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Journal of Chemical Physics

Volumn 135, Issue 3, 2011, Pages

Does amino acid sequence determine the properties of Aβ dimer?

(4) Lockhart, Christopher a Kim, Seongwon a Kumar, Rashmi a Klimov, Dmitri K a

a GEORGE MASON UNIVERSITY (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; END-TO-END DISTANCES; GAUSSIAN STATISTICS; IMPLICIT SOLVENT MODEL; NON-LOCAL INTERACTIONS; NONBONDED INTERACTION; REPLICA EXCHANGE MOLECULAR DYNAMICS; THEORETICAL STUDY; UNITED ATOMS;

AMINO ACIDS; MOLECULAR DYNAMICS; PEPTIDES; POLYMER MELTS; THERMODYNAMICS;

DIMERS;

AMYLOID BETA PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; DIMERIZATION; MOLECULAR DYNAMICS; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMYLOID BETA-PEPTIDES; DIMERIZATION; MOLECULAR DYNAMICS SIMULATION; THERMODYNAMICS;

EID: 79960904377 PISSN: 00219606 EISSN: None Source Type: Journal
DOI: 10.1063/1.3610427 Document Type: Article

Times cited : (4)

References (50)

1
- 0347357617
- Protein folding and misfolding
- DOI 10.1038/nature02261
- C. M. Dobson, Nature (London) 426, 884 (2003). 10.1038/nature02261 (Pubitemid 38056880)
- (2003) Nature , vol.426 , Issue.6968 , pp. 884-890
- Dobson, C.M.¹

2
- 0042467550
- Rationalization of the effects of mutations on peptide and protein aggregation rates
- DOI 10.1038/nature01891
- F. Chiti, M. Stefani, N. Taddei, G. Ramponi, and C. M. Dobson, Nature (London) 424, 805 (2003). 10.1038/nature01891 (Pubitemid 37021713)
- (2003) Nature , vol.424 , Issue.6950 , pp. 805-808
- Chiti, F.¹ Stefani, M.² Taddel, N.³ Ramponi, G.⁴ Dobson, C.M.⁵

3
- 2442718759
- 10.1039/b402126f
- Y. Song, S. R. Challa, C. J. Medforth, Y. Qiu, R. K. Watt, D. Pea, J. E. Miller, F. van Swolab, and J. A. Shelnutt, Chem. Commun., 1044 (2004). 10.1039/b402126f
- (2004) Chem. Commun. , pp. 1044
- Song, Y.¹ Challa, S.R.² Medforth, C.J.³ Qiu, Y.⁴ Watt, R.K.⁵ Pea, D.⁶ Miller, J.E.⁷ Van Swolab, F.⁸ Shelnutt, J.A.⁹

4
- 33645522802
- 10.1088/1478-3975/3/1/S02
- M. Reches and E. Gazit, Phys. Biol. 3, S10 (2006). 10.1088/1478-3975/3/1/ S02
- (2006) Phys. Biol. , vol.3 , pp. 10
- Reches, M.¹ Gazit, E.²

5
- 0347987853
- Folding proteins in fatal ways
- DOI 10.1038/nature02264
- D. J. Selkoe, Nature (London) 426, 900 (2003). 10.1038/nature02264 (Pubitemid 38056883)
- (2003) Nature , vol.426 , Issue.6968 , pp. 900-904
- Selkoe, D.J.¹

6
- 34247899121
- Functional amyloid - from bacteria to humans
- DOI 10.1016/j.tibs.2007.03.003, PII S096800040700059X
- D. M. Fowler, A. V. Koulov, W. E. Balch, and J. W. Kelly, Trends Biochem. Sci. 32, 217 (2007). 10.1016/j.tibs.2007.03.003 (Pubitemid 46694328)
- (2007) Trends in Biochemical Sciences , vol.32 , Issue.5 , pp. 217-224
- Fowler, D.M.¹ Koulov, A.V.² Balch, W.E.³ Kelly, J.W.⁴

7
- 0036708168
- Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: The emerging role of oligomeric assemblies
- DOI 10.1002/jnr.10328
- M. D. Kirkitadze, G. Bitan, and D. B. Teplow, J. Neurosci. Res. 69, 567 (2002). 10.1002/jnr.10328 (Pubitemid 34966869)
- (2002) Journal of Neuroscience Research , vol.69 , Issue.5 , pp. 567-577
- Kirkitadze, M.D.¹ Bitan, G.² Teplow, D.B.³

8
- 0036407227
- Peptide aggregation in neurodegenerative disease
- DOI 10.1146/annurev.bioeng.4.092801.094202
- R. M. Murphy, Annu. Rev. Biomed. Eng. 4, 155 (2002). 10.1146/annurev. bioeng.4.092801.094202 (Pubitemid 35217418)
- (2002) Annual Review of Biomedical Engineering , vol.4 , pp. 155-174
- Murphy, R.M.¹

9
- 12244285938
- Molecular basis for amyloid fibril formation and stability
- DOI 10.1073/pnas.0406847102
- O. S. Makin, E. Atkins, P. Sikorski, J. Johansson, and L. C. Serpell, Proc. Natl. Acad. Sci. U.S.A. 102, 315 (2005). 10.1073/pnas.0406847102 (Pubitemid 40116764)
- (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.2 , pp. 315-320
- Makin, O.S.¹ Atkins, E.² Sikorski, P.³ Johansson, J.⁴ Serpell, L.C.⁵

10
- 0026597063
- 10.1126/science.1566067
- J. Hardy and G. A. Higgins, Science 256, 184 (1992). 10.1126/science. 1566067
- (1992) Science , vol.256 , pp. 184
- Hardy, J.¹ Higgins, G.A.²

11
- 13444310701
- Characterization of chemical exchange between soluble and aggregated states of β-amyloid by solution-state NMR upon variation of salt conditions
- DOI 10.1021/bi048264b
- S. Narayanan and B. Reif, Biochemistry 44, 1444 (2005). 10.1021/bi048264b (Pubitemid 40204388)
- (2005) Biochemistry , vol.44 , Issue.5 , pp. 1444-1452
- Narayanan, S.¹ Reif, B.²

12
- 0041816383
- Elucidation of primary structure elements controlling early amyloid β-protein oligomerization
- DOI 10.1074/jbc.M300825200
- G. Bitan, S. S. Vollers, and D. B. Teplow, J. Biol. Chem. 278, 34882 (2003). 10.1074/jbc.M300825200 (Pubitemid 37102247)
- (2003) Journal of Biological Chemistry , vol.278 , Issue.37 , pp. 34882-34889
- Bitan, G.¹ Vollers, S.S.² Teplow, D.B.³

13
- 70349295278
- 10.1073/pnas.0905127106
- K. Ono, M. M. Condron, and D. B. Teplow, Proc. Natl. Acad. Sci. U.S.A. 106, 14745 (2009). 10.1073/pnas.0905127106
- (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 14745
- Ono, K.¹ Condron, M.M.² Teplow, D.B.³

14
- 33847662852
- Soluble protein oligomers in neurodegeneration: Lessons from the Alzheimer's amyloid β-peptide
- DOI 10.1038/nrm2101, PII NRM2101
- C. Haass and D. J. Selkoe, Nat. Rev. Mol. Cell. Biol. 8, 101 (2007). 10.1038/nrm2101 (Pubitemid 46432529)
- (2007) Nature Reviews Molecular Cell Biology , vol.8 , Issue.2 , pp. 101-112
- Haass, C.¹ Selkoe, D.J.²

15
- 49149124343
- 10.1038/nm1782
- G. M. Shankar, S. Li, T. H. Mehta, A. Garcia-Munoz, N. E. Shepardson, I. Smith, F. M. Brett, M. A. Farrell, M. J. Rowan, C. A. Lemere, C. M. Regan, D. M. Walsh, B. L. Sabatini, and D. J. Selkoe, Nat. Med. 14, 837 (2008). 10.1038/nm1782
- (2008) Nat. Med. , vol.14 , pp. 837
- Shankar, G.M.¹ Li, S.² Mehta, T.H.³ Garcia-Munoz, A.⁴ Shepardson, N.E.⁵ Smith, I.⁶ Brett, F.M.⁷ Farrell, M.A.⁸ Rowan, M.J.⁹ Lemere, C.A.¹⁰ Regan, C.M.¹¹ Walsh, D.M.¹² Sabatini, B.L.¹³ Selkoe, D.J.¹⁴

16
- 0035173352
- ox
- DOI 10.1046/j.0014-2956.2001.02537.x
- R. Riek, P. Guntert, H. Dobeli, B. Wipf, and K. Wuthrich, Eur. J. Biochem. 268, 5930 (2001). 10.1046/j.0014-2956.2001.02537.x (Pubitemid 33079329)
- (2001) European Journal of Biochemistry , vol.268 , Issue.22 , pp. 5930-5936
- Riek, R.¹ Guntert, P.² Dobeli, H.³ Wipf, B.⁴ Wuthrich, K.⁵

17
- 10744219665
- 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
- DOI 10.1021/ja036813f
- L. Hou, H. Shao, Y. Zhang, H. Li, N. K. Menon, E. B. Neuhaus, J. M. Brewer, I.-J. L. Byeon, D. G. Ray, M. P. Vitek, T. Iwashita, R. A. Makula, A. B. Przybyla, and M. G. Zagorski, J. Am. Chem. Soc. 126, 1992 (2004). 10.1021/ja036813f (Pubitemid 38228879)
- (2004) Journal of the American Chemical Society , vol.126 , Issue.7 , pp. 1992-2005
- Hou, L.¹ Shao, H.² Zhang, Y.³ Li, H.⁴ Menon, N.K.⁵ Neuhaus, E.B.⁶ Brewer, J.M.⁷ Byeon, I.-J.L.⁸ Ray, D.G.⁹ Vitek, M.P.¹⁰ Iwashita, T.¹¹ Makula, R.A.¹² Przybyla, A.B.¹³ Zagorski, M.G.¹⁴

18
- 30744433878
- Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils
- DOI 10.1021/bi051952q
- A. T. Petkova, W.-M. Yau, and R. Tycko, Biochemistry 45, 498 (2006). 10.1021/bi051952q (Pubitemid 43100415)
- (2006) Biochemistry , vol.45 , Issue.2 , pp. 498-512
- Petkova, A.T.¹ Yau, W.-M.² Tycko, R.³

19
- 57449091884
- 10.1073/pnas.0806270105
- A. K. Paravastua, R. D. Leapman, W.-M. Yaua, and R. Tycko, Proc. Natl. Acad. Sci. U.S.A. 105, 18349 (2008). 10.1073/pnas.0806270105
- (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 18349
- Paravastua, A.K.¹ Leapman, R.D.² Yaua, W.-M.³ Tycko, R.⁴

20
- 33748689799
- B. Ma and R. Nussinov, Curr. Opin. Chem. Biol. 10, 445 (2006).
- (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 445
- Ma, B.¹ Nussinov, R.²

21
- 33748525884
- Computational models for the prediction of polypeptide aggregation propensity
- DOI 10.1016/j.cbpa.2006.07.009, PII S1367593106001104, Analytical Techniques/Mechanisms
- A. Caflisch, Curr. Opin. Chem. Biol. 10, 437 (2006). 10.1016/j.cbpa.2006. 07.009 (Pubitemid 44375058)
- (2006) Current Opinion in Chemical Biology , vol.10 , Issue.5 , pp. 437-444
- Caflisch, A.¹

22
- 34247234602
- The Alzheimer's Peptides Aβ40 and 42 Adopt Distinct Conformations in Water: A Combined MD / NMR Study
- DOI 10.1016/j.jmb.2007.02.093, PII S0022283607003105
- N. G. Sgourakis, Y. Yan, S. A. McCallum, C. Wang, and A. E. Garcia, J. Mol. Biol. 368, 1448 (2007). 10.1016/j.jmb.2007.02.093 (Pubitemid 46617600)
- (2007) Journal of Molecular Biology , vol.368 , Issue.5 , pp. 1448-1457
- Sgourakis, N.G.¹ Yan, Y.² McCallum, S.A.³ Wang, C.⁴ Garcia, A.E.⁵

23
- 33748121600
- Folding Landscapes of the Alzheimer Amyloid-β(12-28) Peptide
- DOI 10.1016/j.jmb.2006.07.032, PII S0022283606009028
- A. Baumketner and J.-E. Shea, J. Mol. Biol. 362, 567 (2006). 10.1016/j.jmb.2006.07.032 (Pubitemid 44307159)
- (2006) Journal of Molecular Biology , vol.362 , Issue.3 , pp. 567-579
- Baumketner, A.¹ Shea, J.-E.²

24
- 33845570428
- 10-35 monomers
- DOI 10.1021/ja064872y
- B. Tarus, J. E. Straub, and D. Thirumalai, J. Am. Chem. Soc. 128, 16159 (2006). 10.1021/ja064872y (Pubitemid 44936609)
- (2006) Journal of the American Chemical Society , vol.128 , Issue.50 , pp. 16159-16168
- Tarus, B.¹ Straub, J.E.² Thirumalai, D.³

25
- 77957256708
- 10.1016/j.jmb.2010.08.003
- A. Vitalis and A. Caflisch, J. Mol. Biol. 403, 148 (2010). 10.1016/j.jmb.2010.08.003
- (2010) J. Mol. Biol. , vol.403 , pp. 148
- Vitalis, A.¹ Caflisch, A.²

26
- 66149189211
- 10.1002/prot.22305
- Y. Lu, P. Derreumaux, Z. Guo, N. Mousseau, and G. Wei, Proteins: Struct., Funct., Bioinf. 75, 954 (2009). 10.1002/prot.22305
- (2009) Proteins: Struct., Funct., Bioinf. , vol.75 , pp. 954
- Lu, Y.¹ Derreumaux, P.² Guo, Z.³ Mousseau, N.⁴ Wei, G.⁵

27
- 61549102795
- 10.1016/j.bpj.2008.10.040
- G. Bellesia and J.-E. Shea, Biophys. J. 96, 875 (2009). 10.1016/j.bpj.2008.10.040
- (2009) Biophys. J. , vol.96 , pp. 875
- Bellesia, G.¹ Shea, J.-E.²

28
- 56849108519
- 10.1063/1.3021062
- F. S. Nandel, P. Anand, and U. H. E. Hansmann, J. Chem. Phys. 129, 195102 (2008). 10.1063/1.3021062
- (2008) J. Chem. Phys. , vol.129 , pp. 195102
- Nandel, F.S.¹ Anand, P.² Hansmann, U.H.E.³

29
- 77953584016
- 10.1063/1.3447894
- S. Kim, T. Takeda, and D. K. Klimov, J. Chem. Phys. 132, 225101 (2010). 10.1063/1.3447894
- (2010) J. Chem. Phys. , vol.132 , pp. 225101
- Kim, S.¹ Takeda, T.² Klimov, D.K.³

30
- 77957329138
- 10.1016/j.bpj.2010.07.008
- S. Kim, T. Takeda, and D. K. Klimov, Biophys. J. 99, 1949 (2010). 10.1016/j.bpj.2010.07.008
- (2010) Biophys. J. , vol.99 , pp. 1949
- Kim, S.¹ Takeda, T.² Klimov, D.K.³

31
- 66749092410
- 10.1021/jp900425e
- Y. Chebaro, N. Mousseau, and P. Derreumaux, J. Phys. Chem. B 113, 7668 (2009). 10.1021/jp900425e
- (2009) J. Phys. Chem. B , vol.113 , pp. 7668
- Chebaro, Y.¹ Mousseau, N.² Derreumaux, P.³

32
- 84986512474
- 10.1002/jcc.540040211
- B. R. Brooks, R. E. Bruccoler, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1982). 10.1002/jcc.540040211
- (1982) J. Comput. Chem. , vol.4 , pp. 187
- Brooks, B.R.¹ Bruccoler, R.E.² Olafson, B.D.³ States, D.J.⁴ Swaminathan, S.⁵ Karplus, M.⁶

33
- 0036138028
- Evaluation of a fast implicit solvent model for molecular dynamics simulations
- DOI 10.1002/prot.10001
- P. Ferrara, J. Apostolakis, and A. Caflisch, Proteins: Struct., Funct., Bioinf. 46, 24 (2002). 10.1002/prot.10001 (Pubitemid 34033573)
- (2002) Proteins: Structure, Function and Genetics , vol.46 , Issue.1 , pp. 24-33
- Ferrara, P.¹ Apostolakis, J.² Caflisch, A.³

34
- 68949122827
- 10.1016/j.bpj.2009.03.015
- T. Takeda and D. K. Klimov, Biophys. J. 96, 4428 (2009). 10.1016/j.bpj.2009.03.015
- (2009) Biophys. J. , vol.96 , pp. 4428
- Takeda, T.¹ Klimov, D.K.²

35
- 69549145714
- 10.1002/prot.22406
- T. Takeda and D. K. Klimov, Proteins: Struct., Funct., Bioinf. 77, 1 (2009). 10.1002/prot.22406
- (2009) Proteins: Struct., Funct., Bioinf. , vol.77 , pp. 1
- Takeda, T.¹ Klimov, D.K.²

36
- 67650079408
- 10.1021/jp9016773
- T. Takeda and D. K. Klimov, J. Phys. Chem. B 113, 6692 (2009). 10.1021/jp9016773
- (2009) J. Phys. Chem. B , vol.113 , pp. 6692
- Takeda, T.¹ Klimov, D.K.²

37
- 0001616080
- 10.1016/S0009-2614(99)01123-9
- Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 114, 141 (1999). 10.1016/S0009-2614(99)01123-9
- (1999) Chem. Phys. Lett. , vol.114 , pp. 141
- Sugita, Y.¹ Okamoto, Y.²

38
- 58849114585
- 10.1016/j.bpj.2008.10.008
- T. Takeda and D. K. Klimov, Biophys. J. 96, 442 (2009). 10.1016/j.bpj.2008.10.008
- (2009) Biophys. J. , vol.96 , pp. 442
- Takeda, T.¹ Klimov, D.K.²

39
- 0020997912
- 10.1002/bi360221211
- W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983). 10.1002/bip.360221211
- (1983) Biopolymers , vol.22 , pp. 2577
- Kabsch, W.¹ Sander, C.²

40
- 33646987405
- 10.1103/PhysRevLett.63.1195
- A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
- (1989) Phys. Rev. Lett. , vol.63 , pp. 1195
- Ferrenberg, A.M.¹ Swendsen, R.H.²

41
- 79960901634
- See supplementary material at E-JCPSA6-135-034127 for applicability of implicit solvent model and REMD convergence.
- See supplementary material at http://dx.doi.org/10.1063/1.3610427 E-JCPSA6-135-034127 for applicability of implicit solvent model and REMD convergence.

42
- 0003858739
- (Butterworth-Heinemann, Oxford)
- L. D. Landau and E. M. Lifshitz, Statistical Physics, Course of Theoretical Physics Vol. 5 (Butterworth-Heinemann, Oxford, 1984)
- (1984) Statistical Physics, Course of Theoretical Physics Vol. 5
- Landau, L.D.¹ Lifshitz, E.M.²

43
- 0003623697
- (American Institute of Physics, Woodbury).
- A. Y. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules (American Institute of Physics, Woodbury, 1994).
- (1994) Statistical Physics of Macromolecules
- Grosberg, A.Y.¹ Khokhlov, A.R.²

44
- 0003411482
- (Cornell University Press, Ithaca).
- P. J. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, 1953).
- (1953) Principles of Polymer Chemistry
- Flory, P.J.¹

45
- 21644435527
- Proteins and polymers
- DOI 10.1063/1.1940059, 234910
- J. R. Banavar, T. X. Hoang, and A. Maritan, J. Chem. Phys. 122, 234910 (2005). 10.1063/1.1940059 (Pubitemid 40925792)
- (2005) Journal of Chemical Physics , vol.122 , Issue.23 , pp. 1-4
- Banavar, J.R.¹ Hoang, T.X.² Maritan, A.³

46
- 0346492907
- Fractal and statistical properties of large compact polymers: A computational study
- DOI 10.1016/j.polymer.2003.10.073
- R. Lua, A. L. Borovinskiy, and A. Y. Grosberg, Polymer 45, 717 (2004). 10.1016/j.polymer.2003.10.073 (Pubitemid 38082205)
- (2004) Polymer , vol.45 , Issue.2 , pp. 717-731
- Lua, R.¹ Borovinskiy, A.L.² Grosberg, A.Yu.³

47
- 34848929022
- Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils
- DOI 10.1371/journal.pcbi.0030173
- M. Cheon, I. Chang, S. Mohanty, L. M. Luheshi, C. M. Dobson, M. Vendruscolo, and G. Favrin, PLOS Comput. Biol. 3, 1727 (2007). 10.1371/journal.pcbi.0030173 (Pubitemid 47502977)
- (2007) PLoS Computational Biology , vol.3 , Issue.9 , pp. 1727-1738
- Cheon, M.¹ Chang, I.² Mohanty, S.³ Luheshi, L.M.⁴ Dobson, C.M.⁵ Vendruscolo, M.⁶ Favrin, G.⁷

48
- 77950219248
- 10.1021/ja9096303
- B. Urbanc, M. Betnel, L. Cruz, G. Bitan, and D. B. Teplow, J. Am. Chem. Soc. 132, 4266 (2010). 10.1021/ja9096303
- (2010) J. Am. Chem. Soc. , vol.132 , pp. 4266
- Urbanc, B.¹ Betnel, M.² Cruz, L.³ Bitan, G.⁴ Teplow, D.B.⁵

49
- 67849095816
- 10.1021/ja804984h
- A. R. Lam, D. B. Teplow, H. E. Stanley, and B. Urbanc, J. Am. Chem, Soc. 130, 17413 (2008). 10.1021/ja804984h
- (2008) J. Am. Chem, Soc. , vol.130 , pp. 17413
- Lam, A.R.¹ Teplow, D.B.² Stanley, H.E.³ Urbanc, B.⁴

50
- 4444221565
- 10.1002/jcc.20084
- E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, J. Comput. Chem. 25, 1605 (2004). 10.1002/jcc.20084
- (2004) J. Comput. Chem. , vol.25 , pp. 1605
- Pettersen, E.F.¹ Goddard, T.D.² Huang, C.C.³ Couch, G.S.⁴ Greenblatt, D.M.⁵ Meng, E.C.⁶ Ferrin, T.E.⁷

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