Structure and dynamics of amyloid-β segmental polymorphisms

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Berhanu, Workalemahu M ^a   Hansmann, Ulrich H E ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; CYTOTOXICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; PROTEIN AGGREGATION; PROTEIN POLYMORPHISM; PROTEIN STRUCTURE; SIMULATION;

ALZHEIMER DISEASE; AMINO ACIDS; AMYLOID BETA-PEPTIDES; HUMANS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; SALTS; SOLVENTS; THERMODYNAMICS; TIME FACTORS;

EID: 84864187173     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041479     Document Type: Article

References (68)

1. Ashe KH, Zahs KR, (2011) Probing the Biology of Alzheimer's Disease in Mice. Neuron 66: 631-645.
2. Xue WF, Hellewell AL, Hewitt EW, Radford SE, (2010) Fibril fragmentation in amyloid assembly and cytotoxicity When size matters. Prion 4: 20-25.
3. Laganowsky A, Liu C, Sawaya MR, Whitelegge JP, Park J, et al. (2012) Atomic View of a Toxic Amyloid Small Oligomer. Science 335: 1228-1231.
4. Hardy J, Selkoe DJ, (2002) Medicine- The amyloid hypothesis of Alzheimer's disease: Progress and problems on the road to therapeutics. Science 297: 353-356.
5. Chiti F, Dobson CM, (2006) Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry. Palo Alto: Annual Reviews pp. 333-366.
6. Sachse C, Fandrich M, Grigorieff N, (2008) Paired beta-sheet structure of an A beta(1-40) amyloid fibril revealed by electron microscopy. Proceedings of the National Academy of Sciences of the United States of America 105: 7462-7466.
7. Schmidt M, Sachse C, Richter W, Xu C, Fandrich M, et al. (2009) Comparison of Alzheimer A beta(1-40) and A beta(1-42) amyloid fibrils reveals similar protofilament structures. Proceedings of the National Academy of Sciences of the United States of America 106: 19813-19818.
8. Petkova AT, Yau WM, Tycko R, (2006) Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochemistry 45: 498-512.
9. Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, et al. (2005) 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proceedings of the National Academy of Sciences of the United States of America 102: 17342-17347.
10. Petkova AT, Leapman RD, Guo ZH, Yau WM, Mattson MP, et al. (2005) Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils. Science 307: 262-265.
11. Paravastu AK, Qahwash I, Leapman RD, Meredith SC, Tycko R, (2009) Seeded growth of beta-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure. Proceedings of the National Academy of Sciences of the United States of America 106: 7443-7448.
12. Miller Y, Ma B, Nussinov R, (2010) Polymorphism in Alzheimer A beta Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape. Chemical Reviews 110: 4820-4838.
13. Hu XY, Crick SL, Bu GJ, Frieden C, Pappu RV, et al. (2009) Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide. Proceedings of the National Academy of Sciences of the United States of America 106: 20324-20329.
14. Greenwald J, Riek R, (2010) Biology of Amyloid: Structure, Function, and Regulation. Structure 18: 1244-1260.
15. Eisenberg D JM, (2012) The amyloid state of proteins in human diseases. Cell 148: 1188-1203.
16. Wiltzius JJW, Landau M, Nelson R, Sawaya MR, Apostol MI, et al. (2009) Molecular mechanisms for protein-encoded inheritance. Nature Structural & Molecular Biology 16: 973-U998.
17. Hu KN, McGlinchey RP, Wickner RB, Tycko R, (2011) Segmental Polymorphism in a Functional Amyloid. Biophysical Journal 101: 2242-2250.
18. Anand P, Hansmann UHE, (2011) Internal and environmental effects on folding and dimerisation of Alzheimer's beta-amyloid peptide. Molecular Simulation 37: 440-448.
19. Huet A, Derreumaux P, (2006) Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations. Biophysical Journal 91: 3829-3840.
20. Baumketner A, Krone MG, Shea JE, (2008) Role of the familial Dutch mutation E22Q in the folding and aggregation of the 15-28 fragment of the Alzheimer amyloid-beta protein. Proceedings of the National Academy of Sciences of the United States of America 105: 6027-6032.
21. Fawzi NL, Kohlstedt KL, Okabe Y, Head-Gordon T, (2008) Protofibril assemblies of the arctic, dutch, and flemish mutants of the Alzheimer's A beta(1-40) peptide. Biophysical Journal 94: 2007-2016.
22. Chebaro Y, Derreumaux P, (2009) Targeting the early steps of A beta 16-22 protofibril disassembly by N-methylated inhibitors: A numerical study. Proteins-Structure Function and Bioinformatics 75: 442-452.
23. Takeda T, Klimov DK, (2008) Temperature-induced dissociation of A beta monomers from amyloid fibril. Biophysical Journal 95: 1758-1772.
24. Takeda T, Klimov DK, (2007) Dissociation of A beta(16-22) amyloid fibrils probed by molecular dynamics. Journal of Molecular Biology 368: 1202-1213.
25. Chebaro Y JP, Zang T, Mu Y, Nguyen PH, Mousseau N, et al. (2012) Structures of Aβ17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational ProcedureJ Phys Chem B dx.doi.org/10.1021/jp2118778.
26. Takeda T, Klimov DK, (2009) Replica Exchange Simulations of the Thermodynamics of A beta Fibril Growth. Biophysical Journal 96: 442-452.
27. Takeda T, Klimov DK, (2009) Probing Energetics of A beta Fibril Elongation by Molecular Dynamics Simulations. Biophysical Journal 96: 4428-4437.
28. Han M, Hansmann UHE, (2011) Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's A beta(42) peptide. Journal of Chemical Physics 135: 6.
29. Rojas A, Liwo A, Browne D, Scheraga HA, (2010) Mechanism of Fiber Assembly: Treatment of A beta Peptide Aggregation with a Coarse-Grained United-Residue Force Field. Journal of Molecular Biology 404: 537-552.
30. Li MS, Co NT, Reddy G, Hu CK, Straub JE, et al. (2010) Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models. Physical Review Letters 105: 4.
31. Wei GH, Mousseau N, Derreumaux P, (2007) Computational Simulations of the Early Steps of Protein Aggregation. Prion 1: 3-8.
32. Ma BY, Nussinov R, (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Current Opinion in Chemical Biology 10: 445-452.
33. Nguyen PH, Li MS, Derreumaux P, (2011) Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Physical Chemistry Chemical Physics 13: 9778-9788.
34. Berryman JT, Radford SE, Harris SA, (2011) Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation. Biophysical Journal 100: 2234-2242.
35. Miller Y, Ma BY, Nussinov R, (2009) Polymorphism of Alzheimer's A beta(17-42) (p3) Oligomers: The Importance of the Turn Location and Its Conformation. Biophysical Journal 97: 1168-1177.
36. Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, et al. (2007) Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447: 453-457.
37. Colletier JP, Laganowsky A, Landau M, Zhao ML, Soriaga AB, et al. (2011) Molecular basis for amyloid-beta polymorphism. Proceedings of the National Academy of Sciences of the United States of America 108: 16938-16943.
38. Tycko R, Sciarretta KL, Orgel J, Meredith SC, (2009) Evidence for Novel beta-Sheet Structures in Iowa Mutant beta-Amyloid Fibrils. Biochemistry 48: 6072-6084.
39. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: Fast, flexible, and free. Journal of Computational Chemistry 26: 1701-1718.
40. Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins-Structure Function and Bioinformatics 78: 1950-1958.
41. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics 79: 926-935.
42. Darden T, York D, Pedersen L, (1993) Particle Mesh Ewald- an n.log(n) method for ewald sums in large systems. Journal of Chemical Physics 98: 10089-10092.
43. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, et al. (1995) A smooth particle mesh ewald method. Journal of Chemical Physics 103: 8577-8593.
44. Hess B, (2008) P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation 4: 116-122.
45. Miyamoto S, Kollman PA, (1992) Settle- an analytical version of the shake and rattle algorithm for rigid water models. Journal of Computational Chemistry 13: 952-962.
46. Bussi G, Donadio D, Parrinello M, (2007) Canonical sampling through velocity rescaling. Journal of Chemical Physics 126: 7.
47. Parrinello M, Rahman A, (1981) Polymorphic transitions in single-crystals- a new molecular-dynamics method. Journal of Applied Physics 52: 7182-7190.
48. Meersman F, Dobson CM, (2006) Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties. Biochimica Et Biophysica Acta-Proteins and Proteomics 1764: 452-460.
49. Berhanu WM, Masunov AE, (2012) Controlling the aggregation and rate of release in order to improve insulin formulation: molecular dynamics study of full-length insulin amyloid oligomer models J Mol Model 18: 1129-1142.
50. Berhanu WM, Masunov AE, (2012) Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants. J Mol Model 18: 891-903.
51. Humphrey W, Dalke A, Schulten K, (1996) VMD: Visual molecular dynamics. Journal of Molecular Graphics & Modelling 14: 33-38.
52. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. Journal of Computational Chemistry 26: 1668-1688.
53. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins-Structure Function and Bioinformatics 65: 712-725.
54. Berhanu WM, Masunov AE, (2011) Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN. Journal of Molecular Modeling 17: 2423-2442.
55. Vitagliano L, Stanzione F, De Simone A, Esposito L, (2009) Dynamics and Stability of Amyloid-Like Steric Zipper Assemblies with Hydrophobic Dry Interfaces. Biopolymers 91: 1161-1171.
56. Workalemahu M Berhanu, Masunov AE, (2012) Alternative Packing Modes Leading to Amyloid Polymorphism in Five Fragments Studied With Molecular Dynamics. Peptide Science 98: 131-144.
57. Wei Qianga W-MY, Yongquan Luob, Mark P Mattsonb, Robert Tyckoa, (2012) Antiparallel β-sheet architecture in Iowa-mutant β-amyloid fibrils. Proc Natl Acad Sci USA (109): 4443-4448.
58. Tarus B, Straub JE, Thirumalai D, (2006) Dynamics of Asp23-Lys28 salt-bridge formation in A beta(10-35) monomers. Journal of the American Chemical Society 128: 16159-16168.
59. Masman MF, Eisel ULM, Csizmadia IG, Penke B, Enriz RD, et al. (2009) In Silico Study of Full-Length Amyloid beta 1-42 Tri- and Penta-Oligomers in Solution. Journal of Physical Chemistry B 113: 11710-11719.
60. Dzubiella J, (2008) Salt-specific stability and denaturation of a short salt-bridge-forming alpha-helix. Journal of the American Chemical Society 130: 14000-14007.
61. Homeyer N, Gohlke H, (2012) Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method. Molecular Informatics 31: 114-122.
62. Berhanu WM, Masunov AE, (2011) Molecular Dynamic Simulation of Wild Type and Mutants of the Polymorphic Amyloid NNQNTF Segments of Elk Prion: Structural Stability and Thermodynamic of Association. Biopolymers 95: 573-590.
63. Berhanu WM, Mikhailov IA, Masunov AE, (2010) Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation? Journal of Molecular Modeling 16: 1093-1101.
64. Knowles TP, Fitzpatrick AW, Meehan S, Mott HR, Vendruscolo M, et al. (2007) Role of intermolecular forces in defining material properties of protein nanofibrils. Science 318: 1900-1903.
65. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure- pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
66. Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R, (2007) Modeling the Alzheimer A beta(17-42) fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophysical Journal 93: 3046-3057.
67. Lemkul JA, Bevan DR, (2010) Assessing the Stability of Alzheimer's Amyloid Protofibrils Using Molecular Dynamics. Journal of Physical Chemistry B 114: 1652-1660.
68. Landau M, Sawaya MR, Faull KF, Laganowsky A, Jiang L, et al. (2011) Towards a Pharmacophore for Amyloid. Plos Biology 9: 13.