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Volumn 31, Issue 5, 2013, Pages 441-452

The intrinsic stability of the human prion β-sheet region investigated by molecular dynamics

Author keywords

Computer simulations; Neurodegenerative diseases; Prion peptide stability; Prion toxicity

Indexed keywords

PRION PROTEIN;

EID: 84879195454     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.703070     Document Type: Article
Times cited : (2)

References (66)
  • 3
    • 77956941468 scopus 로고    scopus 로고
    • Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease
    • Apostol, M.I., Sawaya, M.R., Cascio, D., & Eisenberg, D. (2010). Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease. The Journal of Biological Chemistry, 285, 29671-29675.
    • (2010) The Journal of Biological Chemistry , vol.285 , pp. 29671-29675
    • Apostol, M.I.1    Sawaya, M.R.2    Cascio, D.3    Eisenberg, D.4
  • 4
    • 79953183597 scopus 로고    scopus 로고
    • Atomic structures suggest determinants of transmission barriers in mammalian prion disease
    • Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., & Eisenberg, D. (2011). Atomic structures suggest determinants of transmission barriers in mammalian prion disease. Biochemistry, 50, 2456-2463.
    • (2011) Biochemistry , vol.50 , pp. 2456-2463
    • Apostol, M.I.1    Wiltzius, J.J.2    Sawaya, M.R.3    Cascio, D.4    Eisenberg, D.5
  • 5
    • 18144416596 scopus 로고    scopus 로고
    • The presence of valine at residue 129 in human prion protein accelerates amyloid formation
    • Baskakov, I., Disterer, P., Breydo, L., Shaw, M., Gill, A., James, W., & Tahiri-Alaoui, A. (2005). The presence of valine at residue 129 in human prion protein accelerates amyloid formation. FEBS Letters, 579, 2589-2596.
    • (2005) FEBS Letters , vol.579 , pp. 2589-2596
    • Baskakov, I.1    Disterer, P.2    Breydo, L.3    Shaw, M.4    Gill, A.5    James, W.6    Tahiri-Alaoui, A.7
  • 7
    • 61749092017 scopus 로고    scopus 로고
    • Structural domains and main-chain flexibility in prion proteins
    • Blinov, N., Berjanskii, M., Wishart, D.S., & Stepanova, M. (2009). Structural domains and main-chain flexibility in prion proteins. Biochemistry, 48, 1488-1497.
    • (2009) Biochemistry , vol.48 , pp. 1488-1497
    • Blinov, N.1    Berjanskii, M.2    Wishart, D.S.3    Stepanova, M.4
  • 8
    • 0028256033 scopus 로고
    • Iatrogenic Creutzfeldt-Jakob disease: An example of the interplay between ancient genes and modern medicine[Raise last author name query]
    • Brown, P., Cervenakova, L., Goldfarb, L.G., McCombie, W.R., Rubenstein, R., Will, R.G., ...Gajdusek, D.C. (1994). Iatrogenic Creutzfeldt-Jakob disease: An example of the interplay between ancient genes and modern medicine[Raise last author name query]. Neurology, 44, 291-293.
    • (1994) Neurology , vol.44 , pp. 291-293
    • Brown, P.1    Cervenakova, L.2    Goldfarb, L.G.3    McCombie, W.R.4    Rubenstein, R.5    Will, R.G.6    Gajdusek, D.C.7
  • 9
    • 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. The Journal of Biological Chemistry, 278, 35592-35596.
    • (2003) The Journal of Biological Chemistry , vol.278 , pp. 35592-35596
    • Calzolai, L.1    Zahn, R.2
  • 11
    • 78149436073 scopus 로고    scopus 로고
    • Diverse effects on the native beta-sheet of the human prion protein due to disease-associated mutations
    • Chen, W., van der Kamp, M.W., & Daggett, V. (2010). Diverse effects on the native beta-sheet of the human prion protein due to disease-associated mutations. Biochemistry, 49, 9874-9881.
    • (2010) Biochemistry , vol.49 , pp. 9874-9881
    • Chen, W.1    Van Der Kamp, M.W.2    Daggett, V.3
  • 12
    • 31944435727 scopus 로고    scopus 로고
    • The determinants of stability in the human prion protein: Insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions
    • Colacino, S., Tiana, G., Broglia, R.A., & Colombo, G. (2006). The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions. Proteins, 62, 698-707.
    • (2006) Proteins , vol.62 , pp. 698-707
    • Colacino, S.1    Tiana, G.2    Broglia, R.A.3    Colombo, G.4
  • 13
    • 0034916581 scopus 로고    scopus 로고
    • Prion diseases of humans and animals: Their causes and molecular basis
    • Collinge, J. (2001). Prion diseases of humans and animals: their causes and molecular basis. Annual Review of Neuroscience, 24, 519-550.
    • (2001) Annual Review of Neuroscience , vol.24 , pp. 519-550
    • Collinge, J.1
  • 14
    • 36049020231 scopus 로고    scopus 로고
    • A general model of prion strains and their pathogenicity
    • Collinge, J., & Clarke, A.R. (2007). A general model of prion strains and their pathogenicity. Science, 318, 930-936.
    • (2007) Science , vol.318 , pp. 930-936
    • Collinge, J.1    Clarke, A.R.2
  • 15
    • 3543030409 scopus 로고    scopus 로고
    • Hydration and packing effects on prion folding and beta-sheet conversion. High pressure spectroscopy and pressure perturbation calorimetry studies
    • Cordeiro, Y., Kraineva, J., Ravindra, R., Lima, L.M., Gomes, M.P., Foguel, D., ...Silva, J.L. (2004). Hydration and packing effects on prion folding and beta-sheet conversion. High pressure spectroscopy and pressure perturbation calorimetry studies. The Journal of Biological Chemistry, 279, 32354-32359.
    • (2004) The Journal of Biological Chemistry , vol.279 , pp. 32354-32359
    • Cordeiro, Y.1    Kraineva, J.2    Ravindra, R.3    Lima, L.M.4    Gomes, M.P.5    Foguel, D.6    Silva, J.L.7
  • 16
    • 69549129200 scopus 로고    scopus 로고
    • Human prion protein helices: Studying their stability by molecular dynamics simulations
    • Costantini, S., & Facchiano, A.M. (2009). Human prion protein helices: Studying their stability by molecular dynamics simulations. Protein and Peptide Letters, 16, 1057-1062.
    • (2009) Protein and Peptide Letters , vol.16 , pp. 1057-1062
    • Costantini, S.1    Facchiano, A.M.2
  • 17
    • 33846823909 scopus 로고
    • Part Mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • Darden, T., York, D. & Pedersen, L. (1993). Part Mesh Ewald: An N-log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089-10092.
    • (1993) Journal of Chemical Physics , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 18
    • 33646528658 scopus 로고    scopus 로고
    • Water molecules as structural determinants among prions of low sequence identity
    • De Simone, A., Dodson, G.G., Fraternali, F., & Zagari, A. (2006). Water molecules as structural determinants among prions of low sequence identity. FEBS Letters, 580, 2488-2494.
    • (2006) FEBS Letters , vol.580 , pp. 2488-2494
    • De Simone, A.1    Dodson, G.G.2    Fraternali, F.3    Zagari, A.4
  • 20
    • 50349099883 scopus 로고    scopus 로고
    • Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses
    • De Simone, A., Esposito, L., Pedone, C., & Vitagliano, L. (2008). Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses. Biophysical Journal, 95, 1965-1973.
    • (2008) Biophysical Journal , vol.95 , pp. 1965-1973
    • De Simone, A.1    Esposito, L.2    Pedone, C.3    Vitagliano, L.4
  • 21
    • 34548221936 scopus 로고    scopus 로고
    • Structural and hydration properties of the partially unfolded states of the prion protein
    • De Simone, A., Zagari, A., & Derreumaux, P. (2007). Structural and hydration properties of the partially unfolded states of the prion protein. Biophysical Journal, 93, 1284-1292.
    • (2007) Biophysical Journal , vol.93 , pp. 1284-1292
    • De Simone, A.1    Zagari, A.2    Derreumaux, P.3
  • 22
    • 7444240183 scopus 로고    scopus 로고
    • Probing the instabilities in the dynamics of helical fragments from mouse PrPC
    • Dima, R.I., & Thirumalai, D. (2004). Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proceedings of the National Academy of Sciences USA, 101, 15335-15340.
    • (2004) Proceedings of the National Academy of Sciences USA , vol.101 , pp. 15335-15340
    • Dima, R.I.1    Thirumalai, D.2
  • 24
    • 79959887638 scopus 로고    scopus 로고
    • A diversity of assembly mechanisms of a generic amyloid fold
    • Eichner, T., & Radford, S.E. (2011). A diversity of assembly mechanisms of a generic amyloid fold. Molecular Cell, 43, 8-18.
    • (2011) Molecular Cell , vol.43 , pp. 8-18
    • Eichner, T.1    Radford, S.E.2
  • 25
    • 43849090507 scopus 로고    scopus 로고
    • Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations
    • Esposito, L., Paladino, A., Pedone, C., & Vitagliano, L. (2008). Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations. Biophysical Journal, 94, 4031-4040.
    • (2008) Biophysical Journal , vol.94 , pp. 4031-4040
    • Esposito, L.1    Paladino, A.2    Pedone, C.3    Vitagliano, L.4
  • 27
    • 73249121817 scopus 로고    scopus 로고
    • Unfolded-state structure and dynamics influence the fibril formation of human prion protein
    • Gerum, C., Silvers, R., Wirmer-Bartoschek, J., & Schwalbe, H. (2009). Unfolded-state structure and dynamics influence the fibril formation of human prion protein. Angewandte Chemie, 48, 9452-9456.
    • (2009) Angewandte Chemie , vol.48 , pp. 9452-9456
    • Gerum, C.1    Silvers, R.2    Wirmer-Bartoschek, J.3    Schwalbe, H.4
  • 28
    • 57649148788 scopus 로고    scopus 로고
    • Structural classification of toxic amyloid oligomers
    • Glabe, C.G. (2008). Structural classification of toxic amyloid oligomers. The Journal of Biological Chemistry, 283, 29639-29643.
    • (2008) The Journal of Biological Chemistry , vol.283 , pp. 29639-29643
    • Glabe, C.G.1
  • 29
    • 0026496257 scopus 로고
    • Fatal familial insomnia and familial Creutzfeldt- Jakob disease: Disease phenotype determined by a DNA polymorphism
    • Goldfarb, L.G., Petersen, R.B., Tabaton, M., Brown, P., LeBlanc, A.C., Montagna, P., ..., Pendelbury, W.W., et al. (1992). Fatal familial insomnia and familial Creutzfeldt- Jakob disease: disease phenotype determined by a DNA polymorphism. Science, 258, 806-808.
    • (1992) Science , vol.258 , pp. 806-808
    • Goldfarb, L.G.1    Petersen, R.B.2    Tabaton, M.3    Brown, P.4    Leblanc, A.C.5    Montagna, P.6    Pendelbury, W.W.7
  • 32
  • 34
    • 3142615402 scopus 로고    scopus 로고
    • The residue 129 polymorphism in human prion protein does not confer susceptibility to Creutzfeldt-Jakob disease by altering the structure or global stability of PrPC
    • Hosszu, L.L., Jackson, G.S., Trevitt, C.R., Jones, S., Batchelor, M., Bhelt, D., ...Collinge, J. (2004). The residue 129 polymorphism in human prion protein does not confer susceptibility to Creutzfeldt-Jakob disease by altering the structure or global stability of PrPC. The Journal of Biological Chemistry, 279, 28515-28521.
    • (2004) The Journal of Biological Chemistry , vol.279 , pp. 28515-28521
    • Hosszu, L.L.1    Jackson, G.S.2    Trevitt, C.R.3    Jones, S.4    Batchelor, M.5    Bhelt, D.6    Collinge, J.7
  • 36
    • 14844284588 scopus 로고    scopus 로고
    • The role of electrostatic interaction in triggering the unraveling of stable helix 1 in normal prion protein. A molecular dynamics simulation investigation
    • Ji, H.F., Zhang, H.Y., & Shen, L. (2005). The role of electrostatic interaction in triggering the unraveling of stable helix 1 in normal prion protein. A molecular dynamics simulation investigation. Journal of Biomolecular Structure & Dynamics, 22, 563-570.
    • (2005) Journal of Biomolecular Structure & Dynamics , vol.22 , pp. 563-570
    • Ji, H.F.1    Zhang, H.Y.2    Shen, L.3
  • 37
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W.L., Maxwell, D.S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118, 11225-11236.
    • (1996) Journal of the American Chemical Society , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 38
    • 0037108168 scopus 로고    scopus 로고
    • Locally disordered conformer of the hamster prion protein: A crucial intermediate to PrPSc?
    • Kuwata, K., Li, H., Yamada, H., Legname, G., Prusiner, S.B., Akasaka, K., & James, T.L. (2002). Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc? Biochemistry, 41, 12277-12283.
    • (2002) Biochemistry , vol.41 , pp. 12277-12283
    • Kuwata, K.1    Li, H.2    Yamada, H.3    Legname, G.4    Prusiner, S.B.5    Akasaka, K.6    James, T.L.7
  • 39
    • 75649120399 scopus 로고    scopus 로고
    • Conformational diversity in prion protein variants influences intermolecular betasheet formation
    • Lee, S., Antony, L., Hartmann, R., Knaus, K.J., Surewicz, K., Surewicz, W.K., & Yee, V.C. (2010). Conformational diversity in prion protein variants influences intermolecular betasheet formation. The EMBO journal, 29, 251-262.
    • (2010) The EMBO Journal , vol.29 , pp. 251-262
    • Lee, S.1    Antony, L.2    Hartmann, R.3    Knaus, K.J.4    Surewicz, K.5    Surewicz, W.K.6    Yee, V.C.7
  • 41
    • 33748689799 scopus 로고    scopus 로고
    • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    • Ma, B., & Nussinov, R. (2006). Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Current Opinion in Chemical Biology, 10, 445-452.
    • (2006) Current Opinion in Chemical Biology , vol.10 , pp. 445-452
    • Ma, B.1    Nussinov, R.2
  • 42
    • 0242684410 scopus 로고    scopus 로고
    • Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics
    • Mead, S., Stumpf, M.P., Whitfield, J., Beck, J.A., Poulter, M., Campbell, T., ...Collinge, J. (2003). Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics. Science, 300, 640-643.
    • (2003) Science , vol.300 , pp. 640-643
    • Mead, S.1    Stumpf, M.P.2    Whitfield, J.3    Beck, J.A.4    Poulter, M.5    Campbell, T.6    Collinge, J.7
  • 44
    • 0025820942 scopus 로고
    • Homozygous prion protein genotype predisposes to sporadic Creutzfeldt-Jakob disease
    • Palmer, M.S., Dryden, A.J., Hughes, J.T., & Collinge, J. (1991). Homozygous prion protein genotype predisposes to sporadic Creutzfeldt-Jakob disease. Nature, 352, 340-342.
    • (1991) Nature , vol.352 , pp. 340-342
    • Palmer, M.S.1    Dryden, A.J.2    Hughes, J.T.3    Collinge, J.4
  • 46
    • 79959442590 scopus 로고    scopus 로고
    • Phenotypic variability of sporadic human prion disease and its molecular basis: Past, present, and future
    • Parchi, P., Strammiello, R., Giese, A., & Kretzschmar, H. (2011). Phenotypic variability of sporadic human prion disease and its molecular basis: past, present, and future. Acta neuropathologica, 121, 91-112.
    • (2011) Acta Neuropathologica , vol.121 , pp. 91-112
    • Parchi, P.1    Strammiello, R.2    Giese, A.3    Kretzschmar, H.4
  • 50
    • 79952916684 scopus 로고    scopus 로고
    • Normal modes of prion proteins: From native to infectious particle
    • Samson, A.O., & Levitt, M. (2011). Normal modes of prion proteins: From native to infectious particle. Biochemistry, 50, 2243-2248.
    • (2011) Biochemistry , vol.50 , pp. 2243-2248
    • Samson, A.O.1    Levitt, M.2
  • 51
    • 0037403022 scopus 로고    scopus 로고
    • Impact of the tail and mutations G131V and M129V on prion protein flexibility
    • Santini, S., Claude, J.B., Audic, S., & Derreumaux, P. (2003). Impact of the tail and mutations G131V and M129V on prion protein flexibility. Proteins, 51, 258-265.
    • (2003) Proteins , vol.51 , pp. 258-265
    • Santini, S.1    Claude, J.B.2    Audic, S.3    Derreumaux, P.4
  • 53
    • 79960065022 scopus 로고    scopus 로고
    • Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
    • Sievers, S.A., Karanicolas, J., Chang, H.W., Zhao, A., Jiang, L., Zirafi, O., ...Eisenberg, D. (2011). Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature, 475, 96-100.
    • (2011) Nature , vol.475 , pp. 96-100
    • Sievers, S.A.1    Karanicolas, J.2    Chang, H.W.3    Zhao, A.4    Jiang, L.5    Zirafi, O.6    Eisenberg, D.7
  • 55
    • 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. Chemical Physics Letters, 314, 141-151.
    • (1999) Chemical Physics Letters , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 56
    • 3843131903 scopus 로고    scopus 로고
    • Methionine 129 variant of human prion protein oligomerizes more rapidly than the valine 129 variant: Implications for disease susceptibility to Creutzfeldt- Jakob disease
    • Tahiri-Alaoui, A., Gill, A.C., Disterer, P., & James, W. (2004). Methionine 129 variant of human prion protein oligomerizes more rapidly than the valine 129 variant: Implications for disease susceptibility to Creutzfeldt- Jakob disease. The Journal of Biological Chemistry, 279, 31390-31397.
    • (2004) The Journal of Biological Chemistry , vol.279 , pp. 31390-31397
    • Tahiri-Alaoui, A.1    Gill, A.C.2    Disterer, P.3    James, W.4
  • 57
    • 33746698975 scopus 로고    scopus 로고
    • The physical basis of how prion conformations determine strain phenotypes
    • Tanaka, M., Collins, S.R., Toyama, B.H., & Weissman, J.S. (2006). The physical basis of how prion conformations determine strain phenotypes. Nature, 442, 585-589.
    • (2006) Nature , vol.442 , pp. 585-589
    • Tanaka, M.1    Collins, S.R.2    Toyama, B.H.3    Weissman, J.S.4
  • 61
    • 77949278013 scopus 로고    scopus 로고
    • Fibril fragmentation in amyloid assembly and cytotoxicity: When size matters
    • Xue, W.F., Hellewell, A.L., Hewitt, E.W., & Radford, S.E. (2010). Fibril fragmentation in amyloid assembly and cytotoxicity: When size matters. Prion, 4, 20-25.
    • (2010) Prion , vol.4 , pp. 20-25
    • Xue, W.F.1    Hellewell, A.L.2    Hewitt, E.W.3    Radford, S.E.4
  • 62
    • 67650421806 scopus 로고    scopus 로고
    • Studies on the structural stability of rabbit prion probed by molecular dynamics simulations
    • Zhang, J. (2009). Studies on the structural stability of rabbit prion probed by molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 27, 159-162.
    • (2009) Journal of Biomolecular Structure & Dynamics , vol.27 , pp. 159-162
    • Zhang, J.1
  • 63
    • 80052186920 scopus 로고    scopus 로고
    • The structural stability of wild-type horse prion protein
    • Zhang, J. (2011). The structural stability of wild-type horse prion protein. Journal of Biomolecular Structure & Dynamics, 29, 369-377.
    • (2011) Journal of Biomolecular Structure & Dynamics , vol.29 , pp. 369-377
    • Zhang, J.1
  • 64
    • 79955524483 scopus 로고    scopus 로고
    • Molecular dynamics studies on the structural stability of wild-type dog prion protein
    • Zhang, J., & Liu, D.D. (2011). Molecular dynamics studies on the structural stability of wild-type dog prion protein. Journal of Biomolecular Structure & Dynamics, 28, 861-869.
    • (2011) Journal of Biomolecular Structure & Dynamics , vol.28 , pp. 861-869
    • Zhang, J.1    Liu, D.D.2
  • 65
    • 66949116095 scopus 로고    scopus 로고
    • Investigation of the effect of glycosylation on human prion protein by molecular dynamics
    • Zhong, L., & Xie, J. (2009). Investigation of the effect of glycosylation on human prion protein by molecular dynamics. Journal of Biomolecular Structure & Dynamics, 26, 525-533.
    • (2009) Journal of Biomolecular Structure & Dynamics , vol.26 , pp. 525-533
    • Zhong, L.1    Xie, J.2


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