Exploration of the mechanism for LPFFD inhibiting the formation of β-sheet conformation of Aβ(1-42) in water

Journal of Molecular Modeling

Volumn 16, Issue 4, 2010, Pages 813-821

  Yang, Cao ^a   Zhu, Xiaolei ^a   Li, Jinyu ^a   Shi, Rongwei ^a  

^a NANJING TECH UNIVERSITY   (China)

Author keywords

A (1 42); Conformational transition; LPFFD; Molecular docking; Molecular dynamics simulation

Indexed keywords

AMYLOID BETA PROTEIN[1-42]; LEUCYLPROLYLPHENYLPHENYLASPARTINE; PENTAPEPTIDE; UNCLASSIFIED DRUG; WATER; AMYLOID BETA PROTEIN; IABETA5 PEPTIDE; PEPTIDE FRAGMENT;

ALZHEIMER DISEASE; ARTICLE; BETA SHEET; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; DRUG ACTIVITY; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR STABILITY; NEUROTOXICITY; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SENILE PLAQUE; CHEMISTRY;

AMYLOID BETA-PROTEIN; BINDING SITES; MOLECULAR DYNAMICS SIMULATION; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; WATER;

EID: 77954611371     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0594-y     Document Type: Article

References (56)

1. Kang J, Lemaire HG, Unterbeck A, Salbaum JM, Masters CL, Grzeschik KH, Multhaup G, Beyreuther K, Muller-Hill B (1987) The precursor of Alzheimer's disease amyloid A4 protein resembles a cell-surface receptor. Nature 325:733-736.
2. Chromy BA, Nowak RJ, Lambert MP, Viola KL, Chang L, Velasco PT, Jone's BW, Fernandez SJ, Laco'r PN, Horowitz P, Finch CE, Krafft GA, Klein WL (2003) Self-assembly of Aβ into globular neurotoxins. Biochemistry 42:12749-12760.
3. Hardy JA, Higgins GA (1992) Alzheimer's disease: the amyloid cascade hypothesis. Science 256:184-185.
4. Iwatsubo T, Odaka A, Suzuki N, Mizusawa H, Nukina N, Ihara Y (1994) Visualization of Aβ42(43) and Aβ40 in senile plaques with end-specific Aβ monoclonals: evidence that an initially deposited species is Aβ42(43). Neuron 13:45-53.
5. Gravina SA, Ho L, Eckman CB, Long KE, Otvos L, Younkin LH, Suzuki N, Younkin SG (1995) Amyloid β protein (Aβ) in Alzheimer's disease brain. J Biol Chem 270:7013-7016.
6. Golde TE, Eckman CB, Younkin SG (2000) Biochemical treatment of Alzheimer's disease. Biochim Biophys Acta 1502:172-187.
7. Barrow CJ, Zagorski MG (1991) Solution structure of β peptide and its constituent fragments: relation to amyloid deposition. Science 253:179-181.
8. Barrow CJ, Yasuda A, Kenny PTM, Zagorski MG (1992) Solution conformations and aggregational properties of synthetic amyloid β-peptides of Alzheimer's disease. J Mol Biol 225:1075-1093.
9. Hilbich C, Kisters-Woide B, Reed J, Masters CL, Beyreuther K (1991) Aggregation and secondary structure of synthetic amyloid βA4 peptides of Alzheimer;s disease. J Mol Biol 218:149-163.
10. Kirchner DA, Inouye H, Duffy LK, Sinclair A, Lind M, Selkoe D (1987) Synthetic peptide homologous to beta protein from Alzheimer disease forms amyloid-like fibrils in vitro. Proc Natl Acad Sci USA 84:6953-6957.
11. Gorevic PD, Castano EM, Sarma R, Frangione B (1987) Ten to fourteen residue peptides of Alzheimer's disease protein are sufficient for amyloid fibril formation and its characteristic x-ray diffraction pattern. Biochem Biophys Res Commun 147:854-862.
12. Shen CL, Murphy RM (1995) Solvent effects on self-assembly of β-amyloid peptide. Biophys J 69:640-651.
13. Behl C, Davis JB, Lesley R, Schubert D (1994) Hydrogen peroxide mediates amyloid β protein toxicity. Cell 77:817-827.
14. Harris ME, Hensley K, Butterfield DA, Leedle RA, Carney JM (1995) Direct evidence of oxidative injure produced by the Alzheimer's β-amyloid peptide (1-40) in culture hippocampal neurons. Exp Neurol 131:193-202.
15. Buchet R, Tavitian E, Ristig D, Swoboda R, Stauss U, Gremlich HU, Fourniere LL, Staufenbiel M, Frey P, Lowe DA (1996) Conformations of synthetic β peptides in solid state and in aqueous solution: relation to toxicity in PC12 cells. Biochim Biophys Acta 1315:40-46.
16. Simmons LK, May PC, Tomaselli KJ, Rydel RE, Fuson KS, Brigham EF, Wright S, Lieberburg I, Becker GW, Brems DN (1994) Secondary structure of amyloid beta peptide correlates with neurotoxic activity in vitro. Mol Pharmacol 45:373-379.
17. Greenfield NJ, Fasman GD (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8:4108-4116.
18. Tomski S, Murphy RM (1992) Kinetics of aggregation of synthetic β-amyloid peptide. Arch Biochem Biophys 294:630- 638.
19. Walencewicz-Wasserman AJ, Kosmoski J, Cribbs DH, Glabe CG, Cotman CW (1995) Structure-activity analyses of β-peptides: conformations of the β25-35 region to aggregation and neurotoxicity. J Neurochem 64:253-265.
20. Lorenzo A, Yankner BA (1994) Beta-amyloid neurotoxicity requires fibril formation and is inhibited by congo red. Proc Natl Acad Sci USA 91:12243-12447.
21. Soto C, Castano EM, Kumar RA, Beavis R, Frangione CB (1995) Fibrillogenesis of synthetic amyloid-β peptides is dependent on their initial secondary structure. Neurosci Lett 200:105-108.
22. Jarrett JT, Berger EP Jr, Lansbury PT (1993) The carboxy terminus of the β amyloid protein is critical for the seeding of amyloid formation: implications for the pathogenesis of Alzheimer's disease. Biochemistry 32:4693-4697.
23. Snyder SW, Ladror US, Wade WS, Wang GT, Barrett LW, Matayoshi ED (1994) Amyloid-β aggregation: selective inhibition of aggregation in mixtures of amyloid with different chain lengths. Biophys J 67:1216-1228.
24. Soto C, Castano EM (1996) The conformation of Alzheimer's β peptide determines the rate of amyloid formation and its resistance to proteolysis. Biochem J 314:701-707.
25. Salomon AR, Marcinowski KJ, Friedland RP, Zagorski MG (1996) Nicotine inhibits amyloid formation by the β-peptide. Biochemistry 35:13568-13578.
26. Moore SA, Huckerby TN, Gibson GL, Fullwood NJ, Turnbull S, Tabner BJ, El-Agnaf OM, Allsop D (2004) Both the D-(+) and L- (-) enantiomers of nicotine inhibit Aβ aggregation and cytotoxicity. Biochemistry 43:819-826.
27. Wood SJ, MacKenzie L, Maleef B, Hurle MR, Wetzel R (1996) Selective inhibition of Aβ fibril formation. J Biol Chem 271:4086-4092.
28. Merlini G, Ascari E, Amboldi N, Belloti V, Arbustini E, Perfetti V, Ferrari M, Zorzoli I, Marinone MG, Garini P, Diegoli M (1995) Interaction of the anthracycline 4'-iodo-4'-deoxyd- oxorubic with amyloid fibrils: inhibition of amyloidogenesis. Proc Natl Acad Sci USA 92:2959-2963.
29. Wang SS, Chen YT, Chou SW (2005) Inhibition of amyloid fibril formation of β-amyloid peptides via the amphiphilic surfactants. Biochim Biophys Acta 1741:307-313.
30. Tjernberg LO, Näslund J, Lindqvist F, Johansson J, Karlström AR, Thyberg J, Terenius L, Nordstedt C (1996) Arrest of β- amyloid fibril formation by a pentapeptide ligand. J Biol Chem 271:8545-8548.
31. Soto C, Sogurdsson EM, Morello L, Kumar RA, Castano EM, Frangione B (1998) B-sheet breaker peptides inhibit fibtillogenesis in a rat brain model of amyloidosis: implications for Alzheimer's therapy. Nat Med 4:822-826.
32. Soto C, Saborio GP, Permanne B (2000) Inhibit the conversion of soluble amyloid-beta peptide into abnormally folded amyloidogenic intermediates: relevance for Alzheimer's disease therapy. Acta Neurol Scand Suppl 176:90-95.
33. Andrew JD (2007) Peptide inhibitors of β-amyloid aggregation. Curr Opin Drug Discov Devel 10:533-539.
34. Hetényi C, Kortvelyesi T, Penke B (2001) Computational studies on the binding of β-sheet breaker (BSB) peptides on amyloid βA (1-42). THEOCHEM 542:25-31.
35. Crescenzi O, Tomaselli S, Guerrini R, Salvadori S, D'Ursi AM, Temussi PA, Picone D (2002) Solution structure of the Alzheimer amyloid β-peptide (1-42) in an apolar microenvironment. Eur J Biochem 269:5642-5648.
36. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.
37. Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43-56.
38. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulations and trajectory analysis. J Mol Model 7:306-317.
39. Daura X, Mark AE, van Gunsteren WF (1998) Parameterization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 19:535-547.
40. Schuttelkopf AW, van-Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D 60:1355-1363.
41. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulation. J Comput Chem 18:1463-1472.
42. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
43. Darden T, York D, Pedersen L (1993) Particle mesh ewald: an N. log(N) method for ewald sums in large systems. J Chem Phys 98:10089-10092.
44. Patra M, Karttunen M, Hyvonen MT, Falck E, Lindqvist P, Vattulainen I (2003) Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interaction. Biophys J 84:3636-3645.
45. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
46. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graphics 14:33-38.
47. Yang C, Li JY, Li Y, Zhu XL (2009) The effect of solvents on the conformations of Amyloid β-peptide (1-42) studied by molecular dynamics simulation. THEOCHEM 895:1-8.
48. Tjernberg LO, Tjernberg A, Bark N, Shi Y, Ruzsicska BP, Bu Z, Thyberg J, Callaway DJE (2002) Assembling amyloid fibrils from designed structures containing a significant amyloid β-peptide fragment. Biochem J 366:343-351.
49. Torok M, Milton S, Kayed R, Wu P, McIntire T, Glabe CG, Langen R (2002) Structure and dynamics features of Alzheimer's Aβ peptide in amyloid fibrils studied by site-directed spin labelling. J Biol Chem 277:40810-40815.
50. Balbach JJ, Petkova AT, Oyler NA, Antzutkin ON, Gordon DJ, Meredith SC, Tycko R (2002) Supramolecular structure in fulllength Alzheimer's β-amyloid fibrils: evidence for a parallel β- sheet organization from solid-state nuclear magnetic resonance. Biophys J 83:1205-1216.
51. Shen L, Ji HF, Zhang HY (2008) Why is the C-terminus of Aβ(1- 42) more unfolded than that of Aβ(1-40)? Clue from hydrophobic interaction. J Phys Chem B 112:3164-3167.
52. Tarus B, Straub JE, Thirumalai DJ (2006) Dynamics of Asp23- Lys28 salt-bridge formation in Aβ10-35 monomers. J Am Chem Soc 128:16159-16168.
53. Lazo ND, Grant MA, Condron MC, Rigby AC, Teplow DB (2005) On the nucleation of amyloid β-protein monomer folding. Protein Sci 14:1581-1596.
54. Sciarretta KL, Gordon DJ, Petkova AT, Tycko R, Meredith SC (2005) Aβ40-lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry 44:6003- 6014.
55. Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Dobeli H, Schubert D, Riek R (2005) 3D structure of Alzheimer's amyloid-β(1-42) fibrils. Proc Natl Acad Sci USA 102:17342-17347.
56. Knecht V, Mhwald H, Lipowsky R (2007) Conformational diversity of the fibrillogenic fusion peptide B18 in different environments from molecular dynamics simulations. J Phys Chem B 111:4161-4170.