메뉴 건너뛰기




Volumn 349, Issue 3, 2005, Pages 648-658

Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein sup35: Simulation by reaction path annealing

Author keywords

Amyloid; Cross beta sheet; Onsager Machlup action; Reaction path annealing; Yeast prion

Indexed keywords

AMYLOID; GLYCYLASPARAGINYLASPARAGINYLGLUTAMINYLGLUTAMINYLASPARAGINYLTYROSINE; PEPTIDE DERIVATIVE; PRION PROTEIN; UNCLASSIFIED DRUG; WATER;

EID: 19444380574     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.03.083     Document Type: Article
Times cited : (61)

References (49)
  • 3
    • 0030908095 scopus 로고    scopus 로고
    • Models of amyloid seeding in Alzheimer's disease and scrapie: Mechanistic truths and physiological consequences of time-dependent solubility of amyloid proteins
    • J.D. Harper, and P.T. Lansbury Models of amyloid seeding in Alzheimer's disease and scrapie: mechanistic truths and physiological consequences of time-dependent solubility of amyloid proteins Annu. Rev. Biochem. 66 1997 385 407
    • (1997) Annu. Rev. Biochem. , vol.66 , pp. 385-407
    • Harper, J.D.1    Lansbury, P.T.2
  • 4
    • 0031711595 scopus 로고    scopus 로고
    • Pathologic conformations of prion proteins
    • F.E. Cohen, and S.B. Prusiner Pathologic conformations of prion proteins Annu. Rev. Biochem. 67 1998 793 819
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 793-819
    • Cohen, F.E.1    Prusiner, S.B.2
  • 6
    • 19444376621 scopus 로고    scopus 로고
    • Prions: Health scare and biological challenge
    • A. Aguzzi, F. Montrasio, and P.S. Kaeser Prions: health scare and biological challenge Cell 93 1998 337 348
    • (1998) Cell , vol.93 , pp. 337-348
    • Aguzzi, A.1    Montrasio, F.2    Kaeser, P.S.3
  • 7
    • 0035956924 scopus 로고    scopus 로고
    • An amyloid-forming peptide from the yeast prion sup35 reveals a dehydrated β-sheet structure for amyloid
    • M. Balbirnie, R. Grothe, and D.S. Eisenberg An amyloid-forming peptide from the yeast prion sup35 reveals a dehydrated β-sheet structure for amyloid Proc. Natl Acad. Sci. USA 98 2001 2375 2380
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 2375-2380
    • Balbirnie, M.1    Grothe, R.2    Eisenberg, D.S.3
  • 9
    • 0028308104 scopus 로고
    • [URE3] as an altered URE2 protein: Evidence for a prion analog in saccharomyces cerevisiae
    • R.B. Wickner [URE3] as an altered URE2 protein: evidence for a prion analog in saccharomyces cerevisiae Science 264 1994 566 569
    • (1994) Science , vol.264 , pp. 566-569
    • Wickner, R.B.1
  • 10
    • 0029780647 scopus 로고    scopus 로고
    • Support for the prion hypothesis for inheritance of a phenotypic trait in yeast
    • M.M. Patino, J.J. Liu, J.R. Glover, and S. Lindquist Support for the prion hypothesis for inheritance of a phenotypic trait in yeast Science 273 1996 622 626
    • (1996) Science , vol.273 , pp. 622-626
    • Patino, M.M.1    Liu, J.J.2    Glover, J.R.3    Lindquist, S.4
  • 11
    • 0028351003 scopus 로고
    • Polypeptide chain termination in Saccharomyces cerevisiae
    • I. Stansfield, and M.F. Tuite Polypeptide chain termination in Saccharomyces cerevisiae Curr. Genet. 25 1994 385 395
    • (1994) Curr. Genet. , vol.25 , pp. 385-395
    • Stansfield, I.1    Tuite, M.F.2
  • 13
    • 0027332116 scopus 로고
    • Conversion of α-helices into β-sheets features in the formation of the scrapie prion proteins
    • K.M. Pan, M. Baldwin, J. Nguyen, M. Gasset, A. Serban, and D. Groth Conversion of α-helices into β-sheets features in the formation of the scrapie prion proteins Proc. Natl Acad. Sci. USA 90 1993 10962 10966
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 10962-10966
    • Pan, K.M.1    Baldwin, M.2    Nguyen, J.3    Gasset, M.4    Serban, A.5    Groth, D.6
  • 14
    • 0035827614 scopus 로고    scopus 로고
    • Folding of prion protein to its native α-helical conformation is under kinetic control
    • I.V. Baskakov, G. Legname, S.B. Prusiner, and F.E. Cohen Folding of prion protein to its native α-helical conformation is under kinetic control J. Biol. Chem. 276 2001 19687 19690
    • (2001) J. Biol. Chem. , vol.276 , pp. 19687-19690
    • Baskakov, I.V.1    Legname, G.2    Prusiner, S.B.3    Cohen, F.E.4
  • 15
    • 0035823222 scopus 로고    scopus 로고
    • Protein refolding versus aggregation: Computer simulations on an intermediate-resolution protein model
    • A.V. Smith, and C.K. Hall Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model J. Mol. Biol. 312 2001 187 202
    • (2001) J. Mol. Biol. , vol.312 , pp. 187-202
    • Smith, A.V.1    Hall, C.K.2
  • 17
    • 0033582587 scopus 로고    scopus 로고
    • Thermodynamics of model prions and its implications for the problem of prion protein folding
    • P.M. Harrison, H.S. Chan, S.B. Prusiner, and F.E. Cohen Thermodynamics of model prions and its implications for the problem of prion protein folding J. Mol. Biol. 286 1999 593 606
    • (1999) J. Mol. Biol. , vol.286 , pp. 593-606
    • Harrison, P.M.1    Chan, H.S.2    Prusiner, S.B.3    Cohen, F.E.4
  • 18
    • 0034275017 scopus 로고    scopus 로고
    • Compactness, aggregation, and prionlike behaviour of protein: A lattice model study
    • G. Giugliarelli, C. Micheletti, J.R. Banavar, and A. Maritan Compactness, aggregation, and prionlike behaviour of protein: a lattice model study J. Chem. Phys. 113 2000 5072 5077
    • (2000) J. Chem. Phys. , vol.113 , pp. 5072-5077
    • Giugliarelli, G.1    Micheletti, C.2    Banavar, J.R.3    Maritan, A.4
  • 19
    • 0035079856 scopus 로고    scopus 로고
    • Conformational propagation with prion-like characteristics in a simple model of protein folding
    • P.M. Harrison, H.S. Chan, S.B. Prusiner, and F.E. Cohen Conformational propagation with prion-like characteristics in a simple model of protein folding Protein Sci. 10 2001 819 835
    • (2001) Protein Sci. , vol.10 , pp. 819-835
    • Harrison, P.M.1    Chan, H.S.2    Prusiner, S.B.3    Cohen, F.E.4
  • 20
    • 0036228167 scopus 로고    scopus 로고
    • Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics
    • R.I. Dima, and D. Thirumalai Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics Protein Sci. 11 2002 1036 1049
    • (2002) Protein Sci. , vol.11 , pp. 1036-1049
    • Dima, R.I.1    Thirumalai, D.2
  • 21
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulation of an amyloid-forming peptide from yeast prion sup35
    • J. Gsponer, U. Haberthaüur, and A. Caflisch The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulation of an amyloid-forming peptide from yeast prion sup35 Proc. Natl Acad. Sci. USA 100 2003 5154 5159
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthaüur, U.2    Caflisch, A.3
  • 23
    • 36149021145 scopus 로고
    • Fluctuations and irreversible processes
    • L. Onsager, and S. Machlup Fluctuations and irreversible processes Phys. Rev. 91 1953 1505 1512
    • (1953) Phys. Rev. , vol.91 , pp. 1505-1512
    • Onsager, L.1    MacHlup, S.2
  • 24
    • 0035250027 scopus 로고    scopus 로고
    • Simulation of protein folding by reaction path annealing
    • P. Eastman, N. Gronbech-Jensen, and S. Doniach Simulation of protein folding by reaction path annealing J. Chem. Phys. 114 2001 3812 3841
    • (2001) J. Chem. Phys. , vol.114 , pp. 3812-3841
    • Eastman, P.1    Gronbech-Jensen, N.2    Doniach, S.3
  • 25
    • 0012021417 scopus 로고    scopus 로고
    • Calculation of classical trajectories with a very large time step: Formalism and numerical examples
    • R. Olender, and R. Elber Calculation of classical trajectories with a very large time step: formalism and numerical examples J. Chem. Phys. 105 1996 9299 9315
    • (1996) J. Chem. Phys. , vol.105 , pp. 9299-9315
    • Olender, R.1    Elber, R.2
  • 27
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 0003932766 scopus 로고
    • W.H. Freeman and Company New York
    • T.E. Creighton Proteins 1993 W.H. Freeman and Company New York
    • (1993) Proteins
    • Creighton, T.E.1
  • 29
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dieletric constants and multivalent ions
    • W. Rocchia, E. Alexov, and B. Honig Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dieletric constants and multivalent ions J. Phys. Chem. B 105 2001 6507 6514
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 30
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Applications to the finite difference Poisson-Boltzmann method
    • W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method J. Comput. Chem. 23 2002 128 137
    • (2002) J. Comput. Chem. , vol.23 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 31
    • 0034710897 scopus 로고    scopus 로고
    • A census of glutamine/asparagine-rich regions: Implications for their conserved function and the prediction of novel prions
    • M.D. Michelitsch, and J.S. Weissman A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions Proc. Natl Acad. Sci. USA 97 2000 11910 11915
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 11910-11915
    • Michelitsch, M.D.1    Weissman, J.S.2
  • 32
    • 0028283985 scopus 로고
    • Glutamine repeats as polar zippers: Theirs possible role in inherited neurodegenerative diseases
    • M.F. Perutz, T. Johnson, M. Suzuki, and J.T. Finch Glutamine repeats as polar zippers: theirs possible role in inherited neurodegenerative diseases Proc. Natl Acad. Sci. USA 91 1994 5355 5358
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5355-5358
    • Perutz, M.F.1    Johnson, T.2    Suzuki, M.3    Finch, J.T.4
  • 33
    • 0029059477 scopus 로고
    • Incorporation of glutamine repeats makes protein oligomerize: Implications for neurodegenrative diseases
    • K. Stott, J.M. Blackburn, P.J.G. Butler, and M.F. Perutz Incorporation of glutamine repeats makes protein oligomerize: implications for neurodegenrative diseases Proc. Natl Acad. Sci. USA 92 1995 6509 6513
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 6509-6513
    • Stott, K.1    Blackburn, J.M.2    Butler, P.J.G.3    Perutz, M.F.4
  • 34
    • 0037117499 scopus 로고    scopus 로고
    • Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine-rich domains of sup35 and of the amyloid β-peptide of amyloid plaques
    • M.F. Perutz, B.J. Pope, D. Owen, E.E. Wanker, and E. Scherzinger Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine-rich domains of sup35 and of the amyloid β-peptide of amyloid plaques Proc. Natl Acad. Sci. USA 99 2002 5596 5600
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 5596-5600
    • Perutz, M.F.1    Pope, B.J.2    Owen, D.3    Wanker, E.E.4    Scherzinger, E.5
  • 35
    • 0036135139 scopus 로고    scopus 로고
    • A possible role for π-stacking in the self-assembly of amyloid fibrils
    • E. Gazit A possible role for π-stacking in the self-assembly of amyloid fibrils FASEB J. 16 2002 77 83
    • (2002) FASEB J. , vol.16 , pp. 77-83
    • Gazit, E.1
  • 37
    • 0036233931 scopus 로고    scopus 로고
    • Origins and kinetic consequences of diversity in sup35 yeast prion fibers
    • A.H. DePace, and J.S. Weissman Origins and kinetic consequences of diversity in sup35 yeast prion fibers Nature Struct. Biol. 9 2002 389 396
    • (2002) Nature Struct. Biol. , vol.9 , pp. 389-396
    • Depace, A.H.1    Weissman, J.S.2
  • 38
    • 0003529419 scopus 로고
    • Oxford University Press Oxford, UK
    • M. Daune Molecular Biophysics 1993 Oxford University Press Oxford, UK
    • (1993) Molecular Biophysics
    • Daune, M.1
  • 39
    • 0037337271 scopus 로고    scopus 로고
    • 16-22 amyloid peptides into antiparallel β sheets
    • 16-22 amyloid peptides into antiparallel β sheets Structure 11 2003 295 307
    • (2003) Structure , vol.11 , pp. 295-307
    • Klimov, D.K.1    Thirumalai, D.2
  • 40
    • 10844230140 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of amyloid peptide aggregation
    • M. Cecchini, F. Rao, M. Seeber, and A. Caisch Replica exchange molecular dynamics simulations of amyloid peptide aggregation J. Chem. Phys. 121 2004 10748 10757
    • (2004) J. Chem. Phys. , vol.121 , pp. 10748-10757
    • Cecchini, M.1    Rao, F.2    Seeber, M.3    Caisch, A.4
  • 43
    • 0034255027 scopus 로고    scopus 로고
    • A systematic exploration if the influence of the protein stability on amyloid fibril formation in vitro
    • M. Ramirez-Alvarado, J.S. Merkel, and L. Regan A systematic exploration if the influence of the protein stability on amyloid fibril formation in vitro Proc. Natl Acad. Sci. USA 97 2000 8979 8984
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 8979-8984
    • Ramirez-Alvarado, M.1    Merkel, J.S.2    Regan, L.3
  • 45
    • 0036845354 scopus 로고    scopus 로고
    • The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation
    • M. Fändrich, and C.M. Dobson The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation EMBO J. 21 2002 5682 5690
    • (2002) EMBO J. , vol.21 , pp. 5682-5690
    • Fändrich, M.1    Dobson, C.M.2
  • 49
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potentials in proteins
    • I.K. McDonald, and J.M. Thornton Satisfying hydrogen bonding potentials in proteins J. Mol. Biol. 238 1994 777 793
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.