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Volumn 10, Issue 5, 2014, Pages

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

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EID: 84901650117     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003606     Document Type: Article
Times cited : (31)

References (95)
  • 1
    • 0037162520 scopus 로고    scopus 로고
    • Crystal structure of monomeric human β-2-microglobulin reveals clues to its amyloidogenic properties
    • Trinh CH, Smith DP, Kalverda AP, Phillips SEV, Radford SE, (2002) Crystal structure of monomeric human β-2-microglobulin reveals clues to its amyloidogenic properties. Proc Natl Acad Sci USA 99: 9771-9776 Available: http://www.pnas.org/content/99/15/9771.abstract.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 9771-9776
    • Trinh, C.H.1    Smith, D.P.2    Kalverda, A.P.3    Phillips, S.E.V.4    Radford, S.E.5
  • 2
    • 68649108349 scopus 로고    scopus 로고
    • Glimpses of the molecular mechanisms of β2-microglobulin fibril formation in vitro: Aggregation on a complex energy landscape
    • Platt GW, Radford SE, (2009) Glimpses of the molecular mechanisms of β2-microglobulin fibril formation in vitro: Aggregation on a complex energy landscape. FEBS Lett 583: 2623-2629 Available: http://www.sciencedirect.com/science/article/pii/S0014579309003718.
    • (2009) FEBS Lett , vol.583 , pp. 2623-2629
    • Platt, G.W.1    Radford, S.E.2
  • 3
    • 20044376283 scopus 로고    scopus 로고
    • β2-microglobulin isoforms display an heterogeneous affinity for type I collagen
    • Giorgetti S, Rossi A, Mangione P, Raimondi S, Marini S, et al. (2005) β2-microglobulin isoforms display an heterogeneous affinity for type I collagen. Protein Sci 14: 696-702 Available: http://dx.doi.org/10.1110/ps.041194005.
    • (2005) Protein Sci , vol.14 , pp. 696-702
    • Giorgetti, S.1    Rossi, A.2    Mangione, P.3    Raimondi, S.4    Marini, S.5
  • 4
    • 70849124339 scopus 로고    scopus 로고
    • β2-microglobulin: from physiology to amyloidosis
    • Heegaard NHH, (2009) β2-microglobulin: from physiology to amyloidosis. Amyloid 16: 151-173 Available: http://dx.doi.org/10.1080/13506120903151775.
    • (2009) Amyloid , vol.16 , pp. 151-173
    • Heegaard, N.H.H.1
  • 5
    • 0000079910 scopus 로고    scopus 로고
    • Establishment of a kinetic model of dialysis-related amyloid fibril extension in vitro
    • Naiki H, Hashimoto N, Suzuki S, Kimura H, Nakakuki K, et al. (1997) Establishment of a kinetic model of dialysis-related amyloid fibril extension in vitro. Amyloid 4: 223-232 Available: http://dx.doi.org/10.3109/13506129709003833.
    • (1997) Amyloid , vol.4 , pp. 223-232
    • Naiki, H.1    Hashimoto, N.2    Suzuki, S.3    Kimura, H.4    Nakakuki, K.5
  • 6
    • 33644813233 scopus 로고    scopus 로고
    • A native to amyloidogenic transition regulated by a backbone trigger
    • Eakin CM, Berman AJ, Miranker AD, (2006) A native to amyloidogenic transition regulated by a backbone trigger. Nat Struct Mol Biol 13: 202-208 Available: http://dx.doi.org/10.1038/nsmb1068.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 202-208
    • Eakin, C.M.1    Berman, A.J.2    Miranker, A.D.3
  • 7
    • 51349128031 scopus 로고    scopus 로고
    • A regulatable switch mediates self-association in an immunoglobulin fold
    • Calabrese MF, Eakin CM, Wang JM, Miranker AD, (2008) A regulatable switch mediates self-association in an immunoglobulin fold. Nat Struct Mol Biol 15: 965-971 Available: http://dx.doi.org/10.1038/nsmb.1483.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 965-971
    • Calabrese, M.F.1    Eakin, C.M.2    Wang, J.M.3    Miranker, A.D.4
  • 8
    • 77955086949 scopus 로고    scopus 로고
    • Folding and fibrillogenesis: Clues from β2-microglobulin
    • Rennella E, Corazza A, Giorgetti S, Fogolari F, Viglino P, et al. (2010) Folding and fibrillogenesis: Clues from β2-microglobulin. J Mol Biol 401: 286-297 Available: http://www.sciencedirect.com/science/article/pii/S0022283610006327.
    • (2010) J Mol Biol , vol.401 , pp. 286-297
    • Rennella, E.1    Corazza, A.2    Giorgetti, S.3    Fogolari, F.4    Viglino, P.5
  • 9
    • 0035861649 scopus 로고    scopus 로고
    • A partially structured species of β2-microglobulin is significantly populated under physiological conditions and involved in fibrillogenesis
    • Chiti F, De Lorenzi E, Grossi S, Mangione P, Giorgetti S, et al. (2001) A partially structured species of β2-microglobulin is significantly populated under physiological conditions and involved in fibrillogenesis. J Biol Chem 276: 46714-46721 Available: http://www.jbc.org/content/276/50/46714.abstract.
    • (2001) J Biol Chem , vol.276 , pp. 46714-46721
    • Chiti, F.1    De Lorenzi, E.2    Grossi, S.3    Mangione, P.4    Giorgetti, S.5
  • 10
    • 33144467755 scopus 로고    scopus 로고
    • Amyloid formation under physiological conditions proceeds via a native-like folding intermediate
    • Jahn TR, Parker MJ, Homans SW, Radford SE, (2006) Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat Struct Mol Biol 13: 195-201 Available: http://dx.doi.org/10.1038/nsmb1058.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 195-201
    • Jahn, T.R.1    Parker, M.J.2    Homans, S.W.3    Radford, S.E.4
  • 11
    • 78651468727 scopus 로고    scopus 로고
    • Conformational conversion during amyloid formation at atomic resolution
    • Eichner T, Kalverda AP, Thompson GS, Homans SW, Radford SE, (2011) Conformational conversion during amyloid formation at atomic resolution. Mol Cell 41: 161-172 Available: http://dx.doi.org/10.1016/j.molcel.2010.11.028.
    • (2011) Mol Cell , vol.41 , pp. 161-172
    • Eichner, T.1    Kalverda, A.P.2    Thompson, G.S.3    Homans, S.W.4    Radford, S.E.5
  • 12
    • 60949106895 scopus 로고    scopus 로고
    • A generic mechanism of β2-microglobulin amyloid assembly at neutral pH involving a specific proline switch
    • Eichner T, Radford SE, (2009) A generic mechanism of β2-microglobulin amyloid assembly at neutral pH involving a specific proline switch. J Mol Biol 386: 1312-1326 Available: http://www.sciencedirect.com/science/article/pii/S0022283609000485.
    • (2009) J Mol Biol , vol.386 , pp. 1312-1326
    • Eichner, T.1    Radford, S.E.2
  • 13
    • 33646685225 scopus 로고    scopus 로고
    • Variants of β2-microglobulin cleaved at lysine-58 retain the main conformational features of the native protein but are more conformationally heterogeneous and unstable at physiological temperature
    • Mimmi MC, Jørgensen TJD, Pettirossi F, Corazza A, Viglino P, et al. (2006) Variants of β2-microglobulin cleaved at lysine-58 retain the main conformational features of the native protein but are more conformationally heterogeneous and unstable at physiological temperature. FEBS J 273: 2461-2474 Available: http://dx.doi.org/10.1111/j.1742-4658.2006.05254.x.
    • (2006) FEBS J , vol.273 , pp. 2461-2474
    • Mimmi, M.C.1    Jørgensen, T.J.D.2    Pettirossi, F.3    Corazza, A.4    Viglino, P.5
  • 14
    • 51549116627 scopus 로고    scopus 로고
    • Kinetic Coupling of Folding and Prolyl Isomerization of β2-Microglobulin Studied by Mutational Analysis
    • Sakata M, Chatani E, Kameda A, Sakurai K, Naiki H, et al. (2008) Kinetic Coupling of Folding and Prolyl Isomerization of β2-Microglobulin Studied by Mutational Analysis. J Mol Biol 382: 1242-1255 Available: http://www.sciencedirect.com/science/article/pii/S0022283608009741.
    • (2008) J Mol Biol , vol.382 , pp. 1242-1255
    • Sakata, M.1    Chatani, E.2    Kameda, A.3    Sakurai, K.4    Naiki, H.5
  • 15
    • 84872118866 scopus 로고    scopus 로고
    • Native-state heterogeneity of β2-microglobulin as revealed by kinetic folding and real-time NMR experiments
    • Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, et al. (2013) Native-state heterogeneity of β2-microglobulin as revealed by kinetic folding and real-time NMR experiments. J Mol Biol 425: 257-272 Available: http://www.sciencedirect.com/science/article/pii/S0022283612008765.
    • (2013) J Mol Biol , vol.425 , pp. 257-272
    • Mukaiyama, A.1    Nakamura, T.2    Makabe, K.3    Maki, K.4    Goto, Y.5
  • 16
    • 84879973682 scopus 로고    scopus 로고
    • Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure
    • Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, et al. (2013) Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. J Mol Biol 425: 2722-2736 Available: http://www.sciencedirect.com/science/article/pii/S0022283613002763.
    • (2013) J Mol Biol , vol.425 , pp. 2722-2736
    • Rennella, E.1    Cutuil, T.2    Schanda, P.3    Ayala, I.4    Gabel, F.5
  • 17
    • 77949320904 scopus 로고    scopus 로고
    • Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-microglobulin revealed by real-time two-dimensional NMR
    • Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, et al. (2010) Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-microglobulin revealed by real-time two-dimensional NMR. J Biol Chem 285: 5827-5835 Available: http://www.jbc.org/content/285/8/5827.abstract.
    • (2010) J Biol Chem , vol.285 , pp. 5827-5835
    • Corazza, A.1    Rennella, E.2    Schanda, P.3    Mimmi, M.C.4    Cutuil, T.5
  • 18
    • 79960550339 scopus 로고    scopus 로고
    • Characterization of β2-microglobulin conformational intermediates associated to different fibrillation conditions
    • Santambrogio C, Ricagno S, Sobott F, Colombo M, Bolognesi M, et al. (2011) Characterization of β2-microglobulin conformational intermediates associated to different fibrillation conditions. J Mass Spectrom 46: 734-741 Available: http://dx.doi.org/10.1002/jms.1946.
    • (2011) J Mass Spectrom , vol.46 , pp. 734-741
    • Santambrogio, C.1    Ricagno, S.2    Sobott, F.3    Colombo, M.4    Bolognesi, M.5
  • 19
    • 84872120842 scopus 로고    scopus 로고
    • The molten globule of β2-microglobulin accumulated at pH 4 and its role in protein folding
    • Mukaiyama A, Nakamura T, Makabe K, Maki K, Goto Y, et al. (2013) The molten globule of β2-microglobulin accumulated at pH 4 and its role in protein folding. J Mol Biol 425: 273-291 Available: http://www.sciencedirect.com/science/article/pii/S0022283612008741.
    • (2013) J Mol Biol , vol.425 , pp. 273-291
    • Mukaiyama, A.1    Nakamura, T.2    Makabe, K.3    Maki, K.4    Goto, Y.5
  • 20
    • 84865957943 scopus 로고    scopus 로고
    • Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation
    • Yoshimura Y, Lin Y, Yagi H, Lee Y-H, Kitayama H, et al. (2012) Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proc Natl Acad Sci USA 109: 14446-14451 Available: http://www.pnas.org/content/109/36/14446.abstract.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 14446-14451
    • Yoshimura, Y.1    Lin, Y.2    Yagi, H.3    Lee, Y.-H.4    Kitayama, H.5
  • 21
    • 84862198496 scopus 로고    scopus 로고
    • Hereditary Systemic Amyloidosis Due to Asp76Asn Variant β2-Microglobulin
    • Valleix S, Gillmore JD, Bridoux F, Mangione PP, Dogan A, et al. (2012) Hereditary Systemic Amyloidosis Due to Asp76Asn Variant β2-Microglobulin. N Engl J Med 366: 2276-2283 Available: http://dx.doi.org/10.1056/NEJMoa1201356.
    • (2012) N Engl J Med , vol.366 , pp. 2276-2283
    • Valleix, S.1    Gillmore, J.D.2    Bridoux, F.3    Mangione, P.P.4    Dogan, A.5
  • 22
    • 84886655678 scopus 로고    scopus 로고
    • Structure, folding dynamics and amyloidogenesis of Asp76Asn β2-microglobulin: roles of shear flow, hydrophobic surfaces and α crystallin
    • Mangione PP, Esposito G, Relini A, Raimondi S, Porcari R, et al. (2013) Structure, folding dynamics and amyloidogenesis of Asp76Asn β2-microglobulin: roles of shear flow, hydrophobic surfaces and α crystallin. J Biol Chem 288: 30917-30 Available: http://www.jbc.org/content/early/2013/09/06/jbc.M113.498857.abstract.
    • (2013) J Biol Chem , vol.288 , pp. 30917-30930
    • Mangione, P.P.1    Esposito, G.2    Relini, A.3    Raimondi, S.4    Porcari, R.5
  • 23
    • 84879039524 scopus 로고    scopus 로고
    • Monitoring the Interaction between β2-Microglobulin and the Molecular Chaperone αB-crystallin by NMR and Mass Spectrometry: αB-CRYSTALLIN DISSOCIATES β2-MICROGLOBULIN OLIGOMERS
    • Esposito G, Garvey M, Alverdi V, Pettirossi F, Corazza A, et al. (2013) Monitoring the Interaction between β2-Microglobulin and the Molecular Chaperone αB-crystallin by NMR and Mass Spectrometry: αB-CRYSTALLIN DISSOCIATES β2-MICROGLOBULIN OLIGOMERS. J Biol Chem 288: 17844-17858 Available: http://www.jbc.org/content/288/24/17844.abstract.
    • (2013) J Biol Chem , vol.288 , pp. 17844-17858
    • Esposito, G.1    Garvey, M.2    Alverdi, V.3    Pettirossi, F.4    Corazza, A.5
  • 24
    • 0035293977 scopus 로고    scopus 로고
    • Dynamic of β2-microglobulin fibril formation and reabsorption: The role of proteolysis
    • Bellotti V, Gallieni M, Giorgetti S, Brancaccio D, (2001) Dynamic of β2-microglobulin fibril formation and reabsorption: The role of proteolysis. Semin Dial 14: 117-122 Available: http://dx.doi.org/10.1046/j.1525-139x.2001.00030.x.
    • (2001) Semin Dial , vol.14 , pp. 117-122
    • Bellotti, V.1    Gallieni, M.2    Giorgetti, S.3    Brancaccio, D.4
  • 25
    • 18244412979 scopus 로고    scopus 로고
    • Removal of the N-terminal hexapeptide from human β2-microglobulin facilitates protein aggregation and fibril formation
    • Esposito G, Michelutti R, Verdone G, Viglino P, Hernández HH, et al. (2000) Removal of the N-terminal hexapeptide from human β2-microglobulin facilitates protein aggregation and fibril formation. Protein Sci 9: 831-845 Available: http://dx.doi.org/10.1110/ps.9.5.831.
    • (2000) Protein Sci , vol.9 , pp. 831-845
    • Esposito, G.1    Michelutti, R.2    Verdone, G.3    Viglino, P.4    Hernández, H.H.5
  • 26
    • 33745224979 scopus 로고    scopus 로고
    • Collagen plays an active role in the aggregation of β2-microglobulin under physiopathological conditions of dialysis-related amyloidosis
    • Relini A, Canale C, De Stefano S, Rolandi R, Giorgetti S, et al. (2006) Collagen plays an active role in the aggregation of β2-microglobulin under physiopathological conditions of dialysis-related amyloidosis. J Biol Chem 281: 16521-16529 Available: http://www.jbc.org/content/281/24/16521.abstract.
    • (2006) J Biol Chem , vol.281 , pp. 16521-16529
    • Relini, A.1    Canale, C.2    De Stefano, S.3    Rolandi, R.4    Giorgetti, S.5
  • 27
    • 79953081933 scopus 로고    scopus 로고
    • Coarse-grained models for protein aggregation
    • Wu C, Shea J-E, (2011) Coarse-grained models for protein aggregation. Curr Opin Struct Biol 21: 209-220 Available: http://www.sciencedirect.com/science/article/pii/S0959440X11000339.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 209-220
    • Wu, C.1    Shea, J.-E.2
  • 28
    • 0036923039 scopus 로고    scopus 로고
    • Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic Amyloidogenesis Mechanism
    • Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI, (2002) Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic Amyloidogenesis Mechanism. J Mol Biol 324: 851-857 Available: http://www.sciencedirect.com/science/article/pii/S0022283602011129.
    • (2002) J Mol Biol , vol.324 , pp. 851-857
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 29
    • 2942748436 scopus 로고    scopus 로고
    • Oligomeric assembly of native-like precursors precedes amyloid formation by β-2 microglobulin
    • Eakin CM, Attenello FJ, Morgan CJ, Miranker AD, (2004) Oligomeric assembly of native-like precursors precedes amyloid formation by β-2 microglobulin. Biochemistry 43: 7808-7815 Available: http://dx.doi.org/10.1021/bi049792q.
    • (2004) Biochemistry , vol.43 , pp. 7808-7815
    • Eakin, C.M.1    Attenello, F.J.2    Morgan, C.J.3    Miranker, A.D.4
  • 30
    • 33750294048 scopus 로고    scopus 로고
    • Direct observation of oligomeric species formed in the early stages of amyloid fibril formation using electrospray ionisation mass spectrometry
    • Smith AM, Jahn TR, Ashcroft AE, Radford SE, (2006) Direct observation of oligomeric species formed in the early stages of amyloid fibril formation using electrospray ionisation mass spectrometry. J Mol Biol 364: 9-19 Available: http://www.sciencedirect.com/science/article/pii/S0022283606011399.
    • (2006) J Mol Biol , vol.364 , pp. 9-19
    • Smith, A.M.1    Jahn, T.R.2    Ashcroft, A.E.3    Radford, S.E.4
  • 31
    • 79952152956 scopus 로고    scopus 로고
    • Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic β2-microglobulin variant
    • Domanska K, Vanderhaegen S, Srinivasan V, Pardon E, Dupeux F, et al. (2011) Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic β2-microglobulin variant. Proc Natl Acad Sci USA 108: 1314-1319 Available: http://www.pnas.org/content/108/4/1314.abstract.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 1314-1319
    • Domanska, K.1    Vanderhaegen, S.2    Srinivasan, V.3    Pardon, E.4    Dupeux, F.5
  • 32
    • 78650982368 scopus 로고    scopus 로고
    • β2-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages
    • Liu C, Sawaya MR, Eisenberg D, (2011) β2-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages. Nat Struct Mol Biol 18: 49-55 Available: http://dx.doi.org/10.1038/nsmb.1948.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 49-55
    • Liu, C.1    Sawaya, M.R.2    Eisenberg, D.3
  • 33
    • 84865691204 scopus 로고    scopus 로고
    • Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants
    • Krobath H, Estácio SG, Faísca PFN, Shakhnovich EI, (2012) Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. J Mol Biol 422: 705-722 Available: http://www.sciencedirect.com/science/article/pii/S0022283612004937.
    • (2012) J Mol Biol , vol.422 , pp. 705-722
    • Krobath, H.1    Estácio, S.G.2    Faísca, P.F.N.3    Shakhnovich, E.I.4
  • 34
    • 84883486569 scopus 로고    scopus 로고
    • Assessing the Effect of Loop Mutations in the Folding Space of β2-Microglobulin with Molecular Dynamics Simulations
    • Estácio SG, Shakhnovich EI, Faísca PFN, (2013) Assessing the Effect of Loop Mutations in the Folding Space of β2-Microglobulin with Molecular Dynamics Simulations. Int J Mol Sci 14: 17256-17278 Available: http://dx.doi.org/10.3390/ijms140917256.
    • (2013) Int J Mol Sci , vol.14 , pp. 17256-17278
    • Estácio, S.G.1    Shakhnovich, E.I.2    Faísca, P.F.N.3
  • 35
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
    • Taketomi H, Ueda Y, Gō N, (1975) Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 7: 445-459.
    • (1975) Int J Pept Protein Res , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 36
    • 84887117718 scopus 로고    scopus 로고
    • Native contacts determine protein folding mechanisms in atomistic simulations
    • Best RB, Hummer G, Eaton WA, (2013) Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci USA 110: 17874-17879 Available: http://www.pnas.org/content/110/44/17874.abstract.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 17874-17879
    • Best, R.B.1    Hummer, G.2    Eaton, W.A.3
  • 37
    • 77957317648 scopus 로고    scopus 로고
    • Constant-pH molecular dynamics simulations reveal a β-rich form of the human prion protein
    • Campos SRR, Machuqueiro M, Baptista AM, (2010) Constant-pH molecular dynamics simulations reveal a β-rich form of the human prion protein. J Phys Chem B 114: 12692-12700 Available: http://dx.doi.org/10.1021/jp104753t.
    • (2010) J Phys Chem B , vol.114 , pp. 12692-12700
    • Campos, S.R.R.1    Machuqueiro, M.2    Baptista, A.M.3
  • 38
    • 84864755277 scopus 로고    scopus 로고
    • Reversibility of prion misfolding: Insights from constant-pH molecular dynamics simulations
    • Vila-Viçosa D, Campos SRR, Baptista AM, Machuqueiro M, (2012) Reversibility of prion misfolding: Insights from constant-pH molecular dynamics simulations. J Phys Chem B 116: 8812-8821 Available: http://dx.doi.org/10.1021/jp3034837.
    • (2012) J Phys Chem B , vol.116 , pp. 8812-8821
    • Vila-Viçosa, D.1    Campos, S.R.R.2    Baptista, A.M.3    Machuqueiro, M.4
  • 39
    • 0041315527 scopus 로고    scopus 로고
    • Influence of pH on NMR structure and stability of the human prion protein globular domain
    • Calzolai L, Zahn R, (2003) Influence of pH on NMR structure and stability of the human prion protein globular domain. J Biol Chem 278: 35592-35596 Available: http://www.jbc.org/content/278/37/35592.abstract.
    • (2003) J Biol Chem , vol.278 , pp. 35592-35596
    • Calzolai, L.1    Zahn, R.2
  • 40
    • 0036732086 scopus 로고    scopus 로고
    • Constant-pH molecular dynamics using stochastic titration
    • Baptista AM, Teixeira VH, Soares CM, (2002) Constant-pH molecular dynamics using stochastic titration. J Chem Phys 117: 4184-4200 Available: http://dx.doi.org/10.1063/1.1497164.
    • (2002) J Chem Phys , vol.117 , pp. 4184-4200
    • Baptista, A.M.1    Teixeira, V.H.2    Soares, C.M.3
  • 41
    • 33644745556 scopus 로고    scopus 로고
    • Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine
    • Machuqueiro M, Baptista AM, (2006) Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine. J Phys Chem B 110: 2927-2933 Available: http://dx.doi.org/10.1021/jp056456q.
    • (2006) J Phys Chem B , vol.110 , pp. 2927-2933
    • Machuqueiro, M.1    Baptista, A.M.2
  • 42
    • 44949173075 scopus 로고    scopus 로고
    • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    • Machuqueiro M, Baptista AM, (2008) Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins: Struct Funct Bioinf 72: 289-298 Available: http://dx.doi.org/10.1002/prot.21923.
    • (2008) Proteins: Struct Funct Bioinf , vol.72 , pp. 289-298
    • Machuqueiro, M.1    Baptista, A.M.2
  • 43
    • 69849094447 scopus 로고    scopus 로고
    • Molecular dynamics at constant pH and reduction potential: Application to cytochrome c3
    • Machuqueiro M, Baptista AM, (2009) Molecular dynamics at constant pH and reduction potential: Application to cytochrome c3. J Am Chem Soc 131: 12586-12594 Available: http://dx.doi.org/10.1021/ja808463e.
    • (2009) J Am Chem Soc , vol.131 , pp. 12586-12594
    • Machuqueiro, M.1    Baptista, A.M.2
  • 44
    • 33748107163 scopus 로고    scopus 로고
    • Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity
    • Tsuchiya Y, Kinoshita K, Nakamura H, (2006) Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng Des Sel 19: 421-429 Available: http://peds.oxfordjournals.org/content/19/9/421.abstract.
    • (2006) Protein Eng Des Sel , vol.19 , pp. 421-429
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 45
    • 84888262555 scopus 로고    scopus 로고
    • The Role of Shape Complementarity in the Protein-Protein Interactions
    • Li Y, Zhang X, Cao D, (2013) The Role of Shape Complementarity in the Protein-Protein Interactions. Sci Rep 3: 3271 Available: http://dx.doi.org/10.1038/srep03271.
    • (2013) Sci Rep , vol.3 , pp. 3271
    • Li, Y.1    Zhang, X.2    Cao, D.3
  • 46
    • 33947398571 scopus 로고    scopus 로고
    • Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
    • Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA, (2006) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput 3: 26-41 Available: http://dx.doi.org/10.1021/ct0502864.
    • (2006) J Chem Theory Comput , vol.3 , pp. 26-41
    • Chodera, J.D.1    Swope, W.C.2    Pitera, J.W.3    Seok, C.4    Dill, K.A.5
  • 47
    • 77954219081 scopus 로고    scopus 로고
    • Relative Importance of Hydrophobicity, Net Charge, and Secondary Structure Propensities in Protein Aggregation
    • Springer US
    • Chiti F (2006) Relative Importance of Hydrophobicity, Net Charge, and Secondary Structure Propensities in Protein Aggregation. Protein Misfolding, Aggregation, and Conformational Diseases- Protein Reviews. Springer US, Vol. 4. pp. 43-59.
    • (2006) Protein Misfolding, Aggregation, and Conformational Diseases - Protein Reviews , vol.4 , pp. 43-59
    • Chiti, F.1
  • 48
    • 18244378561 scopus 로고    scopus 로고
    • The solution structure of human β2-microglobulin reveals the prodromes of its amyloid transition
    • Verdone G, Corazza A, Viglino P, Pettirossi F, Giorgetti S, et al. (2002) The solution structure of human β2-microglobulin reveals the prodromes of its amyloid transition. Protein Sci 11: 487-499 Available: http://dx.doi.org/10.1110/ps.29002.
    • (2002) Protein Sci , vol.11 , pp. 487-499
    • Verdone, G.1    Corazza, A.2    Viglino, P.3    Pettirossi, F.4    Giorgetti, S.5
  • 49
    • 0034254241 scopus 로고    scopus 로고
    • Partially unfolded states of β2-microglobulin and amyloid formation in vitro
    • McParland V, Kad N, Kalverda A, Brown A, Kirwin-Jones P, et al. (2000) Partially unfolded states of β2-microglobulin and amyloid formation in vitro. Biochemistry 39: 8735-8746 Available: http://dx.doi.org/10.1021/bi000276j.
    • (2000) Biochemistry , vol.39 , pp. 8735-8746
    • McParland, V.1    Kad, N.2    Kalverda, A.3    Brown, A.4    Kirwin-Jones, P.5
  • 50
    • 0036240398 scopus 로고    scopus 로고
    • Structural properties of an amyloid precursor of [beta]2-microglobulin
    • McParland VJ, Kalverda AP, Homans SW, Radford SE, (2002) Structural properties of an amyloid precursor of [beta]2-microglobulin. Nat Struct Biol 9: 326-331 Available: http://dx.doi.org/10.1038/nsb791.
    • (2002) Nat Struct Biol , vol.9 , pp. 326-331
    • McParland, V.J.1    Kalverda, A.P.2    Homans, S.W.3    Radford, S.E.4
  • 51
    • 10744219788 scopus 로고    scopus 로고
    • Properties of Some Variants of Human β2-Microglobulin and Amyloidogenesis
    • Corazza A, Pettirossi F, Viglino P, Verdone G, Garcia J, et al. (2004) Properties of Some Variants of Human β2-Microglobulin and Amyloidogenesis. J Biol Chem 279: 9176-9189 Available: http://www.jbc.org/content/279/10/9176.abstract.
    • (2004) J Biol Chem , vol.279 , pp. 9176-9189
    • Corazza, A.1    Pettirossi, F.2    Viglino, P.3    Verdone, G.4    Garcia, J.5
  • 52
    • 0035367287 scopus 로고    scopus 로고
    • Kidney dialysis-associated amyloidosis: a molecular role for copper in fiber formation
    • Morgan CJ, Gelfand M, Atreya C, Miranker AD, (2001) Kidney dialysis-associated amyloidosis: a molecular role for copper in fiber formation. J Mol Biol 309: 339-345 Available: http://www.sciencedirect.com/science/article/pii/S0022283601946613.
    • (2001) J Mol Biol , vol.309 , pp. 339-345
    • Morgan, C.J.1    Gelfand, M.2    Atreya, C.3    Miranker, A.D.4
  • 53
    • 33751198084 scopus 로고    scopus 로고
    • Solvation thermodynamics of amino acids: Assessment of the electrostatic contribution and force-field dependence
    • Dixit SB, Bhasin R, Rajasekaran E, Jayaram B, (1997) Solvation thermodynamics of amino acids: Assessment of the electrostatic contribution and force-field dependence. J Chem Soc, Faraday Trans 93: 1105-1113 Available: http://dx.doi.org/10.1039/A603913H.
    • (1997) J Chem Soc, Faraday Trans , vol.93 , pp. 1105-1113
    • Dixit, S.B.1    Bhasin, R.2    Rajasekaran, E.3    Jayaram, B.4
  • 54
    • 84859476261 scopus 로고    scopus 로고
    • Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations
    • Bershtein S, Wu W, Shakhnovich EI, (2012) Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proc Natl Acad Sci USA 109: 4857-62 Available: http://www.pnas.org/content/early/2012/03/05/1118157109.abstract.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 4857-4862
    • Bershtein, S.1    Wu, W.2    Shakhnovich, E.I.3
  • 55
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • Xiang Z, Honig B, (2001) Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 311: 421-430 Available: http://www.sciencedirect.com/science/article/pii/S002228360194865X.
    • (2001) J Mol Biol , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 56
    • 77953994609 scopus 로고    scopus 로고
    • DE-loop mutations affect beta2 microglobulin stability, oligomerization, and the low-pH unfolded form
    • Santambrogio C, Ricagno S, Colombo M, Barbiroli A, Bonomi F, et al. (2010) DE-loop mutations affect beta2 microglobulin stability, oligomerization, and the low-pH unfolded form. Protein Sci 19: 1386-1394 Available: http://dx.doi.org/10.1002/pro.419.
    • (2010) Protein Sci , vol.19 , pp. 1386-1394
    • Santambrogio, C.1    Ricagno, S.2    Colombo, M.3    Barbiroli, A.4    Bonomi, F.5
  • 57
    • 84858446912 scopus 로고    scopus 로고
    • A recurrent D-strand association interface is observed in β-2 microglobulin oligomers
    • Colombo M, de Rosa M, Bellotti V, Ricagno S, Bolognesi M, (2012) A recurrent D-strand association interface is observed in β-2 microglobulin oligomers. FEBS J 279: 1131-1143 Available: http://dx.doi.org/10.1111/j.1742-4658.2012.08510.x.
    • (2012) FEBS J , vol.279 , pp. 1131-1143
    • Colombo, M.1    de Rosa, M.2    Bellotti, V.3    Ricagno, S.4    Bolognesi, M.5
  • 58
    • 65849165676 scopus 로고    scopus 로고
    • Competition between intramolecular and intermolecular interactions in an amyloid-forming protein
    • Routledge KE, Tartaglia GG, Platt GW, Vendruscolo M, Radford SE, (2009) Competition between intramolecular and intermolecular interactions in an amyloid-forming protein. J Mol Biol 389: 776-786 Available: http://www.sciencedirect.com/science/article/pii/S0022283609004872.
    • (2009) J Mol Biol , vol.389 , pp. 776-786
    • Routledge, K.E.1    Tartaglia, G.G.2    Platt, G.W.3    Vendruscolo, M.4    Radford, S.E.5
  • 59
    • 33847785526 scopus 로고    scopus 로고
    • Molecular dynamics simulation suggests possible interaction patterns at early steps of β2-microglobulin aggregation
    • Fogolari F, Corazza A, Viglino P, Zuccato P, Pieri L, et al. (2007) Molecular dynamics simulation suggests possible interaction patterns at early steps of β2-microglobulin aggregation. Biophys J 92: 1673-1681 Available: http://www.sciencedirect.com/science/article/pii/S000634950770975X.
    • (2007) Biophys J , vol.92 , pp. 1673-1681
    • Fogolari, F.1    Corazza, A.2    Viglino, P.3    Zuccato, P.4    Pieri, L.5
  • 60
    • 3242735504 scopus 로고    scopus 로고
    • An amyloid-forming segment of β2-microglobulin suggests a molecular model for the fibril
    • Ivanova MI, Sawaya MR, Gingery M, Attinger A, Eisenberg D, (2004) An amyloid-forming segment of β2-microglobulin suggests a molecular model for the fibril. Proc Natl Acad Sci USA 101: 10584-10589 Available: http://www.pnas.org/content/101/29/10584.abstract.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 10584-10589
    • Ivanova, M.I.1    Sawaya, M.R.2    Gingery, M.3    Attinger, A.4    Eisenberg, D.5
  • 61
    • 84864913316 scopus 로고    scopus 로고
    • Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: On-the-fly string method calculations
    • Stober ST, Abrams CF, (2012) Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: On-the-fly string method calculations. J Phys Chem B 116: 9371-9375 Available: http://dx.doi.org/10.1021/jp304805v.
    • (2012) J Phys Chem B , vol.116 , pp. 9371-9375
    • Stober, S.T.1    Abrams, C.F.2
  • 62
    • 73249133310 scopus 로고    scopus 로고
    • Self-aggregation of a polyalanine octamer promoted by its C-terminal tyrosine and probed by a strongly enhanced vibrational circular dichroism signal
    • Measey TJ, Smith KB, Decatur SM, Zhao L, Yang G, et al. (2009) Self-aggregation of a polyalanine octamer promoted by its C-terminal tyrosine and probed by a strongly enhanced vibrational circular dichroism signal. J Am Chem Soc 131: 18218-18219 Available: http://dx.doi.org/10.1021/ja908324m.
    • (2009) J Am Chem Soc , vol.131 , pp. 18218-18219
    • Measey, T.J.1    Smith, K.B.2    Decatur, S.M.3    Zhao, L.4    Yang, G.5
  • 63
    • 79953230499 scopus 로고    scopus 로고
    • The molecular basis of distinct aggregation pathways of islet amyloid polypeptide
    • Wei L, Jiang P, Xu W, Li H, Zhang H, et al. (2011) The molecular basis of distinct aggregation pathways of islet amyloid polypeptide. J Biol Chem 286: 6291-6300 Available: http://www.jbc.org/content/286/8/6291.abstract.
    • (2011) J Biol Chem , vol.286 , pp. 6291-6300
    • Wei, L.1    Jiang, P.2    Xu, W.3    Li, H.4    Zhang, H.5
  • 64
    • 58149476769 scopus 로고    scopus 로고
    • A summary of the measured pK values of the ionizable groups in folded proteins
    • Grimsley GR, Scholtz JM, Pace CN, (2009) A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci 18: 247-251 Available: http://dx.doi.org/10.1002/pro.19.
    • (2009) Protein Sci , vol.18 , pp. 247-251
    • Grimsley, G.R.1    Scholtz, J.M.2    Pace, C.N.3
  • 65
    • 31444450716 scopus 로고    scopus 로고
    • Histidine-aromatic interactions in proteins and protein-ligand complexes: Quantum chemical study of X-ray and model structures
    • Cauët E, Rooman M, Wintjens R, Liévin J, Biot C, (2005) Histidine-aromatic interactions in proteins and protein-ligand complexes: Quantum chemical study of X-ray and model structures. J Chem Theory Comput 1: 472-483 Available: http://dx.doi.org/10.1021/ct049875k.
    • (2005) J Chem Theory Comput , vol.1 , pp. 472-483
    • Cauët, E.1    Rooman, M.2    Wintjens, R.3    Liévin, J.4    Biot, C.5
  • 66
    • 79955766939 scopus 로고    scopus 로고
    • Aromatic rings in chemical and biological recognition: Energetics and structures
    • Salonen LM, Ellermann M, Diederich F, (2011) Aromatic rings in chemical and biological recognition: Energetics and structures. Angew Chem Int Ed 50: 4808-4842 Available: http://dx.doi.org/10.1002/anie.201007560.
    • (2011) Angew Chem Int Ed , vol.50 , pp. 4808-4842
    • Salonen, L.M.1    Ellermann, M.2    Diederich, F.3
  • 67
    • 84871046431 scopus 로고    scopus 로고
    • Cation-π interaction: Its role and relevance in chemistry, biology, and material science
    • Mahadevi AS, Sastry GN, (2012) Cation-π interaction: Its role and relevance in chemistry, biology, and material science. Chem Rev 113: 2100-2138 Available: http://dx.doi.org/10.1021/cr300222d.
    • (2012) Chem Rev , vol.113 , pp. 2100-2138
    • Mahadevi, A.S.1    Sastry, G.N.2
  • 68
    • 84884696538 scopus 로고    scopus 로고
    • Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family
    • Song J, Ng SC, Tompa P, Lee KAW, Chan HS, (2013) Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family. PLoS Comput Biol 9: e1003239 Available: http://dx.doi.org/10.1371/journal.pcbi.1003239.
    • (2013) PLoS Comput Biol , vol.9
    • Song, J.1    Ng, S.C.2    Tompa, P.3    Lee, K.A.W.4    Chan, H.S.5
  • 69
    • 84860013075 scopus 로고    scopus 로고
    • Structure of an intermediate state in protein folding and aggregation
    • Neudecker P, Robustelli P, Cavalli A, Walsh P, Lundström P, et al. (2012) Structure of an intermediate state in protein folding and aggregation. Science 336: 362-366 Available: http://www.sciencemag.org/content/336/6079/362.abstract.
    • (2012) Science , vol.336 , pp. 362-366
    • Neudecker, P.1    Robustelli, P.2    Cavalli, A.3    Walsh, P.4    Lundström, P.5
  • 70
    • 4644285228 scopus 로고    scopus 로고
    • Protein folding in the cell: reshaping the folding funnel
    • Clark PL, (2004) Protein folding in the cell: reshaping the folding funnel. Trends in Biochemical Sciences 29: 527-534 Available: http://www.sciencedirect.com/science/article/pii/S0968000404002099.
    • (2004) Trends in Biochemical Sciences , vol.29 , pp. 527-534
    • Clark, P.L.1
  • 71
    • 84874832163 scopus 로고    scopus 로고
    • Protein homeostasis as a therapeutic target for diseases of protein conformation
    • Calamini B, Morimoto RI, (2012) Protein homeostasis as a therapeutic target for diseases of protein conformation. Curr Top Med Chem 12: 2623-2640 Available: http://dx.doi.org/10.2174/1568026611212220014.
    • (2012) Curr Top Med Chem , vol.12 , pp. 2623-2640
    • Calamini, B.1    Morimoto, R.I.2
  • 72
    • 57749098600 scopus 로고    scopus 로고
    • Amyloid formation by globular proteins under native conditions
    • Chiti F, Dobson CM, (2009) Amyloid formation by globular proteins under native conditions. Nat Chem Biol 5: 15-22 Available: http://dx.doi.org/10.1038/nchembio.131.
    • (2009) Nat Chem Biol , vol.5 , pp. 15-22
    • Chiti, F.1    Dobson, C.M.2
  • 73
    • 84860143066 scopus 로고    scopus 로고
    • Is there an en route folding intermediate for cold shock proteins?
    • Huang L, Shakhnovich EI, (2012) Is there an en route folding intermediate for cold shock proteins? Protein Sci 21: 677-685 Available: http://dx.doi.org/10.1002/pro.2053.
    • (2012) Protein Sci , vol.21 , pp. 677-685
    • Huang, L.1    Shakhnovich, E.I.2
  • 74
    • 0035917318 scopus 로고    scopus 로고
    • The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
    • Shimada J, Kussell EL, Shakhnovich EI, (2001) The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J Mol Biol 308: 79-95 Available: http://www.sciencedirect.com/science/article/pii/S0022283601945863.
    • (2001) J Mol Biol , vol.308 , pp. 79-95
    • Shimada, J.1    Kussell, E.L.2    Shakhnovich, E.I.3
  • 75
    • 84865722488 scopus 로고    scopus 로고
    • Robustness of atomistic Gō models in predicting native-like folding intermediates
    • Estácio SG, Fernandes CS, Krobath H, Faísca PFN, Shakhnovich EI, (2012) Robustness of atomistic Gō models in predicting native-like folding intermediates. J Chem Phys 137: 085102 Available: http://dx.doi.org/10.1063/1.4747492.
    • (2012) J Chem Phys , vol.137 , pp. 085102
    • Estácio, S.G.1    Fernandes, C.S.2    Krobath, H.3    Faísca, P.F.N.4    Shakhnovich, E.I.5
  • 76
    • 0032443390 scopus 로고    scopus 로고
    • Discrete molecular dynamics studies of the folding of a protein-like model
    • Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI, (1998) Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 3: 577-587.
    • (1998) Fold Des , vol.3 , pp. 577-587
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Stanley, H.E.3    Shakhnovich, E.I.4
  • 77
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y, (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314: 141-151 Available: http://dx.doi.org/10.1016/s0009-2614(99)01123-9.
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 78
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig M, Karanicolas J, Brooks CL III, (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graphics Modell 22: 377-395 Available: http://www.sciencedirect.com/science/article/pii/S1093326303001943.
    • (2004) J Mol Graphics Modell , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 79
    • 73649194755 scopus 로고
    • Stereochemistry of polypeptide chain configurations
    • Ramachandran GN, Ramakrishnan C, Sasisekharan V, (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7: 95-99 Available: http://www.sciencedirect.com/science/article/pii/S0022283663800236.
    • (1963) J Mol Biol , vol.7 , pp. 95-99
    • Ramachandran, G.N.1    Ramakrishnan, C.2    Sasisekharan, V.3
  • 80
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen HJC, van der Spoel D, van Drunen R, (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications 91: 43-56 Available: http://www.sciencedirect.com/science/article/pii/001046559500042E.
    • (1995) Computer Physics Communications , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 81
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D, (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 83
    • 79959713919 scopus 로고    scopus 로고
    • Definition and testing of the GROMOS force-field versions 54A7 and 54B7
    • Schmid N, Eichenberger A, Choutko A, Riniker S, Winger M, et al. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J Biophys Lett 40: 843-856 Available: http://dx.doi.org/10.1007/s00249-011-0700-9.
    • (2011) Eur Biophys J Biophys Lett , vol.40 , pp. 843-856
    • Schmid, N.1    Eichenberger, A.2    Choutko, A.3    Riniker, S.4    Winger, M.5
  • 84
    • 84990424072 scopus 로고
    • A consistent empirical potential for water-protein interactions
    • Hermans J, Berendsen HJC, Van Gunsteren WF, Postma JPM, (1984) A consistent empirical potential for water-protein interactions. Biopolymers 23: 1513-1518 Available: http://dx.doi.org/10.1002/bip.360230807.
    • (1984) Biopolymers , vol.23 , pp. 1513-1518
    • Hermans, J.1    Berendsen, H.J.C.2    Van Gunsteren, W.F.3    Postma, J.P.M.4
  • 85
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi IG, Sperb R, Smith PE, van Gunsteren WF, (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102: 5451-5459.
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    van Gunsteren, W.F.4
  • 86
    • 2242491482 scopus 로고
    • Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K
    • Smith PE, van Gunsteren WF, (1994) Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J Chem Phys 100: 3169-3174.
    • (1994) J Chem Phys , vol.100 , pp. 3169-3174
    • Smith, P.E.1    van Gunsteren, W.F.2
  • 88
    • 23844500381 scopus 로고    scopus 로고
    • On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium
    • Teixeira VH, Cunha CA, Machuqueiro M, Oliveira ASF, Victor BL, et al. (2005) On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium. J Phys Chem B 109: 14691-14706 Available: http://dx.doi.org/10.1021/jp052259f.
    • (2005) J Phys Chem B , vol.109 , pp. 14691-14706
    • Teixeira, V.H.1    Cunha, C.A.2    Machuqueiro, M.3    Oliveira, A.S.F.4    Victor, B.L.5
  • 89
    • 28744457124 scopus 로고    scopus 로고
    • Protein surface dynamics: Interaction with water and small solutes
    • Friedman R, Nachliel E, Gutman M, (2005) Protein surface dynamics: Interaction with water and small solutes. J Biol Phys 31: 433-452 Available: http://dx.doi.org/10.1007/s10867-005-0171-2.
    • (2005) J Biol Phys , vol.31 , pp. 433-452
    • Friedman, R.1    Nachliel, E.2    Gutman, M.3
  • 90
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson MK, Sharp KA, Honig BH, (1988) Calculating the electrostatic potential of molecules in solution: Method and error assessment. J Comput Chem 9: 327-335 Available: http://dx.doi.org/10.1002/jcc.540090407.
    • (1988) J Comput Chem , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 91
    • 0035120969 scopus 로고    scopus 로고
    • Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins
    • Baptista AM, Soares CM, (2000) Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J Phys Chem B 105: 293-309 Available: http://dx.doi.org/10.1021/jp002763e.
    • (2000) J Phys Chem B , vol.105 , pp. 293-309
    • Baptista, A.M.1    Soares, C.M.2
  • 92
    • 0033001692 scopus 로고    scopus 로고
    • Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics
    • Baptista AM, Martel PJ, Soares CM, (1999) Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics. Biophys J 76: 2978-2998.
    • (1999) Biophys J , vol.76 , pp. 2978-2998
    • Baptista, A.M.1    Martel, P.J.2    Soares, C.M.3
  • 94
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 95
    • 84861217855 scopus 로고    scopus 로고
    • Impact of chemical heterogeneity on protein self-assembly in water
    • Chong S-H, Ham S, (2012) Impact of chemical heterogeneity on protein self-assembly in water. Proc Natl Acad Sci USA 109: 7636-7641 Available: http://www.pnas.org/content/109/20/7636.abstract.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 7636-7641
    • Chong, S.-H.1    Ham, S.2


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