias, D. J., S. F. Sneddon, and C. L. Brooks. 1990. Reverse turns in blocked dipeptides are intrinsically unstable in water. J. Mol. Biol. 216:783-796.
38. van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. O. Scott, and I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Hochschulverlag AG an der ETH, Zurich, Switzerland.
39. Venables, W. N., and B. D. Ripley. 1999. Modern Applied Statistics with S-PLUS, 3rd ed. Springer, New York.
40. Williams, M. A., J. M. Thornton, and J. M. Goodfellow. 1997. Modelling protein unfolding: hen egg-white lysozyme. Protein Eng. 10:895-903.
41. Worth, G. A., F. Nardi, and R. C. Wade. 1998. Use of multiple molecular dynamics trajectories to study biomolecules in solution: the YTGP peptide. J. Phys. Chem. B. 102:6260-6272.
42. Yang, A., B. Hitz, and B. Honig. 1996. Free energy determinants of secondary structure formation: III. β-turns and their role in protein folding. J. Mol. Biol. 259:873-882.
43. Zimmerman, S. S., and H. A. Scheraga. 1977. Local interactions in bends of proteins. Proc. Natl. Acad. Sci. USA. 74:4126-4129.