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The Intrinsic Stability Of The Human Prion Beta-Sheet Region Investigated By Molecular Dynamics (144 visite)

De Simonea A, Stanzione F, Marasco D, Vitagliano L, Esposito L

Journal Of Biomolecular Structure & Dynamics, 2013 May 1; 31(5): 441-452.

Tipo di articolo: Journal Article,

Impact factor: 2.983

Impact factor a 5 anni: 2.165


Parole chiave: Computer Simulations, Neurodegenerative Diseases, Prion Peptide Stability, Prion Toxicity, Prion Protein, Article, Beta Sheet, Carboxy Terminal Sequence, Cytotoxicity, Dimerization, Homozygosity, Human, Molecular Dynamics, Molecular Interaction, Point Mutation, Prion Disease, Priority Journal, Protein Aggregation, Protein Analysis, Protein Assembly, Protein Conformation, Protein Folding, Protein Stability, Protein Structure, Amino Acid Sequence, Hydrogen Bonding, Molecular Dynamics Simulation, Missense, Secondary, Thermodynamics,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84879195454&partnerID=40&md5=6898649c6a239c30d693017e4f7f93d8

Human prion diseases are neurodegenerative disorders associated to the misfolding of the prion protein (PrP). Common features of prion disorders are the fibrillar amyloid deposits and the formation of prefibrillar oligomeric species also suggested as the origin of cytotoxicity associated with diseases. Although the process of PrP misfolding has been extensively investigated, many crucial aspects of this process remain unclear. We have here carried out a molecular dynamics study to evaluate the intrinsic dynamics of PrP β-sheet, a region that is believed to play a crucial role in prion aggregation. Moreover, as this region mediates protein association in dimeric assemblies frequently observed in prion crystallographic investigations, we also analyzed the dynamics of these intermolecular interactions. The extensive sampling of replica exchange shows that the native antiparallel β-structure of the prion is endowed with a remarkable stability. Therefore, upon unfolding, the persistence of a structured β-region may seed molecular association and influence the subsequent phases of the aggregation process. The analysis of the four-stranded β-sheet detected in the dimeric assemblies of PrP shows a tendency of this region to form dynamical structured states. The impact on the β-sheet structure and dynamics of disease associated point mutations has also been evaluated. © 2012 Taylor & Francis.
*** IBB - CNR ***

Division of Molecular Biosciences, Imperial College South Kensington Campus, London, SW7 2AZ, United Kingdom

Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy

Dipartimento Delle Scienze Biologiche, Universit di Napoli Federico II, Napoli, Italy
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Apostol, M.I., Sawaya, M.R., Cascio, D., Eisenberg, D., Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease (2010) The Journal of Biological Chemistry, 285, pp. 29671-29675

Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D., Atomic structures suggest determinants of transmission barriers in mammalian prion disease (2011) Biochemistry, 50, pp. 2456-2463

Dima, R.I., Thirumalai, D., Probing the instabilities in the dynamics of helical fragments from mouse PrPC (2004) Proceedings of the National Academy of Sciences USA, 101, pp. 15335-15340

Glabe, C.G., Structural classification of toxic amyloid oligomers (2008) The Journal of Biological Chemistry, 283, pp. 29639-29643

Goldfarb, L.G., Petersen, R.B., Tabaton, M., Brown, P., Leblanc, A.C., Montagna, P., Pendelbury, W.W., Fatal familial insomnia and familial Creutzfeldt- Jakob disease: Disease phenotype determined by a DNA polymorphism (1992) Science, 258, pp. 806-808

Haire, L.F., Whyte, S.M., Vasisht, N., Gill, A.C., Verma, C., Bayley, P.M., The crystal structure of the globular domain of sheep prion protein (2004) Journal of Molecular Biology, 336, pp. 1175-1183

Hauw, J.J., Sazdovitch, V., Laplanche, J.L., Peoc'H, K., Kopp, N., Kemeny, J., Alperovitch, A., Neuropathologic variants of sporadic Creutzfeldt-Jakob disease and codon 129 of PrP gene (2000) Neurology, 54, pp. 1641-1646

Hosszu, L.L., Baxter, N.J., Jackson, G.S., Power, A., Clarke, A.R., Waltho, J.P., Collinge, J., Structural mobility of the human prion protein probed by backbone hydrogen exchange (1999) Nature Structural & Molecular Biology, 6, pp. 740-743

Hosszu, L.L., Jackson, G.S., Trevitt, C.R., Jones, S., Batchelor, M., Bhelt, D., Collinge, J., 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 (2004) The Journal of Biological Chemistry, 279, pp. 28515-28521

Ji, H.F., Zhang, H.Y., Shen, L., The role of electrostatic interaction in triggering the unraveling of stable helix 1 in normal prion protein. A molecular dynamics simulation investigation (2005) Journal of Biomolecular Structure & Dynamics, 22, pp. 563-570

Jorgensen, W.L., Maxwell, D.S., Tirado-Rives, J., Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids (1996) Journal of the American Chemical Society, 118, pp. 11225-11236

Liu, C., Sawaya, M.R., Cheng, P.N., Zheng, J., Nowick, J.S., Eisenberg, D., Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic beta-sheet mimics (2011) Journal of the American Chemical Society, 133, pp. 6736-6744

O'Brien, E.P., Okamoto, Y., Straub, J.E., Brooks, B.R., Thirumalai, D., Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils (2009) The Journal of Physical Chemistry B, 113, pp. 14421-14430

Palmer, M.S., Dryden, A.J., Hughes, J.T., Collinge, J., Homozygous prion protein genotype predisposes to sporadic Creutzfeldt-Jakob disease (1991) Nature, 352, pp. 340-342

Panegyres, P.K., Toufexis, K., Kakulas, B.A., Cernevakova, L., Brown, P., Ghetti, B., Dlouhy, S.R., A new PRNP mutation (G131V) associated with Gerstmann- Straussler-Scheinker disease (2001) Archives of Neurology, 58, pp. 1899-1902

Prusiner, S.B., Prions (1998) Proceedings of the National Academy of Sciences USA, 95, pp. 13363-13383

Richardson, J.S., Richardson, D.C., Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation (2002) Proceedings of the National Academy of Sciences USA, 99, pp. 2754-2759

Samson, A.O., Levitt, M., Normal modes of prion proteins: From native to infectious particle (2011) Biochemistry, 50, pp. 2243-2248

Sievers, S.A., Karanicolas, J., Chang, H.W., Zhao, A., Jiang, L., Zirafi, O., Eisenberg, D., Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation (2011) Nature, 475, pp. 96-100

Viles, J.H., Donne, D., Kroon, G., Prusiner, S.B., Cohen, F.E., Dyson, H.J., Wright, P.E., Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics (2001) Biochemistry, 40, pp. 2743-2753

Xue, W.F., Hellewell, A.L., Hewitt, E.W., Radford, S.E., Fibril fragmentation in amyloid assembly and cytotoxicity: When size matters (2010) Prion, 4, pp. 20-25

Zhang, J., Liu, D.D., Molecular dynamics studies on the structural stability of wild-type dog prion protein (2011) Journal of Biomolecular Structure & Dynamics, 28, pp. 861-869

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Bonomo RP, Di Natale G, Rizzarelli E, Tabbì G, Vagliasindi LI
* Copper(II) complexes of prion protein PEG11-tetraoctarepeat fragment: spectroscopic and voltammetric studies (88 visite)
Dalton Trans (ISSN: 1477-9226, 1477-7922, 1477-9234), 2009 Apr 14; (14): 2637-2646.
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Calabrese V, Cornelius C, Mancuso C, Barone E, Calafato S, Bates T, Rizzarelli E, Kostova AT
* Vitagenes, dietary antioxidants and neuroprotection in neurodegenerative diseases (151 visite)
Frontiers In Bioscience (ISSN: 1093-4715, 1093-9946), 2009 Jan 1; 14: 376-397.
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Ronga L, Palladino P, Ragone R, Benedetti E, Rossi F
* A thermodynamic approach to the conformational preferences of the 180-195 segment derived from the human prion protein α2-helix (94 visite)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009; 15(1): 30-35.
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La Mendola D, Pietropaolo A, Pappalardo G, Zannoni C, Rizzarelli E
* Prion proteins leading to neurodegeneration (129 visite)
Current Alzheimer Research (ISSN: 1567-2050), 2008 Dec; 5(6): 579-590.
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Bonomo RP, Pappalardo G, Rizzarelli E, Tabbì G, Vagliasindi LI
* Studies of nitric oxide interaction with mono- and dinuclear copper(II) complexes of prion protein bis-octarepeat fragments (131 visite)
Dalton Trans (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2008 Sep 7; (29): 3805-3816.
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Ronga L, Palladino P, Saviano G, Tancredi T, Benedetti E, Ragone R, Rossi F
* Structural characterization of a neurotoxic threonine-rich peptide corresponding to the human prion protein α2-helical 180-195 segment and comparison with full-length α2-helix-derived peptides (128 visite)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2008; 14(10): 1096-1102.
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Bonomo RP, Pappalardo G, Rizzarelli E, Santoro AM, Tabbì G, Vagliasindi LI
* Nitrogen oxide interaction with copper complexes formed by small peptides belonging to the prion protein octa-repeat region (133 visite)
Dalton Trans (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2007 Apr 14; (14): 1400-1408.
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Ronga L, Langella E, Palladino P, Marasco D, Tizzano B, Saviano M, Pedone C, Improta R, Ruvo M
* Does Tetracycline Bind Helix 2 Of Prion? An Integrated Spectroscopical And Computational Study Of The Interaction Between The Antibiotic And Alpha Helix 2 Human Prion Protein Fragments (143 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Feb 15; 66(3): 707-715.
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Rao M, Russo F, Granata V, Berisio R, Zagari A, Gianfreda L
* Fate of prions in soil: Interaction of a recombinant ovine prion protein with synthetic humic-like mineral complexes (90 visite)
Soil Biol Biochem (ISSN: 0038-0717), 2007 Feb; 39(2): 493-504.
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Ronga L, Tizzano B, Palladino P, Ragone R, Urso E, Maffia M, Ruvo M, Benedetti E, Rossi F
* The prion protein: structural features and related toxic peptides (119 visite)
Chem Biol Drug Des Chemical Biology And Drug Design (ISSN: 1747-0277, 1747-0285), 2006 Sep; 68(3): 139-147.
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Langella E, Improta R, Crescenzi O, Barone V
* Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (148 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.
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Granata V, Palladino P, Tizzano B, Negro A, Berisio R, Zagari A
* The effect of the osmolyte trimethylamine N-oxide on the stability of the prion protein at low pH (75 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2006 Jun 15; 82(3): 234-240.
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Palladino P, Ronga L, Tizzano B, Rossi F, Ragone R, Tancredi T, Saviano G, Facchiano A, Costantini S, Ruvo M, Benedetti E
* Prion protein misfolding: Conformational stability of the alpha 2-helix (81 visite)
Understanding Biology Using Peptides, 2006; N/D: N/D-N/D.
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Tizzano B, Palladino P, De Capua A, Marasco D, Rossi F, Benedetti E, Pedone C, Ragone R, Ruvo M
* The Human Prion Protein Alpha2 Helix: A Thermodynamic Study Of Its Conformational Preferences (106 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2005 Apr 1; 59(1): 72-79.
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Di Natale G, Impellizzeri G, Pappalardo G
* Conformational properties of peptide fragments homologous to the 106-114 and 106-126 residues of the human prion protein: a CD and NMR spectroscopic study (115 visite)
Org Biomol Chem (ISSN: 1477-0520, 1477-0539, 1477-0539electronic), 2005 Feb 7; 3(3): 490-497.
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Bonomo RP, Cucinotta V, Giuffrida A, Impellizzeri G, Magrì A, Pappalardo G, Rizzarelli E, Santoro AM, Tabbì G, Vagliasindi LI
* A re-investigation of copper coordination in the octa-repeats region of the prion protein (111 visite)
Dalton Trans (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2005 Jan 7; (1): 150-158.
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Langella E, Improta R, Barone V
* Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues (113 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.
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Brown DR, Guantieri V, Grasso G, Impellizzeri G, Pappalardo G, Rizzarelli E
* Copper(II) complexes of peptide fragments of the prion protein. Conformation changes induced by copper(II) and the binding motif in C-terminal protein region (124 visite)
J Chem Res (ISSN: 0162-0134, 1873-3344, 0162-0134print), 2004 Jan; 98(1): 133-143.
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Tizzano B, Marasco D, Benedetti E, De Capua A, Palladino P, Pedone C, Perretta G, Rossi F, Ragone R, Ruvo M
* Conformational conversion of prion proteins: Role synthetic PRP 173-195 fibrillogenic peptide (108 visite)
Peptide Revolution, 2004; N/D: N/D-N/D.
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Pappalardo G, Impellizzeri G, Campagna T
* Copper(II) binding of prion protein's octarepeat model peptides (141 visite)
Inorg Chim Acta (ISSN: 0020-1693), 2004; 357(1): 185-194.
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La Mendola D, Bonomo R, Maccarrone G, Pappalardo G, Rizzarelli E
* A thermodynamic and spectroscopic study on the copper(II) complexes with hexarepeats fragments of the avian prion protein (124 visite)
J Chem Res (ISSN: 0162-0134, 1873-3344, 0162-0134print), 2003 Jul 15; 96(1): N/D-N/D.
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Bonomo RP, Grasso D, Grasso G, Guantieri V, Impellizzeri G, La Rosa C, Milardi D, Pappalardo G, Tabbì G, Rizzarelli E
* Metal binding to prion protein (116 visite)
Metal-Ligand Interactions - Molecular Nano- Micro- And Macro-Systems In Complex Environments, 2003 Jan 01; 116: 21-39.
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Menziani MC, De Benedetti PG, Langella E, Barone V
* Seeking for binding determinants of the prion protein to human plasminogen (82 visite)
Mol Phys (ISSN: 0026-8976), 2003; 101(17): 2763-2773.
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36 Records (29 escludendo Abstract e Conferenze).
Impact factor totale: 110.413 (90.508 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 113.703 (92.419 escludendo Abstract e Conferenze).







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