메뉴 건너뛰기




Volumn 79, Issue 1, 2011, Pages 1-22

Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces

Author keywords

Amyloid; Molecular dynamics simulations; Peptide self aggregation; Protein folding

Indexed keywords

AMYLOID; OCTANE; OCTAPEPTIDE; POLYPEPTIDE; WATER;

EID: 78649801398     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22854     Document Type: Article
Times cited : (35)

References (108)
  • 1
    • 34548729144 scopus 로고    scopus 로고
    • Ranking the factors that contribute to protein β-sheet folding
    • Parisien M, Major F. Ranking the factors that contribute to protein β-sheet folding. Proteins 2007; 68: 824-829.
    • (2007) Proteins , vol.68 , pp. 824-829
    • Parisien, M.1    Major, F.2
  • 2
    • 0027998757 scopus 로고
    • Context is a major determinant of β-sheet propensity
    • Minor DL, Kim PS. Context is a major determinant of β-sheet propensity. Nature 1994; 371: 264-267.
    • (1994) Nature , vol.371 , pp. 264-267
    • Minor, D.L.1    Kim, P.S.2
  • 3
    • 4644264473 scopus 로고    scopus 로고
    • Alanine-scanning mutagenesis of the b-sheet region of T4 lysozyme suggests that tertiary context has a dominant effect on β-sheet propensity
    • He MM, Wood ZA, Baase WA, Xiao H, Matthews BM. Alanine-scanning mutagenesis of the b-sheet region of T4 lysozyme suggests that tertiary context has a dominant effect on β-sheet propensity. Protein Sci 2004; 13: 2716-2724.
    • (2004) Protein Sci , vol.13 , pp. 2716-2724
    • He, M.M.1    Wood, Z.A.2    Baase, W.A.3    Xiao, H.4    Matthews, B.M.5
  • 4
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson CM. Protein folding and misfolding. Nature 2003; 426: 884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 5
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75: 333-366.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 7
    • 0033790878 scopus 로고    scopus 로고
    • Molecular structure of a fibrillar Alzheimer's Aβ fragment
    • Serpell LC, Blake CCF, Fraser PE. Molecular structure of a fibrillar Alzheimer's Aβ fragment. Biochemistry 2000; 39: 13269-13275.
    • (2000) Biochemistry , vol.39 , pp. 13269-13275
    • Serpell, L.C.1    Blake, C.C.F.2    Fraser, P.E.3
  • 13
    • 0029861772 scopus 로고    scopus 로고
    • Membrane disruption by Alzheimer beta-amyloid peptides mediated through specific binding to either phospholipids or gangliosides
    • McLaurin JA, Chakrabartty A. Membrane disruption by Alzheimer beta-amyloid peptides mediated through specific binding to either phospholipids or gangliosides. J Biol Chem 1996; 280: 30001-30008.
    • (1996) J Biol Chem , vol.280 , pp. 30001-30008
    • McLaurin, J.A.1    Chakrabartty, A.2
  • 14
    • 67650325176 scopus 로고    scopus 로고
    • The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes
    • Hebda JA, Miranker AD. The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes. Annu Rev Biophys 2009; 38: 125-152.
    • (2009) Annu Rev Biophys , vol.38 , pp. 125-152
    • Hebda, J.A.1    Miranker, A.D.2
  • 15
    • 0035800097 scopus 로고    scopus 로고
    • Vesicle permeabilization by protofibrillar α-synuclein: implications for the pathogenesis and treatment of Parkinson's disease
    • Volles MJ, Lee SJ, Rochet JC, Shtilerman MD, Ding TT, Kessler JC, Lansbury PT, Jr. Vesicle permeabilization by protofibrillar α-synuclein: implications for the pathogenesis and treatment of Parkinson's disease. Biochemistry 2001; 40: 7812-7819.
    • (2001) Biochemistry , vol.40 , pp. 7812-7819
    • Volles, M.J.1    Lee, S.J.2    Rochet, J.C.3    Shtilerman, M.D.4    Ding, T.T.5    Kessler, J.C.6    Lansbury Jr, P.T.7
  • 16
    • 0037930855 scopus 로고    scopus 로고
    • Lipid binding inhibits alpha-synuclein fibril formation
    • Zhu M, Fink AL. Lipid binding inhibits alpha-synuclein fibril formation. J Biol Chem 2003; 278: 16873-16877.
    • (2003) J Biol Chem , vol.278 , pp. 16873-16877
    • Zhu, M.1    Fink, A.L.2
  • 18
    • 0037016741 scopus 로고    scopus 로고
    • Membrane-bound α-synuclein has a high aggregation propensity and the ability to seed the aggregation of the cytosolic form
    • Lee HJ, Choi C, Lee SJ. Membrane-bound α-synuclein has a high aggregation propensity and the ability to seed the aggregation of the cytosolic form. J Biol Chem 2002; 277: 671-678.
    • (2002) J Biol Chem , vol.277 , pp. 671-678
    • Lee, H.J.1    Choi, C.2    Lee, S.J.3
  • 19
    • 0034602296 scopus 로고    scopus 로고
    • George-Hyslop P, Fraser PE. α-Synuclein membrane interactions and lipid specificity
    • Jo E, McLaurin JA, Yip CM, St. George-Hyslop P, Fraser PE. α-Synuclein membrane interactions and lipid specificity. J Biol Chem 2000; 275: 34328-34334.
    • (2000) J Biol Chem , vol.275 , pp. 34328-34334
    • Jo, E.1    McLaurin, J.A.2    Yip St, C.M.3
  • 20
    • 58149277415 scopus 로고    scopus 로고
    • Soluble amyloid β-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity
    • Valincius G, Heinrich F, Budvytyte R, Vanderah DJ, Sokolov Y, Hall JE, Lösche M. Soluble amyloid β-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity. Biophys J 2008; 95: 4845-4861.
    • (2008) Biophys J , vol.95 , pp. 4845-4861
    • Valincius, G.1    Heinrich, F.2    Budvytyte, R.3    Vanderah, D.J.4    Sokolov, Y.5    Hall, J.E.6    Lösche, M.7
  • 22
    • 33845395215 scopus 로고    scopus 로고
    • Natively folded HypF-N and its early amyloid aggregates interact with phospholipid monolayers and destabilize supported phospholipid bilayers
    • Canale C, Torrassa S, Rispoli P, Relini A, Rolandi R, Bucciantini M, Stefani M, Gliozzi A. Natively folded HypF-N and its early amyloid aggregates interact with phospholipid monolayers and destabilize supported phospholipid bilayers. Biophys J 2006; 91: 4575.
    • (2006) Biophys J , vol.91 , pp. 4575
    • Canale, C.1    Torrassa, S.2    Rispoli, P.3    Relini, A.4    Rolandi, R.5    Bucciantini, M.6    Stefani, M.7    Gliozzi, A.8
  • 23
    • 4043100348 scopus 로고    scopus 로고
    • Formation of amyloid fibers triggered by phosphatidylserine-containing membranes
    • Zhao H, Tuominen EKJ, Kinnunen PKJ. Formation of amyloid fibers triggered by phosphatidylserine-containing membranes. Biochemistry 2004; 43: 10302-10307.
    • (2004) Biochemistry , vol.43 , pp. 10302-10307
    • Zhao, H.1    Tuominen, E.K.J.2    Kinnunen, P.K.J.3
  • 25
    • 0036019210 scopus 로고    scopus 로고
    • Abeta-peptide assembly on lipid bilayers
    • Yip CM, Darabie AA, McLaurin JA. Abeta-peptide assembly on lipid bilayers. J Mol Biol 2002; 318: 97-107.
    • (2002) J Mol Biol , vol.318 , pp. 97-107
    • Yip, C.M.1    Darabie, A.A.2    McLaurin, J.A.3
  • 26
    • 61949248657 scopus 로고    scopus 로고
    • Effect of dehydration on the aggregation kinetics of two amyloid peptides
    • Mukherjee S, Chowdhury P, Gai F. Effect of dehydration on the aggregation kinetics of two amyloid peptides. J Phys Chem B 2009; 113: 531-535.
    • (2009) J Phys Chem B , vol.113 , pp. 531-535
    • Mukherjee, S.1    Chowdhury, P.2    Gai, F.3
  • 27
    • 47749146102 scopus 로고    scopus 로고
    • Instantaneous amyloid fibril formation of α-synuclein from the oligomeric granular structures in the presence of hexane
    • Lee J, Bhak G, Lee SG, Paik SR. Instantaneous amyloid fibril formation of α-synuclein from the oligomeric granular structures in the presence of hexane. Biophys J 2008; 95: L16-L18.
    • (2008) Biophys J , vol.95
    • Lee, J.1    Bhak, G.2    Lee, S.G.3    Paik, S.R.4
  • 29
    • 34547481020 scopus 로고    scopus 로고
    • Nanoparticles as catalysts for protein fibrillation
    • Colvin VL, Kulinowski KM. Nanoparticles as catalysts for protein fibrillation. Proc Natl Acad Sci USA 2007; 104: 8679-8680.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 8679-8680
    • Colvin, V.L.1    Kulinowski, K.M.2
  • 30
    • 11844249291 scopus 로고    scopus 로고
    • Rapid assembly of amyloid-beta peptide at a liquid/liquid interface produces unstable beta-sheet fibers
    • Nichols MR, Moss MA, Reed DK, Hoh JH, Rosenberry TL. Rapid assembly of amyloid-beta peptide at a liquid/liquid interface produces unstable beta-sheet fibers. Biochemistry 2005; 44: 165-173.
    • (2005) Biochemistry , vol.44 , pp. 165-173
    • Nichols, M.R.1    Moss, M.A.2    Reed, D.K.3    Hoh, J.H.4    Rosenberry, T.L.5
  • 31
    • 0032796425 scopus 로고    scopus 로고
    • Amyloid-β-sheet formation at the air-water interface
    • Schladitz C, Vieira EP, Hermel H, Möhwald H. Amyloid-β-sheet formation at the air-water interface. Biophys J 1999; 77: 3305-3310.
    • (1999) Biophys J , vol.77 , pp. 3305-3310
    • Schladitz, C.1    Vieira, E.P.2    Hermel, H.3    Möhwald, H.4
  • 34
    • 75149180052 scopus 로고    scopus 로고
    • Competing discrete interfacial effects are critical for amyloidogenesis
    • Jean L, Lee CF, Lee C, Shaw M, Vaux DJ. Competing discrete interfacial effects are critical for amyloidogenesis. FASEB J 2010; 24: 309-317.
    • (2010) FASEB J , vol.24 , pp. 309-317
    • Jean, L.1    Lee, C.F.2    Lee, C.3    Shaw, M.4    Vaux, D.J.5
  • 35
    • 58149216444 scopus 로고    scopus 로고
    • Protein folding and misfolding on surfaces
    • Stefani M. Protein folding and misfolding on surfaces. Int J Mol Sci 2008; 9: 2515-2542.
    • (2008) Int J Mol Sci , vol.9 , pp. 2515-2542
    • Stefani, M.1
  • 36
    • 33749642847 scopus 로고    scopus 로고
    • Computational approaches to fibril structure and formation
    • Hall CK, Wagoner VA. Computational approaches to fibril structure and formation. Meth Enzymol 2006; 412: 338-365.
    • (2006) Meth Enzymol , vol.412 , pp. 338-365
    • Hall, C.K.1    Wagoner, V.A.2
  • 37
    • 33748689799 scopus 로고    scopus 로고
    • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    • Ma J, Nussinov R. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol 2006; 10: 445-452.
    • (2006) Curr Opin Chem Biol , vol.10 , pp. 445-452
    • Ma, J.1    Nussinov, R.2
  • 38
  • 39
    • 19544375553 scopus 로고    scopus 로고
    • Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations
    • López de la Paz M, de Mori M, Serrano L, Colombo G. Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol 2005; 349: 583-596.
    • (2005) J Mol Biol , vol.349 , pp. 583-596
    • López de la Paz, M.1    de Mori, M.2    Serrano, L.3    Colombo, G.4
  • 40
    • 33644536691 scopus 로고    scopus 로고
    • Atomic-level description of amyloid beta-dimer formation
    • Gnanakaran S, Nussinov R, García AE. Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc 2006; 128: 2158-2159.
    • (2006) J Am Chem Soc , vol.128 , pp. 2158-2159
    • Gnanakaran, S.1    Nussinov, R.2    García, A.E.3
  • 42
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen HD, Hall CK. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci USA 2004; 101: 16180-16185.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 43
    • 33745727173 scopus 로고    scopus 로고
    • Interpreting the aggregation kinetics of amyloid peptides
    • Pellarin R, Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol 2006; 360: 882-892.
    • (2006) J Mol Biol , vol.360 , pp. 882-892
    • Pellarin, R.1    Caflisch, A.2
  • 44
    • 35748943830 scopus 로고    scopus 로고
    • Pathways and intermediates of amyloid fibril formation
    • Pellarin R, Guarnera E, Caflisch A. Pathways and intermediates of amyloid fibril formation. J Mol Biol 2007; 374: 917-924.
    • (2007) J Mol Biol , vol.374 , pp. 917-924
    • Pellarin, R.1    Guarnera, E.2    Caflisch, A.3
  • 45
    • 33845652619 scopus 로고    scopus 로고
    • Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations
    • Marchut AJ, Hall CK. Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations. Proteins 2007; 66: 96-109.
    • (2007) Proteins , vol.66 , pp. 96-109
    • Marchut, A.J.1    Hall, C.K.2
  • 46
    • 62549097355 scopus 로고    scopus 로고
    • Characterization of the nucleation barriers for protein aggregation and amyloid formation
    • Auer S, Dobson CM, Vendruscolo M. Characterization of the nucleation barriers for protein aggregation and amyloid formation. HFSP J 2007; 1: 137-146.
    • (2007) HFSP J , vol.1 , pp. 137-146
    • Auer, S.1    Dobson, C.M.2    Vendruscolo, M.3
  • 47
    • 65249190783 scopus 로고    scopus 로고
    • Effect of β-sheet propensity on peptide aggregation
    • Bellesia G, Shea JE. Effect of β-sheet propensity on peptide aggregation. J Chem Phys 2009; 130: 145103.
    • (2009) J Chem Phys , vol.130 , pp. 145103
    • Bellesia, G.1    Shea, J.E.2
  • 48
    • 72949120775 scopus 로고    scopus 로고
    • Diversity of kinetic pathways in amyloid fibril formation
    • Bellesia G, Shea JE. Diversity of kinetic pathways in amyloid fibril formation. J Chem Phys 2009; 131: 111102.
    • (2009) J Chem Phys , vol.131 , pp. 111102
    • Bellesia, G.1    Shea, J.E.2
  • 49
    • 22144448838 scopus 로고    scopus 로고
    • The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent
    • Wu C, Lei H, Duan Y. The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J 2005; 88: 2897-2906.
    • (2005) Biophys J , vol.88 , pp. 2897-2906
    • Wu, C.1    Lei, H.2    Duan, Y.3
  • 50
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
    • Gsponer J, Haberthur U, Caflisch A. The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc Natl Acad Sci USA 2003; 100: 5154.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 5154
    • Gsponer, J.1    Haberthur, U.2    Caflisch, A.3
  • 51
    • 27644540293 scopus 로고    scopus 로고
    • A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide
    • Han W, Wu YD. A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide. J Am Chem Soc 2005; 127: 15408-15416.
    • (2005) J Am Chem Soc , vol.127 , pp. 15408-15416
    • Han, W.1    Wu, Y.D.2
  • 52
    • 61549084018 scopus 로고    scopus 로고
    • Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study
    • Davis CH, Berkowitz ML. Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study. Biophys J 2009; 96: 785-797.
    • (2009) Biophys J , vol.96 , pp. 785-797
    • Davis, C.H.1    Berkowitz, M.L.2
  • 53
    • 70350397192 scopus 로고    scopus 로고
    • Structure of the amyloid-b (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study
    • Davis CH, Berkowitz ML. Structure of the amyloid-b (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study. J Phys Chem B 2009; 113: 14480-14486.
    • (2009) J Phys Chem B , vol.113 , pp. 14480-14486
    • Davis, C.H.1    Berkowitz, M.L.2
  • 55
    • 34548788549 scopus 로고    scopus 로고
    • Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process
    • Jang H, Zheng J, Nussinov R. Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J 2007; 93: 1938.
    • (2007) Biophys J , vol.93 , pp. 1938
    • Jang, H.1    Zheng, J.2    Nussinov, R.3
  • 56
    • 49649122274 scopus 로고    scopus 로고
    • β-hairpin folding by a model amyloid peptide in solution and at an interface
    • Knecht V. β-hairpin folding by a model amyloid peptide in solution and at an interface. J Phys Chem B 2008; 112: 9476-9483.
    • (2008) J Phys Chem B , vol.112 , pp. 9476-9483
    • Knecht, V.1
  • 57
    • 38349077350 scopus 로고    scopus 로고
    • A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer
    • Lemkul JA, Bevan DR. A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer. Arch Biochem Biophys 2008; 470: 54-63.
    • (2008) Arch Biochem Biophys , vol.470 , pp. 54-63
    • Lemkul, J.A.1    Bevan, D.R.2
  • 58
    • 65549152828 scopus 로고    scopus 로고
    • Perturbation of membranes by the amyloid b-peptide-A molecular dynamics study
    • Lemkul JA, Bevan DR. Perturbation of membranes by the amyloid b-peptide-A molecular dynamics study. FEBS J 2009; 276: 3060-3075.
    • (2009) FEBS J , vol.276 , pp. 3060-3075
    • Lemkul, J.A.1    Bevan, D.R.2
  • 59
    • 71749085062 scopus 로고    scopus 로고
    • Structures of beta-amyloid peptide 1-40, 1-42, and the 672-726 fragment of APP in a membrane environment with implications for interactions with gamma-secretase
    • Miyashita N, Straub JE, Thirumalai D. Structures of beta-amyloid peptide 1-40, 1-42, and the 672-726 fragment of APP in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 2009; 131: 17843-17852.
    • (2009) J Am Chem Soc , vol.131 , pp. 17843-17852
    • Miyashita, N.1    Straub, J.E.2    Thirumalai, D.3
  • 63
    • 0035250292 scopus 로고    scopus 로고
    • Nanostructure formation through β-sheet self-assembly in silk-based materials
    • Rathore O, Sogah DY. Nanostructure formation through β-sheet self-assembly in silk-based materials. Macromolecules 2001; 34: 1477-1486.
    • (2001) Macromolecules , vol.34 , pp. 1477-1486
    • Rathore, O.1    Sogah, D.Y.2
  • 64
    • 33646365344 scopus 로고    scopus 로고
    • Metallopolymer-peptide conjugates: synthesis and self-assembly of polyferrocenylsilane graft and block copolymers containing a β-sheet forming Gly-Ala-Gly-Ala tetrapeptide segment
    • Vandermeulen GWM, Kim KT, Wang Z, Manners I. Metallopolymer-peptide conjugates: synthesis and self-assembly of polyferrocenylsilane graft and block copolymers containing a β-sheet forming Gly-Ala-Gly-Ala tetrapeptide segment. Biomacromol 2006; 7: 1005-1010.
    • (2006) Biomacromol , vol.7 , pp. 1005-1010
    • Vandermeulen, G.W.M.1    Kim, K.T.2    Wang, Z.3    Manners, I.4
  • 65
    • 33846250450 scopus 로고    scopus 로고
    • Proline and glycine control protein self-organization into elastomeric or amyloid fibrils
    • Rauscher S, Baud S, Miao M, Keeley FW, Pomès R. Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. Structure 2006; 14: 1667-1676.
    • (2006) Structure , vol.14 , pp. 1667-1676
    • Rauscher, S.1    Baud, S.2    Miao, M.3    Keeley, F.W.4    Pomès, R.5
  • 66
    • 0035132984 scopus 로고    scopus 로고
    • Voltage-dependent insertion of alamethicin at phosholipid/water and octane/water interfaces
    • Tieleman DP, Berendsen HJC, Sansom MSP. Voltage-dependent insertion of alamethicin at phosholipid/water and octane/water interfaces. Biophys J 2001; 80: 331-346.
    • (2001) Biophys J , vol.80 , pp. 331-346
    • Tieleman, D.P.1    Berendsen, H.J.C.2    Sansom, M.S.P.3
  • 67
    • 3142747401 scopus 로고    scopus 로고
    • Direct simulation of transmembrane helix association: role of asparagines
    • Stockner T, Ash WL, MacCallum JL, Tieleman DP. Direct simulation of transmembrane helix association: role of asparagines. Biophys J 2004; 87: 1650-1656.
    • (2004) Biophys J , vol.87 , pp. 1650-1656
    • Stockner, T.1    Ash, W.L.2    MacCallum, J.L.3    Tieleman, D.P.4
  • 68
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force-field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force-field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 70
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001; 7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 71
    • 0029633168 scopus 로고
    • GROMACS: a message-passing parallel molecular dynamics implementation
    • Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp Phys Comm 1995; 91: 43-56.
    • (1995) Comp Phys Comm , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 75
    • 84986440341 scopus 로고
    • Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto S, Kollman PA. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comp Chem 1992; 13: 952-962.
    • (1992) J Comp Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 77
    • 54849417403 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding affinities using distributed replica sampling
    • Rodinger T, Howell PL, Pomès R. Calculation of absolute protein-ligand binding affinities using distributed replica sampling. J Chem Phys 2008; 129: 155102.
    • (2008) J Chem Phys , vol.129 , pp. 155102
    • Rodinger, T.1    Howell, P.L.2    Pomès, R.3
  • 78
    • 73949096788 scopus 로고    scopus 로고
    • Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling
    • Rauscher S, Neale C, Pomès R. Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling. J Chem Theory Comput 2009; 5: 2640-2662.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2640-2662
    • Rauscher, S.1    Neale, C.2    Pomès, R.3
  • 79
    • 84943502952 scopus 로고
    • A molecular-dynamics method for simulations in the canonical ensemble
    • Nosé S. A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys 1984; 52: 255-268.
    • (1984) Mol Phys , vol.52 , pp. 255-268
    • Nosé, S.1
  • 80
    • 0001538909 scopus 로고
    • Canonical dynamics-equilibrium phase-space distributions
    • Hoover WG. Canonical dynamics-equilibrium phase-space distributions. Phys Rev A 1985; 31: 1695-1697.
    • (1985) Phys Rev A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 81
    • 0041706333 scopus 로고    scopus 로고
    • An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface
    • Pandit SA, Bostick D, Berkowitz ML. An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface. J Chem Phys 2003; 119: 2199.
    • (2003) J Chem Phys , vol.119 , pp. 2199
    • Pandit, S.A.1    Bostick, D.2    Berkowitz, M.L.3
  • 82
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 83
    • 0003451443 scopus 로고
    • Computer Simulation of Liquids
    • Clarendon Press; Oxford
    • Allen MP, Tildesley DJ. Computer Simulation of Liquids. Clarendon Press; Oxford 1987.
    • (1987)
    • Allen, M.P.1    Tildesley, D.J.2
  • 84
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
    • Radzicka A, Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988; 27: 1664-1670.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 85
    • 34247626293 scopus 로고    scopus 로고
    • Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment
    • MacCallum JL, Bennett WF, Tieleman DP. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 2007; 129: 371-377.
    • (2007) J Gen Physiol , vol.129 , pp. 371-377
    • MacCallum, J.L.1    Bennett, W.F.2    Tieleman, D.P.3
  • 86
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996; 35: 5109-5124.
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 87
    • 61649121892 scopus 로고    scopus 로고
    • Amyloid aggregation on lipid bilayers and its impact on membrane permeability
    • Friedman R, Pellarin R, Caflisch A. Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J Mol Biol 2009; 378: 407-415.
    • (2009) J Mol Biol , vol.378 , pp. 407-415
    • Friedman, R.1    Pellarin, R.2    Caflisch, A.3
  • 88
    • 70049090008 scopus 로고    scopus 로고
    • A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation
    • Auer S, Trovato A, Vendruscolo M. A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation. PLoS Comput Biol 2009; 5: e1000458.
    • (2009) PLoS Comput Biol , vol.5
    • Auer, S.1    Trovato, A.2    Vendruscolo, M.3
  • 89
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75: 333-336.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-336
    • Chiti, F.1    Dobson, C.M.2
  • 90
    • 34547156274 scopus 로고    scopus 로고
    • Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins
    • Murphy RM. Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins. Biochim Biophys Acta 2007; 1768: 1923-1934.
    • (2007) Biochim Biophys Acta , vol.1768 , pp. 1923-1934
    • Murphy, R.M.1
  • 91
    • 48249092311 scopus 로고    scopus 로고
    • Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly
    • Xue W-F, Homans SW, Radford SE. Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly. Proc Natl Acad Sci USA 2008; 105: 8926-8931.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 8926-8931
    • Xue, W.1    Homans, S.W.2    Radford, S.E.3
  • 92
    • 67651098677 scopus 로고    scopus 로고
    • Aggregation of amyloidogenic peptides near hydrophobic and hydrophillic surfaces
    • Brovchenko I, Singh G, Winter R. Aggregation of amyloidogenic peptides near hydrophobic and hydrophillic surfaces. Langmuir 2009; 25: 8111-8116.
    • (2009) Langmuir , vol.25 , pp. 8111-8116
    • Brovchenko, I.1    Singh, G.2    Winter, R.3
  • 93
    • 0037207098 scopus 로고    scopus 로고
    • Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces
    • Sharp JS, Forrest JA, Jones RAL. Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces. Biochemistry 2002; 41: 15810-15819.
    • (2002) Biochemistry , vol.41 , pp. 15810-15819
    • Sharp, J.S.1    Forrest, J.A.2    Jones, R.A.L.3
  • 94
    • 43649094583 scopus 로고    scopus 로고
    • Distribution of amino acids in a lipid bilayer from computer simulations
    • MacCallum JL, Bennett WF, Tieleman DP. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J 2008; 94: 3393-3404.
    • (2008) Biophys J , vol.94 , pp. 3393-3404
    • MacCallum, J.L.1    Bennett, W.F.2    Tieleman, D.P.3
  • 95
    • 39749132236 scopus 로고    scopus 로고
    • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    • Johansson AC, Lindahl E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 2008; 70: 1332-1344.
    • (2008) Proteins , vol.70 , pp. 1332-1344
    • Johansson, A.C.1    Lindahl, E.2
  • 97
    • 36248932202 scopus 로고    scopus 로고
    • Computer simulation of antimicrobial peptides
    • Matyus E, Kandt C, Tieleman DP. Computer simulation of antimicrobial peptides. Curr Med Chem 2008; 14: 2789-2798.
    • (2008) Curr Med Chem , vol.14 , pp. 2789-2798
    • Matyus, E.1    Kandt, C.2    Tieleman, D.P.3
  • 98
    • 31544474881 scopus 로고    scopus 로고
    • Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces
    • Aliste MP, Tieleman DP. Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC Biochem 2005; 6: 30.
    • (2005) BMC Biochem , vol.6 , pp. 30
    • Aliste, M.P.1    Tieleman, D.P.2
  • 99
    • 0034598954 scopus 로고    scopus 로고
    • Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis
    • Broome BM, Hecht MH. Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol 2000; 296: 961-968.
    • (2000) J Mol Biol , vol.296 , pp. 961-968
    • Broome, B.M.1    Hecht, M.H.2
  • 100
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: physical principles
    • White SH, Wimley WC. Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 1999; 28: 319-365.
    • (1999) Annu Rev Biophys Biomol Struct , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 102
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Prot Chem 1959; 14: 1-63.
    • (1959) Adv Prot Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 103
    • 0019052221 scopus 로고
    • Hydrophobic basis of packing in soluble proteins
    • Rose GD, Roy S. Hydrophobic basis of packing in soluble proteins. Proc Natl Acad Sci USA 1980; 77: 4643-4647.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 4643-4647
    • Rose, G.D.1    Roy, S.2
  • 105
    • 0036404919 scopus 로고    scopus 로고
    • On the significance of alternating patterns of polar and non-polar residues in β-strands
    • Mandel-Gutfreund Y, Gregoret LM. On the significance of alternating patterns of polar and non-polar residues in β-strands. J Mol Biol 2002; 323: 453-461.
    • (2002) J Mol Biol , vol.323 , pp. 453-461
    • Mandel-Gutfreund, Y.1    Gregoret, L.M.2
  • 106
    • 67149096041 scopus 로고    scopus 로고
    • Folding by numbers: primary sequence statistics and their use in studying protein folding
    • Wathen B, Jia Z. Folding by numbers: primary sequence statistics and their use in studying protein folding. Int J Mol Sci 2009; 10: 1567-1589.
    • (2009) Int J Mol Sci , vol.10 , pp. 1567-1589
    • Wathen, B.1    Jia, Z.2
  • 107
    • 34547631623 scopus 로고    scopus 로고
    • Prevention of amyloid-like aggregation as a driving force of protein evolution
    • Monsellier E, Chiti F. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep 2007; 8: 737-742.
    • (2007) EMBO Rep , vol.8 , pp. 737-742
    • Monsellier, E.1    Chiti, F.2
  • 108
    • 7044247850 scopus 로고    scopus 로고
    • Folding and assembly of β-barrel membrane proteins
    • Tamm LK, Hong H, Liang B. Folding and assembly of β-barrel membrane proteins. Biochim Biophys Acta 2004; 1666: 250-263.
    • (2004) Biochim Biophys Acta , vol.1666 , pp. 250-263
    • Tamm, L.K.1    Hong, H.2    Liang, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.