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Collegamenti



Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association (143 visite)

Vitagliano L, Esposito L, Pedone C, De Simone A

Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Dec 26; 377(4): 1036-1041.

Tipo di articolo: Journal Article, Research Support, Non-U. S. Gov'T,

Impact factor: 2.648

Impact factor a 5 anni: 2.823


Parole chiave: Amyloid, Neurodegenerative Diseases, Protein Aggregation, Yeast Prion, Glycylasparaginylasparaginylglutaminylglutaminylasparaginyltyrosine, Peptide, Unclassified Drug, Article, Beta Sheet, Molecular Dynamics, Peptide Analysis, Priority Journal, Protein Interaction, Protein Stability, Amino Acid Sequence, Humans, Protein Structure, Secondary,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-56349091416&partnerID=40&md5=a280de3e705594e8f8eff363be369913

Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel beta-sheets. The data show that GNNQQNY preference for parallel or antiparallel beta-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.
*** IBB - CNR ***

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

Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
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Walsh, D.M., Selkoe, D.J., A beta oligomers-a decade of discovery (2007) J. Neurochem., 101, pp. 1172-1184

Nelson, R., Sawaya, M.R., Balbirnie, M., Madsen, A.O., Riekel, C., Grothe, R., Eisenberg, D., Structure of the cross-beta spine of amyloid-like fibrils (2005) Nature, 435, pp. 773-778

Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Eisenberg, D., Atomic structures of amyloid cross-beta spines reveal varied steric zippers (2007) Nature, 447, pp. 453-457

Gsponer, J., Haberthur, U., Caflisch, A., The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35 (2003) Proc. Natl. Acad. Sci. USA, 100, pp. 5154-5159

De Simone, A., Esposito, L., Pedone, C., Vitagliano, L., Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses (2008) Biophys. J., 95, pp. 1965-1973

Meli, M., Morra, G., Colombo, G., Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations (2008) Biophys. J., 94, pp. 4414-4426

Esposito, L., Paladino, A., Pedone, C., Vitagliano, L., Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations (2008) Biophys. J., 94, pp. 4031-4040

Strodel, B., Whittleston, C.S., Wales, D.J., Thermodynamics and kinetics of aggregation for the GNNQQNY peptide (2007) J. Am. Chem. Soc., 129, pp. 16005-16014

Zhang, Z., Chen, H., Bai, H., Lai, L., Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35 (2007) Biophys. J., 93, pp. 1484-1492

van der Wel, P.C., Lewandowski, J.R., Griffin, R.G., Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p (2007) J. Am. Chem. Soc., 129, pp. 5117-5130

Zheng, J., Ma, B., Tsai, C.J., Nussinov, R., Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35 (2006) Biophys. J., 91, pp. 824-833

Lipfert, J., Franklin, J., Wu, F., Doniach, S., Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing (2005) J. Mol. Biol., 349, pp. 648-658

Diaz-Avalos, R., Long, C., Fontano, E., Balbirnie, M., Grothe, R., Eisenberg, D., Caspar, D.L., Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide (2003) J. Mol. Biol., 330, pp. 1165-1175

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Guo, Z., Eisenberg, D., The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold (2008) Protein Sci., 17, pp. 1617-1623

Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E., GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation (2008) J. Chem. Theory Comput., 4, pp. 435-447

De Simone, A., Zagari, A., Derreumaux, P., Structural and hydration properties of the partially unfolded states of the prion protein (2007) Biophys. J., 93, pp. 1284-1292

Santini, S., Mousseau, N., Derreumaux, P., In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets (2004) J. Am. Chem. Soc., 126, pp. 11509-11516

Colombo, G., Meli, M., De Simone, A., Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A (2008) Proteins, 70, pp. 863-872

Strodel, B., Wales, D.J., Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide (2008) J. Chem. Theor. Comput., 4, pp. 657-672

Chimon, S., Shaibat, M.A., Jones, C.R., Calero, D.C., Aizezi, B., Ishii, Y., Evidence of fibril-like beta-sheet structures in a neurotoxic amyloid intermediate of Alzheimer's beta-amyloid (2007) Nat. Struct. Mol. Biol., 14, pp. 1157-1164


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5 Records (4 escludendo Abstract e Conferenze).
Impact factor totale: 12.716 (12.716 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 12.225 (12.225 escludendo Abstract e Conferenze).







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