메뉴 건너뛰기




Volumn 412, Issue , 2006, Pages 314-338

Ab initio Discrete Molecular Dynamics Approach to Protein Folding and Aggregation

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN;

EID: 33749601705     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)12019-4     Document Type: Review
Times cited : (68)

References (67)
  • 4
    • 33749518696 scopus 로고    scopus 로고
    • Structural study of metastable amyloidogenic protien oligomers by photo-induced cross-linking of unmodified protiens
    • in press
    • Bitan G. Structural study of metastable amyloidogenic protien oligomers by photo-induced cross-linking of unmodified protiens. Methods Enzymol. 413 (2006) in press
    • (2006) Methods Enzymol. , vol.413
    • Bitan, G.1
  • 6
    • 0041816383 scopus 로고    scopus 로고
    • Elucidation of primary structure elements controlling early amyloid β-protein oligomerization
    • Bitan G., Vollers S.S., and Teplow D.B. Elucidation of primary structure elements controlling early amyloid β-protein oligomerization. J. Biol. Chem. 278 (2003) 34882-34889
    • (2003) J. Biol. Chem. , vol.278 , pp. 34882-34889
    • Bitan, G.1    Vollers, S.S.2    Teplow, D.B.3
  • 11
    • 0032483035 scopus 로고    scopus 로고
    • Solution structure of amyloid-β peptide (1-40) in a water-micelle environment. Is the membrane spanning domain where we think it is?
    • Coles M., Bicknell W., Watson A.A., Fairlie D.P., and Craik D.J. Solution structure of amyloid-β peptide (1-40) in a water-micelle environment. Is the membrane spanning domain where we think it is?. Biochemistry 37 (1998) 11064-11077
    • (1998) Biochemistry , vol.37 , pp. 11064-11077
    • Coles, M.1    Bicknell, W.2    Watson, A.A.3    Fairlie, D.P.4    Craik, D.J.5
  • 13
    • 0036438914 scopus 로고    scopus 로고
    • Solution structure of the Alzheimer amyloid β-peptide (1-42) in an apolar microenvironment. Similarity with a virus fusion domain
    • Crescenzi O., Tomaselli S., Guerrini R., Salvatori S., D'Ursi A.M., Temussi P.A., and Picone D. Solution structure of the Alzheimer amyloid β-peptide (1-42) in an apolar microenvironment. Similarity with a virus fusion domain. Eur. J. Biochem. 269 (2002) 5642-5648
    • (2002) Eur. J. Biochem. , vol.269 , pp. 5642-5648
    • Crescenzi, O.1    Tomaselli, S.2    Guerrini, R.3    Salvatori, S.4    D'Ursi, A.M.5    Temussi, P.A.6    Picone, D.7
  • 15
    • 0036927818 scopus 로고    scopus 로고
    • Direct molecular dynamics observation of protein folding transition state ensemble
    • Ding F., Dokholyan N.V., Buldyrev S.V., Stanley H.E., and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83 (2002) 3525-3532
    • (2002) Biophys. J. , vol.83 , pp. 3525-3532
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 17
    • 11244291006 scopus 로고    scopus 로고
    • Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model
    • Ding F., Buldyrev S.V., and Dokholyan N.V. Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys. J. 88 (2005) 147-155
    • (2005) Biophys. J. , vol.88 , pp. 147-155
    • Ding, F.1    Buldyrev, S.V.2    Dokholyan, N.V.3
  • 18
    • 0842281551 scopus 로고    scopus 로고
    • Principles of protein folding, misfolding, and aggregation
    • Dobson C.M. Principles of protein folding, misfolding, and aggregation. Cell Dev. Biol. 15 (2004) 3-16
    • (2004) Cell Dev. Biol. , vol.15 , pp. 3-16
    • Dobson, C.M.1
  • 22
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig M., and Brooks III C.L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14 (2004) 217-224
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 23
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • Fersht A.R., and Daggett V. Protein folding and unfolding at atomic resolution. Cell 108 (2002) 573-582
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 24
    • 4644293577 scopus 로고    scopus 로고
    • Conformation-dependent antibodies target diseases of protein misfolding
    • Glabe C.G. Conformation-dependent antibodies target diseases of protein misfolding. Trends Biochem. Sci. 29 (2004) 542-547
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 542-547
    • Glabe, C.G.1
  • 25
    • 0028892389 scopus 로고
    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
    • Godzik A., Kolinski A., and Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Prot. Sci. 4 (1995) 2107-2117
    • (1995) Prot. Sci. , vol.4 , pp. 2107-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 26
    • 33749642847 scopus 로고    scopus 로고
    • Computational approaches to fibril structure and formation
    • Hall C.K., and Wagoner V.A. Computational approaches to fibril structure and formation. Methods Enzymol. 412 (2006) 338-365
    • (2006) Methods Enzymol. , vol.412 , pp. 338-365
    • Hall, C.K.1    Wagoner, V.A.2
  • 27
    • 3242887525 scopus 로고    scopus 로고
    • STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
    • Heinig M., and Frishman D. STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Nucl. Aci. Res. 32 (2004) W500-W502
    • (2004) Nucl. Aci. Res. , vol.32
    • Heinig, M.1    Frishman, D.2
  • 28
    • 0028929583 scopus 로고
    • Free energy balance in protein folding
    • Honig B., and Yang A.S. Free energy balance in protein folding. Adv. Protein Chem. 46 (1995) 27-58
    • (1995) Adv. Protein Chem. , vol.46 , pp. 27-58
    • Honig, B.1    Yang, A.S.2
  • 29
    • 0026587310 scopus 로고
    • Co-operative interactions during protein folding
    • Horovitz A., and Fersht A.R. Co-operative interactions during protein folding. J. Mol. Biol. 224 (1992) 733-740
    • (1992) J. Mol. Biol. , vol.224 , pp. 733-740
    • Horovitz, A.1    Fersht, A.R.2
  • 31
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9 (2002) 646-652
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 33
    • 2542455537 scopus 로고    scopus 로고
    • Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease
    • Klein W.L., Stine Jr. W.B., and Teplow D.B. Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease. Neurobiol. Aging 25 (2004) 569-580
    • (2004) Neurobiol. Aging , vol.25 , pp. 569-580
    • Klein, W.L.1    Stine Jr., W.B.2    Teplow, D.B.3
  • 34
    • 0033621165 scopus 로고    scopus 로고
    • Amyloid diseases: Abnormal protein aggregation in neurodegeneration
    • Koo E.H., Lansbury Jr. P.T., and Kelly J.W. Amyloid diseases: Abnormal protein aggregation in neurodegeneration. Proc. Natl. Acad. Sci. USA 96 (1999) 9989-9990
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9989-9990
    • Koo, E.H.1    Lansbury Jr., P.T.2    Kelly, J.W.3
  • 35
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 38
    • 27244440859 scopus 로고    scopus 로고
    • From computational quantum chemistry to computational biology: Experiments and computations are (full) partners
    • Ma B., and Nussinov R. From computational quantum chemistry to computational biology: Experiments and computations are (full) partners. Phys. Biol. 1 (2004) P23-P26
    • (2004) Phys. Biol. , vol.1
    • Ma, B.1    Nussinov, R.2
  • 39
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen H.D., and Hall C.K. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA 101 (2004) 16180-16185
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 40
    • 10044280719 scopus 로고    scopus 로고
    • Phase diagrams describing fibrillization by polyalanine peptides
    • Nguyen H.D., and Hall C.K. Phase diagrams describing fibrillization by polyalanine peptides. Biophys. J. 87 (2004) 4122-4134
    • (2004) Biophys. J. , vol.87 , pp. 4122-4134
    • Nguyen, H.D.1    Hall, C.K.2
  • 41
    • 15744382287 scopus 로고    scopus 로고
    • Kinetics of fibril formation by polyalanine peptides
    • Nguyen H.D., and Hall C.K. Kinetics of fibril formation by polyalanine peptides. J. Biol. Chem. 280 (2005) 9074-9082
    • (2005) J. Biol. Chem. , vol.280 , pp. 9074-9082
    • Nguyen, H.D.1    Hall, C.K.2
  • 45
    • 17644397372 scopus 로고    scopus 로고
    • Aβ40-Lactam (D23/K28) models a conformation highly favorable for nucleation of amyloid
    • Sciarretta K.L., Gordon D.J., Petkova A.T., Tycko R., and Meredith S.C. Aβ40-Lactam (D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry 44 (2005) 6003-6014
    • (2005) Biochemistry , vol.44 , pp. 6003-6014
    • Sciarretta, K.L.1    Gordon, D.J.2    Petkova, A.T.3    Tycko, R.4    Meredith, S.C.5
  • 46
    • 0033596337 scopus 로고    scopus 로고
    • Energetics of weak interactions in a β-hairpin peptide: Electrostatic and hydrophobic contributions to stability from lysine salt bridges
    • Searle M.S., Griffiths-Jones S.R., and Skinner-Smith H. Energetics of weak interactions in a β-hairpin peptide: Electrostatic and hydrophobic contributions to stability from lysine salt bridges. J. Acad. Chem. Soc. 121 (1999) 11615-11620
    • (1999) J. Acad. Chem. Soc. , vol.121 , pp. 11615-11620
    • Searle, M.S.1    Griffiths-Jones, S.R.2    Skinner-Smith, H.3
  • 47
    • 0035066332 scopus 로고    scopus 로고
    • Alzheimer's disease: Genes, proteins, and therapy
    • Selkoe D.J. Alzheimer's disease: Genes, proteins, and therapy. Physiol. Rev. 81 (2001) 741-766
    • (2001) Physiol. Rev. , vol.81 , pp. 741-766
    • Selkoe, D.J.1
  • 48
    • 0035882559 scopus 로고    scopus 로고
    • α-Helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model
    • Smith A.V., and Hall C.K. α-Helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model. Proteins 44 (2001) 344-360
    • (2001) Proteins , vol.44 , pp. 344-360
    • Smith, A.V.1    Hall, C.K.2
  • 49
    • 0035882537 scopus 로고    scopus 로고
    • Assembly of a tetrameric α-helical bundle: Computer simulations on an intermediate-resolution protein model
    • Smith A.V., and Hall C.K. Assembly of a tetrameric α-helical bundle: Computer simulations on an intermediate-resolution protein model. Proteins 44 (2001) 376-391
    • (2001) Proteins , vol.44 , pp. 376-391
    • Smith, A.V.1    Hall, C.K.2
  • 50
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow C.D., Nguyen N., Pande V.S., and Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420 (2002) 102-106
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, N.2    Pande, V.S.3    Gruebele, M.4
  • 51
    • 0032606941 scopus 로고    scopus 로고
    • Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
    • Takada S., Luthey-Schulten Z., and Wolynes P.G. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer. J. Chem. Phys. 110 (1999) 11616-11629
    • (1999) J. Chem. Phys. , vol.110 , pp. 11616-11629
    • Takada, S.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 52
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulations
    • Taketomi H., Ueda Y., and Gō N. Studies on protein folding, unfolding and fluctuations by computer simulations. Int. J. Peptide Protein Res. 7 (1975) 445-459
    • (1975) Int. J. Peptide Protein Res. , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 53
    • 0033516705 scopus 로고    scopus 로고
    • The packing density in proteins: Standard radii and volumes
    • Tsai J., Taylor R., Chothia C., and Gerstein M. The packing density in proteins: Standard radii and volumes. J. Mol. Biol. 290 (1999) 253-266
    • (1999) J. Mol. Biol. , vol.290 , pp. 253-266
    • Tsai, J.1    Taylor, R.2    Chothia, C.3    Gerstein, M.4
  • 54
    • 33749509894 scopus 로고    scopus 로고
    • Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy
    • in press
    • Tycko R. Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy. Methods Enzymol. 413 (2006) in press
    • (2006) Methods Enzymol. , vol.413
    • Tycko, R.1
  • 57
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to molecular dynamics of proteins in solution
    • Wesson L., and Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1 (1992) 227-235
    • (1992) Protein Sci. , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2
  • 59
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic B., Snow C.D., Shirts M.R., and Pande V.S. Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323 (2002) 927-937
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 60
    • 0042561888 scopus 로고    scopus 로고
    • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    • Zagrovic B., and Pande V.S. Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study. J. Comput. Chem. 24 (2003) 1432-1436
    • (2003) J. Comput. Chem. , vol.24 , pp. 1432-1436
    • Zagrovic, B.1    Pande, V.S.2
  • 61
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang C., Vasmatzis G., Cornette J.L., and DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267 (1997) 707-726
    • (1997) J. Mol. Biol. , vol.267 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4
  • 62
    • 2942694535 scopus 로고    scopus 로고
    • The dependence of all-atom statistical potentials on structural training database
    • Zhang C., Liu S., Zhou H., and Zhou Y. The dependence of all-atom statistical potentials on structural training database. Biophys. J. 86 (2004) 3349-3358
    • (2004) Biophys. J. , vol.86 , pp. 3349-3358
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 64
    • 0001351693 scopus 로고    scopus 로고
    • First-order disorder-to-order transition in an isolated homopolymer model
    • Zhou Y., Hall C.K., and Karplus M. First-order disorder-to-order transition in an isolated homopolymer model. Phys. Rev. Lett. 77 (1996) 2822-2825
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 2822-2825
    • Zhou, Y.1    Hall, C.K.2    Karplus, M.3
  • 65
    • 0001015060 scopus 로고    scopus 로고
    • Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte-Carlo simulations of system with square-well interactions
    • Zhou Y., Karplus M., Wichert J.M., and Hall C.K. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte-Carlo simulations of system with square-well interactions. J. Chem. Phys. 107 (1997) 10691-10708
    • (1997) J. Chem. Phys. , vol.107 , pp. 10691-10708
    • Zhou, Y.1    Karplus, M.2    Wichert, J.M.3    Hall, C.K.4
  • 66
    • 0031475159 scopus 로고    scopus 로고
    • Folding thermodynamics of a three-helix-bundle protein
    • Zhou Y., and Karplus M. Folding thermodynamics of a three-helix-bundle protein. Proc. Natl. Acad. Sci. USA 94 (1997) 14429-14432
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 14429-14432
    • Zhou, Y.1    Karplus, M.2
  • 67
    • 0033527768 scopus 로고    scopus 로고
    • Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis
    • Zhou Y., and Karplus M. Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis. J. Mol. Biol. 293 (1999) 917-951
    • (1999) J. Mol. Biol. , vol.293 , pp. 917-951
    • Zhou, Y.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.