-
1
-
-
0035961329
-
The structural basis of protein folding and its links with human disease
-
Dobson, C. M. 2001. The structural basis of protein folding and its links with human disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356:133-145.
-
(2001)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.356
, pp. 133-145
-
-
Dobson, C.M.1
-
2
-
-
0037551741
-
Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders
-
Caughey, B., and P. T. Lansbury. 2003. Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu. Rev. Neurosci. 26:267-298.
-
(2003)
Annu. Rev. Neurosci
, vol.26
, pp. 267-298
-
-
Caughey, B.1
Lansbury, P.T.2
-
3
-
-
36749078792
-
Folding versus aggregation: Polypeptide conformations on competing pathways
-
Jahn, T. R., and S. E. Radford. 2008. Folding versus aggregation: polypeptide conformations on competing pathways. Arch. Biochem. Biophys. 469:100-117.
-
(2008)
Arch. Biochem. Biophys
, vol.469
, pp. 100-117
-
-
Jahn, T.R.1
Radford, S.E.2
-
4
-
-
33748857338
-
Pathogenesis of prion diseases: Current status and future outlook
-
Aguzzi, A., and M. Heikenwalder. 2006. Pathogenesis of prion diseases: current status and future outlook. Nat. Rev. Microbiol. 4:765-775.
-
(2006)
Nat. Rev. Microbiol
, vol.4
, pp. 765-775
-
-
Aguzzi, A.1
Heikenwalder, M.2
-
5
-
-
34249941302
-
Copper and the prion protein: Methods, structures, function, and disease
-
Millhauser, G. L. 2007. Copper and the prion protein: methods, structures, function, and disease. Annu. Rev. Phys. Chem. 58:299-320.
-
(2007)
Annu. Rev. Phys. Chem
, vol.58
, pp. 299-320
-
-
Millhauser, G.L.1
-
6
-
-
24644448839
-
The most infectious prion protein particles
-
Silveira, J. R., G. J. Raymond, A. G. Hughson, R. E. Race, V. L. Sim, S. F. Hayes, and B. Caughey. 2005. The most infectious prion protein particles. Nature. 437:257-261.
-
(2005)
Nature
, vol.437
, pp. 257-261
-
-
Silveira, J.R.1
Raymond, G.J.2
Hughson, A.G.3
Race, R.E.4
Sim, V.L.5
Hayes, S.F.6
Caughey, B.7
-
7
-
-
0036377156
-
Amyloid fibril formation. proposed mechanisms and relevance to conformational disease
-
Zerovnik, E. 2002. Amyloid fibril formation. proposed mechanisms and relevance to conformational disease. Eur. J. Biochem. 269:3362-3371.
-
(2002)
Eur. J. Biochem
, vol.269
, pp. 3362-3371
-
-
Zerovnik, E.1
-
8
-
-
0033849738
-
Review: History of the amyloid fibril
-
Sipe, J. D., and A. S. Cohen. 2000. Review: history of the amyloid fibril. J. Struct. Biol. 130:88-98.
-
(2000)
J. Struct. Biol
, vol.130
, pp. 88-98
-
-
Sipe, J.D.1
Cohen, A.S.2
-
9
-
-
62549097355
-
Characterization of the nucleation barriers for protein aggregation and amyloid formation
-
Auer, S., C. M. Dobson, and M. Vendruscolo. 2007. Characterization of the nucleation barriers for protein aggregation and amyloid formation. HFSP J. 1:137-146.
-
(2007)
HFSP J
, vol.1
, pp. 137-146
-
-
Auer, S.1
Dobson, C.M.2
Vendruscolo, M.3
-
10
-
-
0027195933
-
Seeding "one-dimensional crystallization" of amyloid: A pathogenic mechanism in Alzheimer's disease and scrapie?
-
Jarrett, J. T., and P. T. Lansbury. 1993. Seeding "one-dimensional crystallization" of amyloid: a pathogenic mechanism in Alzheimer's disease and scrapie? Cell. 73:1055-1058.
-
(1993)
Cell
, vol.73
, pp. 1055-1058
-
-
Jarrett, J.T.1
Lansbury, P.T.2
-
11
-
-
34249782573
-
Similarities in the thermodynamics and kinetics of aggregation of disease-related Aβ(1-40) peptides
-
Meinhardt, J., G. G. Tartaglia, A. Pawar, T. Christopeit, P. Hortschansky, V. Schroeckh, C. M. Dobson, M. Vendruscolo, and M. Fandrich. 2007. Similarities in the thermodynamics and kinetics of aggregation of disease-related Aβ(1-40) peptides. Protein Sci. 16:1214-1222.
-
(2007)
Protein Sci
, vol.16
, pp. 1214-1222
-
-
Meinhardt, J.1
Tartaglia, G.G.2
Pawar, A.3
Christopeit, T.4
Hortschansky, P.5
Schroeckh, V.6
Dobson, C.M.7
Vendruscolo, M.8
Fandrich, M.9
-
12
-
-
0031592945
-
Common core structure of amyloid fibrils by synchrotron x-ray diffraction
-
Sunde, M., L. C. Serpell, M. Bartlam, P. E. Fraser, M. B. Pepys, and C. C. F. Blake. 1997. Common core structure of amyloid fibrils by synchrotron x-ray diffraction. J. Mol. Biol. 273:729-739.
-
(1997)
J. Mol. Biol
, vol.273
, pp. 729-739
-
-
Sunde, M.1
Serpell, L.C.2
Bartlam, M.3
Fraser, P.E.4
Pepys, M.B.5
Blake, C.C.F.6
-
13
-
-
34047157022
-
Hydrophobic cooperativity as a mechanism for amyloid nucleation
-
Hills, R. D., Jr., and C. L. Brooks III. 2007. Hydrophobic cooperativity as a mechanism for amyloid nucleation. J. Mol. Biol. 368:894-901.
-
(2007)
J. Mol. Biol
, vol.368
, pp. 894-901
-
-
Hills Jr., R.D.1
Brooks III, C.L.2
-
14
-
-
26844435756
-
Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments
-
Buchete, N.-V., R. Tycko, and G. Hummer. 2005. Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J. Mol. Biol. 353:804-821.
-
(2005)
J. Mol. Biol
, vol.353
, pp. 804-821
-
-
Buchete, N.-V.1
Tycko, R.2
Hummer, G.3
-
15
-
-
34247637243
-
Structure and dynamics of parallel β-sheets, hydrophobic core, and loops in Alzheimer's Aβ fibrils
-
Buchete, N.-V., and G. Hummer. 2007. Structure and dynamics of parallel β-sheets, hydrophobic core, and loops in Alzheimer's Aβ fibrils. Biophys. J. 92:3032-3039.
-
(2007)
Biophys. J
, vol.92
, pp. 3032-3039
-
-
Buchete, N.-V.1
Hummer, G.2
-
16
-
-
4444346811
-
Kinetic control of dimer structure formation in amyloid fibrillogenesis
-
Hwang, W., S. Zhang, R. D. Kamm, and M. Karplus. 2004. Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc. Natl. Acad. Sci. USA. 101:12916-12921.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 12916-12921
-
-
Hwang, W.1
Zhang, S.2
Kamm, R.D.3
Karplus, M.4
-
17
-
-
0037337271
-
16-22 amyloid peptides into antiparallel β sheets
-
16-22 amyloid peptides into antiparallel β sheets. Structure. 11:295-307.
-
(2003)
Structure
, vol.11
, pp. 295-307
-
-
Klimov, D.K.1
Thirumalai, D.2
-
18
-
-
33646192684
-
The stability of monomeric intermediates controls amyloid formation: Aβ25-35 and its N27Q mutant
-
Ma, B., and R. Nussinov. 2006. The stability of monomeric intermediates controls amyloid formation: Aβ25-35 and its N27Q mutant. Biophys. J. 90:3365-3374.
-
(2006)
Biophys. J
, vol.90
, pp. 3365-3374
-
-
Ma, B.1
Nussinov, R.2
-
19
-
-
36148983867
-
17-42 fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities
-
17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys. J. 93:3046-3057.
-
(2007)
Biophys. J
, vol.93
, pp. 3046-3057
-
-
Zheng, J.1
Jang, H.2
Ma, B.3
Tsai, C.-J.4
Nussinov, R.5
-
20
-
-
33846036362
-
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism
-
Nguyen, P. H., M. S. Li, G. Stock, J. E. Straub, and D. Thirumalai. 2007. Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism. Proc. Natl. Acad. Sci. USA. 104:111-116.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 111-116
-
-
Nguyen, P.H.1
Li, M.S.2
Stock, G.3
Straub, J.E.4
Thirumalai, D.5
-
21
-
-
7444240183
-
Probing the instabilities in the dynamics of helical fragments from mouse PrPC
-
Dima, R. I., and D. Thirumalai. 2004. Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc. Natl. Acad. Sci. USA. 101:15335-15340.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15335-15340
-
-
Dima, R.I.1
Thirumalai, D.2
-
22
-
-
33947379177
-
Molecular mechanism for low pH triggered misfolding of the human prion protein
-
DeMarco, M., and V. Daggett. 2007. Molecular mechanism for low pH triggered misfolding of the human prion protein. Biochemistry. 46:3045-3054.
-
(2007)
Biochemistry
, vol.46
, pp. 3045-3054
-
-
DeMarco, M.1
Daggett, V.2
-
23
-
-
1442330474
-
From conversion to aggregation: Protofibril formation of the prion protein
-
DeMarco, M. L., and V. Daggett. 2004. From conversion to aggregation: protofibril formation of the prion protein. Proc. Natl. Acad. Sci. USA. 101:2293-2298.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2293-2298
-
-
DeMarco, M.L.1
Daggett, V.2
-
24
-
-
10044227281
-
Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues
-
Langella, E., R. Improta, and V. Barone. 2004. Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: effect of protonation of histidine residues. Biophys. J. 87:3623-3632.
-
(2004)
Biophys. J
, vol.87
, pp. 3623-3632
-
-
Langella, E.1
Improta, R.2
Barone, V.3
-
25
-
-
34548221936
-
Structural and hydration properties of the partially unfolded states of the prion protein
-
De Simone, A., A. Zagari, and P. Derreumaux. 2007. Structural and hydration properties of the partially unfolded states of the prion protein. Biophys. J. 93:1284-1292.
-
(2007)
Biophys. J
, vol.93
, pp. 1284-1292
-
-
De Simone, A.1
Zagari, A.2
Derreumaux, P.3
-
26
-
-
30344461291
-
Misfolding of the amyloid β-protein: A molecular dynamics study
-
Flöck, D., S. Colacino, G. Colombo, and A. D. Nola. 2006. Misfolding of the amyloid β-protein: a molecular dynamics study. Proteins. 62:183-192.
-
(2006)
Proteins
, vol.62
, pp. 183-192
-
-
Flöck, D.1
Colacino, S.2
Colombo, G.3
Nola, A.D.4
-
27
-
-
20444363123
-
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of ASN ladder
-
Tsai, H.-H. G., M. Reches, C.-J. Tsai, K. Gunasekaran, E. Gazit, and R. Nussinov. 2005. Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of ASN ladder. Proc. Natl. Acad. Sci. USA. 102:8174-8179.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 8174-8179
-
-
Tsai, H.-H.G.1
Reches, M.2
Tsai, C.-J.3
Gunasekaran, K.4
Gazit, E.5
Nussinov, R.6
-
28
-
-
0037195098
-
Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16-22, Aβ 16-35, and Aβ 10-35): Sequence effects
-
Ma, B., and R. Nussinov. 2002. Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ 16-22, Aβ 16-35, and Aβ 10-35): sequence effects. Proc. Natl. Acad. Sci. USA. 99:14126-14131.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14126-14131
-
-
Ma, B.1
Nussinov, R.2
-
29
-
-
42449155493
-
Amyloid-β(29-42) dimer formations studied by a multicanonical-multioverlap molecular dynamics simulation
-
Itoh, S., and Y. Okamoto. 2008. Amyloid-β(29-42) dimer formations studied by a multicanonical-multioverlap molecular dynamics simulation. J. Phys. Chem. B. 112:2767-2770.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 2767-2770
-
-
Itoh, S.1
Okamoto, Y.2
-
30
-
-
4444267407
-
β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations
-
Daidone, I., F. Simona, D. Roccatano, R. A. Broglia, G. Tiana, G. Colombo, and A. D. Nola. 2004. β-Hairpin conformation of fibrillogenic peptides: structure and α-β transition mechanism revealed by molecular dynamics simulations. Proteins. 57:198-204.
-
(2004)
Proteins
, vol.57
, pp. 198-204
-
-
Daidone, I.1
Simona, F.2
Roccatano, D.3
Broglia, R.A.4
Tiana, G.5
Colombo, G.6
Nola, A.D.7
-
31
-
-
34548804689
-
Computational simulations of the early steps of protein aggregation
-
Wei, G., N. Mousseau, and P. Derreumaux. 2007. Computational simulations of the early steps of protein aggregation. Prion. 1:3-8.
-
(2007)
Prion
, vol.1
, pp. 3-8
-
-
Wei, G.1
Mousseau, N.2
Derreumaux, P.3
-
32
-
-
33749642847
-
Computational approaches to fibril structure and formation
-
Hall, C. K., and V. A. Wagoner. 2006. Computational approaches to fibril structure and formation. Methods Enzymol. 412:338-365.
-
(2006)
Methods Enzymol
, vol.412
, pp. 338-365
-
-
Hall, C.K.1
Wagoner, V.A.2
-
33
-
-
33751248251
-
Stability and structure of oligomers of the Alzheimer peptide Aβ16-22: From the dimer to the 32-mer
-
Röhrig, U. F., A. Laio, N. Tantalo, M. Parrinello, and R. Petronzio. 2006. Stability and structure of oligomers of the Alzheimer peptide Aβ16-22: from the dimer to the 32-mer. Biophys. J. 91:3217-3229.
-
(2006)
Biophys. J
, vol.91
, pp. 3217-3229
-
-
Röhrig, U.F.1
Laio, A.2
Tantalo, N.3
Parrinello, M.4
Petronzio, R.5
-
34
-
-
0036784617
-
Molecular dynamics simulations of alanine rich β-sheet oligomers: Insight into amyloid formation
-
Ma, B., and R. Nussinov. 2002. Molecular dynamics simulations of alanine rich β-sheet oligomers: insight into amyloid formation. Protein Sci. 11:2335-2350.
-
(2002)
Protein Sci
, vol.11
, pp. 2335-2350
-
-
Ma, B.1
Nussinov, R.2
-
35
-
-
85031347127
-
-
Kovalenko, A. 2003. Three-dimensional RISM theory for molecular liquids and solid-liquid interfaces. In Molecular Theory of Solvation. 24 of Understanding Chemical Reactivity. F. Hirata, editor. Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
Kovalenko, A. 2003. Three-dimensional RISM theory for molecular liquids and solid-liquid interfaces. In Molecular Theory of Solvation. Vol. 24 of Understanding Chemical Reactivity. F. Hirata, editor. Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
-
-
-
36
-
-
0003184548
-
Numerical solution of the hypernetted chain equation for a solute of arbitrary geometry in three dimensions
-
Beglov, D., and B. Roux. 1995. Numerical solution of the hypernetted chain equation for a solute of arbitrary geometry in three dimensions. J. Chem. Phys. 103:360-364.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 360-364
-
-
Beglov, D.1
Roux, B.2
-
37
-
-
0032568751
-
Three-dimensional density profiles of water in contact with a solute of arbitrary shape: A RISM approach
-
Kovalenko, A., and F. Hirata. 1998. Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach. Chem. Phys. Lett. 290:237-244.
-
(1998)
Chem. Phys. Lett
, vol.290
, pp. 237-244
-
-
Kovalenko, A.1
Hirata, F.2
-
38
-
-
0001324288
-
Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model
-
Kovalenko, A., and F. Hirata. 1999. Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model. J. Chem. Phys. 110:10095-10112.
-
(1999)
J. Chem. Phys
, vol.110
, pp. 10095-10112
-
-
Kovalenko, A.1
Hirata, F.2
-
39
-
-
0033691158
-
Potentials of mean force of simple ions in ambient aqueous solution. I. three-dimensional reference interaction site model approach
-
Kovalenko, A., and F. Hirata. 2000. Potentials of mean force of simple ions in ambient aqueous solution. I. three-dimensional reference interaction site model approach. J. Chem. Phys. 112:10391-10402.
-
(2000)
J. Chem. Phys
, vol.112
, pp. 10391-10402
-
-
Kovalenko, A.1
Hirata, F.2
-
40
-
-
33846411078
-
Microtubule stability studied by three-dimensional molecular theory of solvation
-
Drabik, P., S. Gusarov, and A. Kovalenko. 2007. Microtubule stability studied by three-dimensional molecular theory of solvation. Biophys. J. 92:394-403.
-
(2007)
Biophys. J
, vol.92
, pp. 394-403
-
-
Drabik, P.1
Gusarov, S.2
Kovalenko, A.3
-
41
-
-
0035366824
-
Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model
-
Harano, Y., T. Imai, A. Kovalenko, M. Kinoshita, and F. Hirata. 2001. Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model. J. Chem. Phys. 114:9506-9511.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 9506-9511
-
-
Harano, Y.1
Imai, T.2
Kovalenko, A.3
Kinoshita, M.4
Hirata, F.5
-
42
-
-
34250693613
-
Theoretical analysis on changes in thermodynamic quantities upon protein folding: Essential role of hydration
-
Imai, T., Y. Harano, M. Kinoshita, A. Kovalenko, and F. Hirata. 2007. Theoretical analysis on changes in thermodynamic quantities upon protein folding: essential role of hydration. J. Chem. Phys. 126:225102.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 225102
-
-
Imai, T.1
Harano, Y.2
Kinoshita, M.3
Kovalenko, A.4
Hirata, F.5
-
43
-
-
0035216619
-
Theoretical study for volume changes associated with the helix-coil transition of polypeptides
-
Imai, T., Y. Harano, A. Kovalenko, and F. Hirata. 2001. Theoretical study for volume changes associated with the helix-coil transition of polypeptides. Biopolymers. 59:512-519.
-
(2001)
Biopolymers
, vol.59
, pp. 512-519
-
-
Imai, T.1
Harano, Y.2
Kovalenko, A.3
Hirata, F.4
-
44
-
-
33745780922
-
Theoretical study of volume changes accompanying xenon-lysozyme binding: Implication for molecular mechanism of pressure reversal of anesthesia
-
Imai, T., H. Isogai, T. Seto, A. Kovalenko, and F. Hirata. 2006. Theoretical study of volume changes accompanying xenon-lysozyme binding: implication for molecular mechanism of pressure reversal of anesthesia. J. Phys. Chem. B. 110:12149-12154.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12149-12154
-
-
Imai, T.1
Isogai, H.2
Seto, T.3
Kovalenko, A.4
Hirata, F.5
-
45
-
-
27644490825
-
Water molecules in a protein cavity detected by a statistical-mechanical theory
-
Imai, T., R. Hiraoka, A. Kovalenko, and F. Hirata. 2005. Water molecules in a protein cavity detected by a statistical-mechanical theory. J. Am. Chem. Soc. 127:15334-15335.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 15334-15335
-
-
Imai, T.1
Hiraoka, R.2
Kovalenko, A.3
Hirata, F.4
-
46
-
-
33847074189
-
Theoretical study of cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation
-
Yamazaki, T., T. Imai, F. Hirata, and A. Kovalenko. 2007. Theoretical study of cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation. J. Phys. Chem. B. 111:1206-1212.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 1206-1212
-
-
Yamazaki, T.1
Imai, T.2
Hirata, F.3
Kovalenko, A.4
-
47
-
-
0010159070
-
Optimized cluster expansions for classical fluids. II. Theory of molecular liquids
-
Chandler, D., and H. C. Andersen. 1972. Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. J. Chem. Phys. 57:1930-1937.
-
(1972)
J. Chem. Phys
, vol.57
, pp. 1930-1937
-
-
Chandler, D.1
Andersen, H.C.2
-
48
-
-
36849102073
-
Derivation of an integral equation for pair correlation functions in molecular fluids
-
Chandler, D. 1973. Derivation of an integral equation for pair correlation functions in molecular fluids. J. Chem. Phys. 59:2742-2746.
-
(1973)
J. Chem. Phys
, vol.59
, pp. 2742-2746
-
-
Chandler, D.1
-
49
-
-
0000755031
-
Solvation thermodynamics: An approach from analytical temperature derivatives
-
Yu, H.-A., B. Roux, and M. Karplus. 1990. Solvation thermodynamics: an approach from analytical temperature derivatives. J. Chem. Phys. 92:5020-5033.
-
(1990)
J. Chem. Phys
, vol.92
, pp. 5020-5033
-
-
Yu, H.-A.1
Roux, B.2
Karplus, M.3
-
51
-
-
40849120669
-
Amyloid fibrils of the HET-s(218-289) prion form a β solenoid with a triangular hydrophobic core
-
Wasmer, C., A. Lange, H. V. Melckebeke, A. B. Siemer, R. Riek, and B. H. Meier. 2008. Amyloid fibrils of the HET-s(218-289) prion form a β solenoid with a triangular hydrophobic core. Science. 319:1523-1526.
-
(2008)
Science
, vol.319
, pp. 1523-1526
-
-
Wasmer, C.1
Lange, A.2
Melckebeke, H.V.3
Siemer, A.B.4
Riek, R.5
Meier, B.H.6
-
52
-
-
0037168655
-
A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR
-
Petkova, A. T., Y. Ishii, J. J. Balbach, O. N. Antzutkin, R. D. Leapman, F. Delaglio, and R. Tycko. 2002. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl. Acad. Sci. USA. 99:16742-16747.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16742-16747
-
-
Petkova, A.T.1
Ishii, Y.2
Balbach, J.J.3
Antzutkin, O.N.4
Leapman, R.D.5
Delaglio, F.6
Tycko, R.7
-
53
-
-
28444442999
-
3D structure of Alzheimer's amyloid-β(1-42) fibrils
-
Lührs, T., C. Ritter, M. Adrian, D. Riek-Loher, B. Bohrmann, H. Döbeli, D. Schubert, and R. Riek. 2005. 3D structure of Alzheimer's amyloid-β(1-42) fibrils. Proc. Natl. Acad. Sci. USA. 102:17342-17347.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 17342-17347
-
-
Lührs, T.1
Ritter, C.2
Adrian, M.3
Riek-Loher, D.4
Bohrmann, B.5
Döbeli, H.6
Schubert, D.7
Riek, R.8
-
54
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A., R. K. Do, and A. Sali. 2000. Modeling of loops in protein structures. Protein Sci. 9:1753-1773.
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
55
-
-
0346882663
-
ModLoop: Automated modeling of loops in protein structures
-
Fiser, A., and A. Sali. 2003. ModLoop: automated modeling of loops in protein structures. Bioinformatics. 19:2500-2501.
-
(2003)
Bioinformatics
, vol.19
, pp. 2500-2501
-
-
Fiser, A.1
Sali, A.2
-
56
-
-
23444454552
-
-
Case, D. A., T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
-
Case, D. A., T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
-
-
-
-
57
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. A. Kollman. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24:1999-2012.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.A.13
-
58
-
-
2442480826
-
Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized Born solvent model
-
Lee, M. C., and Y. Duan. 2004. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins. 55:620-634.
-
(2004)
Proteins
, vol.55
, pp. 620-634
-
-
Lee, M.C.1
Duan, Y.2
-
59
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev, A., D. Bashford, and D. A. Case. 2004. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins. 55:383-394.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
60
-
-
0346971105
-
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig, M., A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks III. 2004. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25:265-284.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
-
61
-
-
36449009271
-
A site-site theory for finite concentration saline solutions
-
Perkyns, J. S., and B. M. Pettitt. 1992. A site-site theory for finite concentration saline solutions. J. Chem. Phys. 97:7656-7666.
-
(1992)
J. Chem. Phys
, vol.97
, pp. 7656-7666
-
-
Perkyns, J.S.1
Pettitt, B.M.2
-
62
-
-
36549095343
-
Alkali halides in water: Ion-solvent correlations and ion-ion potentials of mean force at infinite dilution
-
Pettitt, B. M., and P. J. Rossky. 1986. Alkali halides in water: ion-solvent correlations and ion-ion potentials of mean force at infinite dilution. J. Chem. Phys. 84:5836-5844.
-
(1986)
J. Chem. Phys
, vol.84
, pp. 5836-5844
-
-
Pettitt, B.M.1
Rossky, P.J.2
-
63
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
64
-
-
61349175335
-
Theory of molecular liquids
-
F. Hirata, editor. Kluwer Academic Publishers, Dordrecht, The Netherlands
-
Hirata, F. 2003. Theory of molecular liquids. In Molecular Theory of Solvation, Understanding Chemical Reactivity, Vol. 24. F. Hirata, editor. Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
(2003)
Molecular Theory of Solvation, Understanding Chemical Reactivity
, vol.24
-
-
Hirata, F.1
-
65
-
-
11244309572
-
Direct measurement of the thermodynamic parameters of amyloid formation by isothermal titration calorimetry
-
Kardos, J., K. Yamamoto, K. Hasegawa, H. Naiki, and Y. Goto. 2004. Direct measurement of the thermodynamic parameters of amyloid formation by isothermal titration calorimetry. J. Biol. Chem. 279:55308-55314.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 55308-55314
-
-
Kardos, J.1
Yamamoto, K.2
Hasegawa, K.3
Naiki, H.4
Goto, Y.5
-
68
-
-
33646088595
-
Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties
-
Meersman, F., and C. M. Dobson. 2006. Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties. Biochim. Biophys. Acta. 1764:452-460.
-
(2006)
Biochim. Biophys. Acta
, vol.1764
, pp. 452-460
-
-
Meersman, F.1
Dobson, C.M.2
-
69
-
-
45749097124
-
Investigation of the mechanism of β-amyloid fibril formation by kinetic and thermodynamic analyses
-
Lin, M.-S., L.-Y. Chen, H.-T. Tsai, S. S.-S. Wang, Y. Chang, A. Higuchi, and W.-Y. Chen. 2008. Investigation of the mechanism of β-amyloid fibril formation by kinetic and thermodynamic analyses. Langmuir. 24:5802-5808.
-
(2008)
Langmuir
, vol.24
, pp. 5802-5808
-
-
Lin, M.-S.1
Chen, L.-Y.2
Tsai, H.-T.3
Wang, S.S.-S.4
Chang, Y.5
Higuchi, A.6
Chen, W.-Y.7
-
70
-
-
1542331496
-
Ordered aggregation of big bodies with high asphericity in small spheres: A possible mechanism of the amyloid fibril formation
-
Kinoshita, M. 2004. Ordered aggregation of big bodies with high asphericity in small spheres: a possible mechanism of the amyloid fibril formation. Chem. Phys. Lett. 387:54-60.
-
(2004)
Chem. Phys. Lett
, vol.387
, pp. 54-60
-
-
Kinoshita, M.1
-
71
-
-
11844255790
-
10-35-protein: Assessing the propensity for peptide dimerization
-
10-35-protein: assessing the propensity for peptide dimerization. J. Mol. Biol. 345:1141-1156.
-
(2005)
J. Mol. Biol
, vol.345
, pp. 1141-1156
-
-
Tarus, B.1
Straub, J.E.2
Thirumalai, D.3
-
72
-
-
0037947523
-
Ultra-high-pressure inactivation of prion infectivity in processed meat: A practical method to prevent human infection
-
Brown, P., R. Meyer, F. Cardone, and M. Pocchiari. 2003. Ultra-high-pressure inactivation of prion infectivity in processed meat: a practical method to prevent human infection. Proc. Natl. Acad. Sci. USA. 100:6093-6097.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 6093-6097
-
-
Brown, P.1
Meyer, R.2
Cardone, F.3
Pocchiari, M.4
-
73
-
-
18744425443
-
Reduced proteinase K resistance and infectivity of prions after pressure treatment at 60°C
-
Fernández García, A., P. Heindl, H. Voigt, M. Büttner, D. Wienhold, P. Butz, J. Stärke, B. Tauscher, and E. Pfaff. 2004. Reduced proteinase K resistance and infectivity of prions after pressure treatment at 60°C. J. Gen. Virol. 85:261-264.
-
(2004)
J. Gen. Virol
, vol.85
, pp. 261-264
-
-
Fernández García, A.1
Heindl, P.2
Voigt, H.3
Büttner, M.4
Wienhold, D.5
Butz, P.6
Stärke, J.7
Tauscher, B.8
Pfaff, E.9
-
74
-
-
15444367217
-
Dual nature of the infectious prion protein revealed by high pressure
-
Fernandez Garcia, A., P. Heindl, H. Voigt, M. Büttner, P. Butz, N. Tauber, B. Tauscher, and E. Pfaff. 2005. Dual nature of the infectious prion protein revealed by high pressure. J. Biol. Chem. 280:9842-9847.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 9842-9847
-
-
Fernandez Garcia, A.1
Heindl, P.2
Voigt, H.3
Büttner, M.4
Butz, P.5
Tauber, N.6
Tauscher, B.7
Pfaff, E.8
-
75
-
-
33645512247
-
High pressure modulates amyloid formation
-
Torrent, J., C. Balny, and R. Lange. 2006. High pressure modulates amyloid formation. Protein Pept. Lett. 13:271-277.
-
(2006)
Protein Pept. Lett
, vol.13
, pp. 271-277
-
-
Torrent, J.1
Balny, C.2
Lange, R.3
-
76
-
-
0037171122
-
High pressure effects on biological macromolecules: From structural changes to alteration of cellular processes
-
Balny, C., P. Masson, and K. Heremans. 2002. High pressure effects on biological macromolecules: from structural changes to alteration of cellular processes. Biochim. Biophys. Acta. 1595:3-10.
-
(2002)
Biochim. Biophys. Acta
, vol.1595
, pp. 3-10
-
-
Balny, C.1
Masson, P.2
Heremans, K.3
-
77
-
-
0037171140
-
Revisiting volume changes in pressure-induced protein unfolding
-
Royer, C. A. 2002. Revisiting volume changes in pressure-induced protein unfolding. Biochim. Biophys. Acta. 1595:201-209.
-
(2002)
Biochim. Biophys. Acta
, vol.1595
, pp. 201-209
-
-
Royer, C.A.1
-
78
-
-
1642488929
-
Pressure-dissociable reversible assembly of intrinsically denatured lysozyme is a precursor for amyloid fibrils
-
Niraula, T. N., T. Konno, H. Yamada, K. Akasaka, and H. Tachibana. 2004. Pressure-dissociable reversible assembly of intrinsically denatured lysozyme is a precursor for amyloid fibrils. Proc. Natl. Acad. Sci. USA. 101:4089-4093.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4089-4093
-
-
Niraula, T.N.1
Konno, T.2
Yamada, H.3
Akasaka, K.4
Tachibana, H.5
-
79
-
-
20344375446
-
Pressure-jump NMR study of dissociation and association of amyloid protofibrils
-
Kamatari, Y. O., S. Yokoyama, H. Tachibana, and K. Akasaka. 2005. Pressure-jump NMR study of dissociation and association of amyloid protofibrils. J. Mol. Biol. 349:916-921.
-
(2005)
J. Mol. Biol
, vol.349
, pp. 916-921
-
-
Kamatari, Y.O.1
Yokoyama, S.2
Tachibana, H.3
Akasaka, K.4
-
80
-
-
33846014251
-
Kinetic analysis of amyloid protofibril dissociation and volumetric properties of the transition state
-
Abdul Latif, A. R., R. Kono, H. Tachibana, and K. Akasaka. 2007. Kinetic analysis of amyloid protofibril dissociation and volumetric properties of the transition state. Biophys. J. 92:323-329.
-
(2007)
Biophys. J
, vol.92
, pp. 323-329
-
-
Abdul Latif, A.R.1
Kono, R.2
Tachibana, H.3
Akasaka, K.4
-
81
-
-
34548669375
-
Amyloid protofibril is highly voluminous and compressible
-
Akasaka, K., A. R. Abdul Latif, A. Nakamura, K. Matsuo, H. Tachibana, and K. Gekko. 2007. Amyloid protofibril is highly voluminous and compressible. Biochemistry. 46:10444-10450.
-
(2007)
Biochemistry
, vol.46
, pp. 10444-10450
-
-
Akasaka, K.1
Abdul Latif, A.R.2
Nakamura, A.3
Matsuo, K.4
Tachibana, H.5
Gekko, K.6
-
82
-
-
0016352763
-
Hydrophobic bonding and accessible surface area in proteins
-
Chothia, C. 1974. Hydrophobic bonding and accessible surface area in proteins. Nature. 248:338-339.
-
(1974)
Nature
, vol.248
, pp. 338-339
-
-
Chothia, C.1
-
83
-
-
26944481188
-
Interfaces and the driving force of hydrophobic assembly
-
Chandler, D. 2005. Interfaces and the driving force of hydrophobic assembly. Nature. 437:640-647.
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
|