Structure of the 21-30 fragment of amyloid β-protein

Protein Science

Volumn 15, Issue 6, 2006, Pages 1239-1247

  Baumketner, Andrij ^a,c   Bernstein, Summer L ^a   Wyttenbach, Thomas ^a   Lazo, Noel D ^b   Teplow, David B ^b   Bowers, Michael T ^a   Shea, Joan Emma ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INSTITUTE FOR CONDENSED MATTER PHYSICS   (Ukraine)

Author keywords

Alzheimer A peptide; Replica exchange molecular dynamics simulations; Sampling of conformational space

Indexed keywords

AMIDE; AMYLOID BETA PROTEIN; HYDROGEN; SODIUM CHLORIDE;

ALZHEIMER DISEASE; ARTICLE; CATALYST; CLUSTER ANALYSIS; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENERGY CONSUMPTION; HUMAN; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN DEGRADATION; PROTEIN STRUCTURE; SIMULATION; TEMPERATURE;

AMYLOID BETA-PROTEIN; HYDROPHOBICITY; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN DENATURATION; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33744467718     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062076806     Document Type: Article

References (45)

1. Antzutkin, O.N., Leapman, R.D., Balbach, J.J., and Tycko, R. 2002. Supramolecular structural constraints on Alzheimer's β-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance. Biochemistry 41: 15436-15450.
2. Berendsen, H.J.C., van der Spoel, D., and van Drunen, R. 1995. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91: 43-56.
3. Borreguero, J.M., Urbanc, B., Lazo, N.D., Buldyrev, S.V., Teplow, D.B., and Stanley, H.E. 2005. Folding events in the 21-30 region of amyloid β-protein (Aβ) studied in silico. Prot. Natl. Acad. Sci. 102: 6015-6020.
4. Bryngelson, J.D. and Wolynes, P.G. 1987. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. 84: 7524-7528.
5. Chimon, S. and Ishii, Y. 2005. Capturing intermediate structures of Alzheimer's β-amyloid, Aβ (1-40), by solid-state NMR spectroscopy. J. Am. Chem. Soc. 127: 13472-13473.
6. Cruz, L., Urbanc, B., Borreguero, J.M., Lazo, N.D., Teplow, D.B., and Stanley, H.E. 2005. Solvent and mutation effects on the nucleation of amyloid β-protein folding. Proc. Natl. Acad. Sci. 102: 18801-18806.
7. Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W.F., and Mark, A.E. 1999. Peptide folding: When simulation meets experiment. Angew. Chem. Int. Ed. Engl. 38: 236-240.
8. Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., and Pedersen, L.G. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593.
9. Garcia, A.E. and Onuchic, J.N. 2003. Folding a protein in a computer: An atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. 100: 13898-13903.
10. Grabowski, T.J., Cho, H.S., Vonsattel, J.P.G., Rebeck, G.W., and Greenberg, S.M. 2001. Novel amyloid precursor protein mutation in an Iowa family with dementia and severe cerebral amyloid angiopathy. Ann. Neurol. 49: 697-705.
11. Guo, J.T.,Wetzel, R., and Ying, X. 2004. Molecular modeling of the core of Aβ amyloid fibrils. Proteins 57: 357-364.
12. Hardy, J. and Selkoe, D.J. 2002. The amyloid hypothesis of Alzheimer's disease: Progress and problems on the road to therapeutics. Science 297: 353-357.
13. Harper, J.D., Wong, S.S., Lieber, C.M., and Lansbury Jr., P.T. 1997. Observation of metastable Aβ amyloid protofibrils by atomic force microscopy. Chem. Biol. 4: 119-125.
14. Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. 1997. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18: 1463-1472.
15. Hou, L., Shao, H., Zhang, Y., Li, H., Menon, N.K., Neuhaus, E.B., Brewer, J.M., Byeona, I.-J.Lx., Ray, D.G., Vitek, M.P., et al. 2004. Solution NMR studies of the Aβ (1-40) and Aβ (1-42) peptides establish that the MET35 oxidation state affects the mechanism of amyloid formation. J. Am. Chem. Soc. 126: 1992-2005.
16. Jolliffe, I.T. 1986. Principal component analysis. Springer-Verlag, New York.
17. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., and Klein, M.L. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79: 926-935.
18. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
19. Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., and Jorgensen, W.L. 2001. Evaluation and reparametrization of the opls-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105: 6474-6487.
20. Kirkitadze, M., Condron, M.M., and Teplow, D.B. 2001. Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis. J. Mol. Biol. 312: 1103-1119.
21. Klein, W.L., Stine Jr., W.B., and Teplow, D.B. 2004. Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease. Neurobiol. Aging 25: 569-580.
22. Lazo, N.D., Grant, M.A., Condron, M.C., Rigby, A.C., and Teplow, D.B. 2005a. On the nucleation of amyloid β-protein monomer folding. Protein Sci. 14: 1581-1596.
23. Lazo, N.D., Maji, S.K., Fradinger, E.A., Bitan, G., and Teplow, D.B. 2005b. The amyloid β-protein. In Amyloid proteins: The β-sheet conformation and disease, Vol. 2, pp. 385-491. Wiley-VCH Verlag GmbH, Weinheim, Germany.
24. Lindahl, E., Hess, B., and van der Spoel, D. 2001. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model 7: 306-317.
25. Lührs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Dobeli, H., Schubert, D., and Riek, R. 2005. Three-dimensional structure of Alzheimer's amyloid-β (1-42) fibrils. Proc. Natl. Acad. Sci. 102: 17342-17347.
26. Lum, K., Chandler, D., and Weeks, J.D. 1999. Hydrophobicity at small and large length scales. J. Phys. Chem. B 103: 4570-4577.
27. Miyamoto, S. and Kollman, P.A. 1992. SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comput. Chem. 13: 952-962.
28. Morimoto, A., Irie, K., Murakami, K., Masuda, Y., Ohigashi, H., Nagao, M., Fukuda, H., Shimizu, T., and Shirasawa, T. 2004. Analysis of the secondary structure of β-amyloid (Aβ 42) fibrils by systematic proline replacement. J. Biol. Chem. 279: 52781-52788.
29. Murakami, K., Irie, K., Morimoto, A., Ohigashi, H., Shindo, M., Nagao, M., Shimizu, T., and Shirasawa, T. 2003. Neurotoxicity and physicochemical properties of Aβ mutant peptides from cerebral amyloid angiopathy: Implication for the pathogenesis of cerebral amyloid angiopathy and Alzheimer's disease. J. Biol. Chem. 278: 46179-46187.
30. Nilsberth, C.,Westlind-Danielsson, A., Eckman, C.B., Condron, M.M., Axelman, K., Forsell, C., Stenh, C., Luthman, J., Teplow, D.B., Younkin, S.G., et al. 2001. The 'arctic' APP mutation (E693G) causes Alzheimer's disease by enhanced Aβ protofibril formation. Nat. Neurosci. 4: 887-893.
31. Nosé, S. 1991. Constant temperature molecular dynamics methods. Prog. Theor. Phys. 103: 1-46.
32. Petkova, A.T., Ishii, Y., Balbach, J.J., Antzutkin, O.N., Leapman, R.D., Delaglio, F., and Tycko, R. 2002. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl. Acad. Sci. 99: 16742-16747.
33. Petkova, A.T., Leapman, R.D., Guo, Z.H., Yau, W.M., Mattson, M.P., and Tycko, R. 2005. Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils. Science 307: 262-265.
34. Rein ten Wolde, P., Sun, S.X., and Chandler, D. 2001. Model of a fluid at small and large length scales and the hydrophobic effect. Phys. Rev. E 65: 011201-1-011201-9.
35. ox. Eur. J. Biochem 268: 5930-5936.
36. Serpell, L.C. 2000. Alzheimer's amyloid fibrils: Structure and assembly. Biochim. Biophys. Acta 1502: 16-30.
37. Sugita, Y. and Okamoto, Y. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314: 141-151.
38. Temussi, P.A., Masino, L., and Pastore, A. 2003. From Alzheimer to Huntington: Why is a structural understanding so difficult? EMBO J. 22: 355-361.
39. Teplow, D.B., Lomakin, A., Benedek, G.B., Kirschner, D.A., and Walsh, D.M. 1997. Effects of β-protein mutations on amyloid fibril nucleation and elongation. In Alzheimer's disease: Biology, diagnosis and therapeutics, pp. 311-319. John Wiley & Sons, Chichester, UK.
40. van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., Feenstra, K.A., van Drunen, R., et al. 2004. GROMACS user manual version 3.2. www.gromacs.org.
41. Van Nostrand, W.E., Melchor, J.P., Cho, H.S., Greenberg, S.M., and Rebeck, G.W. 2001. Pathogenic effects of D23N Iowa mutant amyloid β-protein. J. Biol. Chem. 276: 32860-32866.
42. Walsh, D.M., Lomakin, A., Benedek, G.B., Condron, M.M., and Teplow, D.B. 1997. Amyloid β-protein fibrillogenesis. detection of a protofibrillar intermediate. J. Biol. Chem. 272: 22364-22372.
43. Williams, A.D., Portelius, E., Kheterpal, I., Guo, J.T., Cook, K.D., Xu, Y., and Wetzel, R. 2004. Mapping Aβ amyloid fibril secondary structure using scanning proline mutagenesis. J. Mol. Biol. 335: 833-842.
44. Wisniewski, T. and Frangione, B. 1992. Molecular biology of Alzheimer's amyloid Dutch variant. Mol. Neurobiol. 6: 75-86.
45. Zhang, S., Iwata, K., Lachenmann, M.J., Peng, J.W., Li, S., Stimson, E.R., Lu, Y.-A., Felix, A.M., Maggio, J.E., and Lee, J.P. 2000. The Alzheimer's peptide: Aβ adopts a collapsed coil structure in water. J. Struct. Biol. 130: 130-141.