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Volumn 14, Issue 9, 2013, Pages 17256-17278

Assessing the effect of loop mutations in the folding space of β2microglobulin with molecular dynamics simulations

Author keywords

Dialysis related amyloidosis; Discrete molecular dynamics; Folding pathways; Intermediate states; Molten globule; Principal component analysis

Indexed keywords

AMYLOID; BETA 2 MICROGLOBULIN; CYSTEINE;

EID: 84883486569     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms140917256     Document Type: Article
Times cited : (15)

References (56)
  • 1
    • 0037162520 scopus 로고    scopus 로고
    • Crystal structure of monomeric human β-2-microglobulin reveals clues to its amyloidogenic properties
    • Trinh, C.H.; Smith, D.P.; Kalverda, A.P.; Phillips, S.E.V.; Radford, S.E. Crystal structure of monomeric human β-2-microglobulin reveals clues to its amyloidogenic properties. Proc. Natl. Acad. Sci. USA 2002, 99, 9771-9776.
    • (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
  • 3
    • 38049187118 scopus 로고    scopus 로고
    • Thiol compounds inhibit the formation of amyloid fibrils by β2-microglobulin at neutral pH
    • Yamamoto, K.; Yagi, H.; Ozawa, D.; Sasahara, K.; Naiki, H.; Goto, Y. Thiol compounds inhibit the formation of amyloid fibrils by β2-microglobulin at neutral pH. J. Mol. Biol. 2008, 376, 258-268.
    • (2008) J. Mol. Biol , vol.376 , pp. 258-268
    • Yamamoto, K.1    Yagi, H.2    Ozawa, D.3    Sasahara, K.4    Naiki, H.5    Goto, Y.6
  • 4
    • 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. Dynamic of β2-microglobulin fibril formation and reabsorption: The role of proteolysis. Semin. Dial. 2001, 14, 117-122.
    • (2001) Semin. Dial , vol.14 , pp. 117-122
    • Bellotti, V.1    Gallieni, M.2    Giorgetti, S.3    Brancaccio, D.4
  • 5
    • 27744437192 scopus 로고    scopus 로고
    • From chance to frequent encounters: Origins of β2-microglobulin fibrillogenesis
    • Eakin, C.M.; Miranker, A.D. From chance to frequent encounters: Origins of β2-microglobulin fibrillogenesis. BBA-Proteins Proteom. 2005, 1753, 92-99.
    • (2005) BBA-Proteins Proteom , vol.1753 , pp. 92-99
    • Eakin, C.M.1    Miranker, A.D.2
  • 6
    • 68649108349 scopus 로고    scopus 로고
    • Glimpses of the molecular mechanisms of β2-microglobulin fibril formation in vitro
    • Platt, G.W.; Radford, S.E. Glimpses of the molecular mechanisms of β2-microglobulin fibril formation in vitro: Aggregation on a complex energy landscape. FEBS Lett. 2009, 583, 2623-2629.
    • (2009) Aggregation On a Complex Energy Landscape. FEBS Lett , vol.583 , pp. 2623-2629
    • Platt, G.W.1    Radford, S.E.2
  • 7
    • 0038575395 scopus 로고    scopus 로고
    • A systematic investigation into the effect of protein destabilisation on beta 2-microglobulin amyloid formation
    • Smith, D.P.; Jones, S.; Serpell, L.C.; Sunde, M.; Radford, S.E. A systematic investigation into the effect of protein destabilisation on beta 2-microglobulin amyloid formation. J. Mol. Biol. 2003, 330, 943-954.
    • (2003) J. Mol. Biol , vol.330 , pp. 943-954
    • Smith, D.P.1    Jones, S.2    Serpell, L.C.3    Sunde, M.4    Radford, S.E.5
  • 8
    • 25444512708 scopus 로고    scopus 로고
    • Ultrasonication-induced amyloid fibril formation of β2-microglobulin
    • Ohhashi, Y.; Kihara, M.; Naiki, H.; Goto, Y. Ultrasonication-induced amyloid fibril formation of β2-microglobulin. J. Biol. Chem. 2005, 280, 32843-32848.
    • (2005) J. Biol. Chem , vol.280 , pp. 32843-32848
    • Ohhashi, Y.1    Kihara, M.2    Naiki, H.3    Goto, Y.4
  • 9
    • 51349128031 scopus 로고    scopus 로고
    • A regulatable switch mediates self-association in an immunoglobulin fold
    • Calabrese, M.F.; Eakin, C.M.; Wang, J.M.; Miranker, A.D. A regulatable switch mediates self-association in an immunoglobulin fold. Nat. Struct. M.l. Biol. 2008, 15, 965-971.
    • (2008) Nat. Struct. M.l. Biol , vol.15 , pp. 965-971
    • Calabrese, M.F.1    Eakin, C.M.2    Wang, J.M.3    Miranker, A.D.4
  • 10
    • 84863644568 scopus 로고    scopus 로고
    • The role of conformational flexibility in β2-microglobulin amyloid fibril formation at neutral pH
    • Hodkinson, J.P.; Radford, S.E.; Ashcroft, A.E. The role of conformational flexibility in β2-microglobulin amyloid fibril formation at neutral pH. Rapid Commun. Mass Spectrom. 2012, 26, 1783-1792.
    • (2012) Rapid Commun. Mass Spectrom , vol.26 , pp. 1783-1792
    • Hodkinson, J.P.1    Radford, S.E.2    Ashcroft, A.E.3
  • 11
    • 0035896018 scopus 로고    scopus 로고
    • Detection of two partially structured species in the folding process of the amyloidogenic protein [beta]2-microglobulin
    • Chiti, F.; Mangione, P.; Andreola, A.; Giorgetti, S.; Stefani, M.; Dobson, C.M.; Bellotti, V.; Taddei N. Detection of two partially structured species in the folding process of the amyloidogenic protein [beta]2-microglobulin. J. Mol. Biol. 2001, 307, 379-391.
    • (2001) J. Mol. Biol , vol.307 , pp. 379-391
    • Chiti, F.1    Mangione, P.2    Andreola, A.3    Giorgetti, S.4    Stefani, M.5    Dobson, C.M.6    Bellotti, V.7    Taddei, N.8
  • 12
  • 13
    • 33144467755 scopus 로고    scopus 로고
    • Amyloid formation under physiological conditions proceeds via a native-like folding intermediate
    • Jahn, T.R.; Parker, M.J.; Homans, S.W.; Radford, S.E. Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat. Struct. Mol. Biol. 2006, 13, 195-201.
    • (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
  • 14
    • 60949106895 scopus 로고    scopus 로고
    • A generic mechanism of β2-microglobulin amyloid assembly at neutral pH involving a specific proline switch
    • Eichner, T.; Radford, S.E. A generic mechanism of β2-microglobulin amyloid assembly at neutral pH involving a specific proline switch. J. Mol. Biol. 2009, 386, 1312-1326.
    • (2009) J. Mol. Biol , vol.386 , pp. 1312-1326
    • Eichner, T.1    Radford, S.E.2
  • 16
    • 78651468727 scopus 로고    scopus 로고
    • Conformational conversion during amyloid formation at atomic resolution
    • Eichner, T.; Kalverda, A.P.; Thompson, G.S.; Homans, S.W.; Radford, S.E. Conformational conversion during amyloid formation at atomic resolution. Mol. Cell 2011, 41, 161-172.
    • (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
  • 17
    • 65849165676 scopus 로고    scopus 로고
    • Competition between intramolecular and intermolecular interactions in an amyloid-forming protein
    • Routledge, K.E.; Tartaglia, G.G.; Platt, G.W.; Vendruscolo, M.; Radford, S.E. Competition between intramolecular and intermolecular interactions in an amyloid-forming protein. J. Mol. Biol. 2009, 389, 776-786.
    • (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
  • 18
    • 77449095000 scopus 로고    scopus 로고
    • Structure of the preamyloid dimer of β-2-microglobulin from covalent labeling and mass spectrometry
    • Mendoza, V.L.; Antwi, K.; Barón-Rodríguez, M.A.; Blanco, C.; Vachet, R.W. Structure of the preamyloid dimer of β-2-microglobulin from covalent labeling and mass spectrometry. Biochemistry 2010, 49, 1522-1532.
    • (2010) Biochemistry , vol.49 , pp. 1522-1532
    • Mendoza, V.L.1    Antwi, K.2    Barón-Rodríguez, M.A.3    Blanco, C.4    Vachet, R.W.5
  • 19
    • 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. A recurrent D-strand association interface is observed in β-2 microglobulin oligomers. FEBS J. 2012, 279, 1131-1143.
    • (2012) FEBS J , vol.279 , pp. 1131-1143
    • Colombo, M.1    de Rosa, M.2    Bellotti, V.3    Ricagno, S.4    Bolognesi, M.5
  • 23
    • 79958178306 scopus 로고    scopus 로고
    • The two tryptophans of beta2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure
    • Raimondi, S.; Barbarini, N.; Mangione, P.; Esposito, G.; Ricagno, S.; Bolognesi, M.; Zorzoli, I.; Marchese, L.; Soria, C.; Bellazzi, R.; et al. The two tryptophans of beta2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure. BMC Evol. Biol. 2011, 11, 159.
    • (2011) BMC Evol. Biol , vol.11 , pp. 159
    • Raimondi, S.1    Barbarini, N.2    Mangione, P.3    Esposito, G.4    Ricagno, S.5    Bolognesi, M.6    Zorzoli, I.7    Marchese, L.8    Soria, C.9    Bellazzi, R.10
  • 26
    • 84883479663 scopus 로고    scopus 로고
    • Emerging Molecular Targets in the Therapy of Dialysis-related Amyloidosis
    • John Wiley & Sons, Inc.: Hoboken, NJ, USA
    • Esposito, G.; Bellotti, V. Emerging Molecular Targets in the Therapy of Dialysis-related Amyloidosis. In Protein Misfolding Diseases; John Wiley & Sons, Inc.: Hoboken, NJ, USA, 2010; pp. 843-865.
    • (2010) Protein Misfolding Diseases , pp. 843-865
    • Esposito, G.1    Bellotti, V.2
  • 27
    • 0037022563 scopus 로고    scopus 로고
    • Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
    • Richardson, J.S.; Richardson, D.C. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. USA 2002, 99, 2754-2759.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 2754-2759
    • Richardson, J.S.1    Richardson, D.C.2
  • 28
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez, J.C.; Pisabarro, M.T.; Serrano, L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Mol. Biol. 1998, 5, 721-729.
    • (1998) Nat. Struct. Mol. Biol , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 29
    • 0021114569 scopus 로고
    • Molten-globule state: A compact form of globular proteins with mobile side-chains
    • Ohgushi, M.; Wada, A. "Molten-globule state": A compact form of globular proteins with mobile side-chains. FEBS Lett. 1983, 164, 21-24.
    • (1983) FEBS Lett , vol.164 , pp. 21-24
    • Ohgushi, M.1    Wada, A.2
  • 30
    • 77954219081 scopus 로고    scopus 로고
    • Relative Importance of Hydrophobicity, Net Charge, and Secondary Structure Propensities in Protein Aggregation
    • Springer: New York, NY, USA
    • Chiti, F. Relative Importance of Hydrophobicity, Net Charge, and Secondary Structure Propensities in Protein Aggregation. In Protein Misfolding, Aggregation, and Conformational Diseases-Protein Reviews; Springer: New York, NY, USA, 2006; Volume 4, pp. 43-59.
    • (2006) Protein Misfolding, Aggregation, and Conformational Diseases-Protein Reviews , vol.4 , pp. 43-59
    • Chiti, F.1
  • 31
  • 32
    • 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.; Kuwajima, K. The molten globule of β2-microglobulin accumulated at pH 4 and its role in protein folding. J. Mol. Biol. 2013, 425, 273-291.
    • (2013) J. Mol. Biol , vol.425 , pp. 273-291
    • Mukaiyama, A.1    Nakamura, T.2    Makabe, K.3    Maki, K.4    Goto, Y.5    Kuwajima, K.6
  • 33
    • 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.; Kuwajima, K. Native-state heterogeneity of β2-microglobulin as revealed by kinetic folding and real-time NMR experiments. J. Mol. Biol. 2013, 425, 257-272.
    • (2013) J. Mol. Biol , vol.425 , pp. 257-272
    • Mukaiyama, A.1    Nakamura, T.2    Makabe, K.3    Maki, K.4    Goto, Y.5    Kuwajima, K.6
  • 36
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li, H.; Robertson, A.D.; Jensen, J.H. Very fast empirical prediction and rationalization of protein pKa values. Proteins: Struct. Funct. Bioinf. 2005, 61, 704-721.
    • (2005) Proteins: Struct. Funct. Bioinf , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 37
    • 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, S.G.; Faísca, P.F.N.; Shakhnovich, E.I. Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. J. Mol. Biol. 2012, 422, 705-722.
    • (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
  • 38
    • 84860143066 scopus 로고    scopus 로고
    • Is there an en route folding intermediate for cold shock proteins?
    • Huang, L.; Shakhnovich, E.I. Is there an en route folding intermediate for cold shock proteins? Protein Sci. 2012, 21, 677-685.
    • (2012) Protein Sci , vol.21 , pp. 677-685
    • Huang, L.1    Shakhnovich, E.I.2
  • 39
    • 0345411345 scopus 로고    scopus 로고
    • Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
    • Tsai, J.; Levitt, M.; Baker, D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J. Mol. Biol. 1999, 291, 215-225.
    • (1999) J. Mol. Biol , vol.291 , pp. 215-225
    • Tsai, J.1    Levitt, M.2    Baker, D.3
  • 40
    • 0019569599 scopus 로고
    • Noninteracting local-structure model of folding and unfolding transition in globular proteins
    • Go, N.; Abe, H. Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers 1981, 20, 991-1011.
    • (1981) I. Formulation. Biopolymers , vol.20 , pp. 991-1011
    • Go, N.1    Abe, H.2
  • 41
    • 0035917318 scopus 로고    scopus 로고
    • The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
    • Shimada, J.; Kussell, E.L.; Shakhnovich, E.I. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 2001, 308, 79-95.
    • (2001) J. Mol. Biol , vol.308 , pp. 79-95
    • Shimada, J.1    Kussell, E.L.2    Shakhnovich, E.I.3
  • 42
    • 0032443390 scopus 로고    scopus 로고
    • Discrete molecular dynamics studies of the folding of a protein-like model
    • Dokholyan, N.V.; Buldyrev, S.V.; Stanley, H.E.; Shakhnovich, E.I. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 1998, 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
  • 43
    • 0031161658 scopus 로고    scopus 로고
    • Molecular dynamics for polymeric fluids using discontinuous potentials
    • Smith, S.W.; Hall, C.K.; Freeman, B.D. Molecular dynamics for polymeric fluids using discontinuous potentials. J. Comput. Phys. 1997, 134, 16-30.
    • (1997) J. Comput. Phys , vol.134 , pp. 16-30
    • Smith, S.W.1    Hall, C.K.2    Freeman, B.D.3
  • 44
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-151.
    • (1999) Chem. Phys. Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 45
    • 33947398571 scopus 로고    scopus 로고
    • Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
    • Chodera, J.D.; Swope, W.C.; Pitera, J.W.; Seok, C.; Dill, K.A. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J. Chem. Theor. Comput. 2007, 3, 26-41.
    • (2007) J. Chem. Theor. 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
  • 46
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig, M.; Karanicolas, J.; Brooks, C.L., III. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph. Model. 2004, 22, 377-395.
    • (2004) J. Mol. Graph. Model , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 49
    • 57749098600 scopus 로고    scopus 로고
    • Amyloid formation by globular proteins under native conditions
    • Chiti, F.; Dobson, C.M. Amyloid formation by globular proteins under native conditions. Nat. Chem. Biol. 2009, 5, 15-22.
    • (2009) Nat. Chem. Biol , vol.5 , pp. 15-22
    • Chiti, F.1    Dobson, C.M.2
  • 50
    • 0038351889 scopus 로고    scopus 로고
    • Role of the N and C-terminal strands of [beta]2-microglobulin in amyloid formation at neutral pH
    • Jones, S.; Smith, D.P.; Radford, S.E. Role of the N and C-terminal strands of [beta]2-microglobulin in amyloid formation at neutral pH. J. Mol. Biol. 2003, 330, 935-941.
    • (2003) J. Mol. Biol , vol.330 , pp. 935-941
    • Jones, S.1    Smith, D.P.2    Radford, S.E.3
  • 51
    • 39749190021 scopus 로고    scopus 로고
    • Solvent effects in the slow dynamics of proteins
    • Hinsen, K.; Kneller, G.R. Solvent effects in the slow dynamics of proteins. Proteins Struct. Funct. Bioinf. 2008, 70, 1235-1242.
    • (2008) Proteins Struct. Funct. Bioinf , vol.70 , pp. 1235-1242
    • Hinsen, K.1    Kneller, G.R.2
  • 52
    • 0025186451 scopus 로고
    • Structural characterization of a partly folded apomyoglobin intermediate
    • Hughson, F.; Wright, P.; Baldwin, R. Structural characterization of a partly folded apomyoglobin intermediate. Science 1990, 249, 1544-1548.
    • (1990) Science , vol.249 , pp. 1544-1548
    • Hughson, F.1    Wright, P.2    Baldwin, R.3
  • 53
    • 13544271033 scopus 로고    scopus 로고
    • Hydrophobic core variant ubiquitin forms a molten globule conformation at acidic pH
    • Park, S.H. Hydrophobic core variant ubiquitin forms a molten globule conformation at acidic pH. J. Biochem. Mol. Biol. 2004, 37, 676-683.
    • (2004) J. Biochem. Mol. Biol , vol.37 , pp. 676-683
    • Park, S.H.1
  • 54
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky, T.; Czodrowski, P.; Li, H.; Nielsen, J.E.; Jensen, J.H.; Klebe, G.; Baker, N. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 2004, 35, W522-W525.
    • (2004) Nucleic Acids Res , vol.35
    • Dolinsky, T.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5    Klebe, G.6    Baker, N.7


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