2005
DOI: 10.1110/ps.051471205
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Prediction of aggregation rate and aggregation‐prone segments in polypeptide sequences

Abstract: The reliable identification of b-aggregating stretches in protein sequences is essential for the development of therapeutic agents for Alzheimer's and Parkinson's diseases, as well as other pathological conditions associated with protein deposition. Here, a model based on physicochemical properties and computational design of b-aggregating peptide sequences is shown to be able to predict the aggregation rate over a large set of natural polypeptide sequences. Furthermore, the model identifies aggregation-prone … Show more

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Cited by 201 publications
(226 citation statements)
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References 81 publications
(138 reference statements)
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“…It has been proposed that PrP c could undergo specific structural rearrangements modulated by binding with specific nucleic acids molecules, such as highly structured RNAs (Deleault et al 2003) or RNA aptamers (Mercey et al 2006). Several studies showed that residues 90-141 are crucial for the conversion from natural to pathological form (Tartaglia et al 2005(Tartaglia et al , 2008. Proske et al (2002) discovered an RNA aptamer, DP7, which binds with great affinity to an epitope located within residues 90-141 of hamster PrP (highly conserved in mouse and human sequences) (Supplemental Table 1).…”
Section: Prions and Rna Aptamersmentioning
confidence: 99%
“…It has been proposed that PrP c could undergo specific structural rearrangements modulated by binding with specific nucleic acids molecules, such as highly structured RNAs (Deleault et al 2003) or RNA aptamers (Mercey et al 2006). Several studies showed that residues 90-141 are crucial for the conversion from natural to pathological form (Tartaglia et al 2005(Tartaglia et al , 2008. Proske et al (2002) discovered an RNA aptamer, DP7, which binds with great affinity to an epitope located within residues 90-141 of hamster PrP (highly conserved in mouse and human sequences) (Supplemental Table 1).…”
Section: Prions and Rna Aptamersmentioning
confidence: 99%
“…[49,50] Conformational heterogeneity provides an additional driving force for the association of globules. For IDPs and partially unfolded proteins, the conformational ensemble in a poor solvent will be heterogeneous because there is no unique way to partition residues in the chain between the interior and the surface of a globule and conformations of equivalent compactness have equivalent stability.…”
Section: Characteristics Of the Dilute Solvent-rich And Concentratementioning
confidence: 99%
“…12,22 A number of different software packages have been developed to predict cross-beta-sheet aggregation-propensities based on the sequence. [23][24][25][26][27][28] There is no single computational method that is able to estimate antibody developability and shelf-life, but a number of established methods, developed for different purposes, can be utilized to assemble important aspects of rate-limiting steps of antibody degradation pathways and provide valuable estimations for antibody developability. Computational methods pinpoint potential liabilities to distinct sequence patterns, paving the way for rational engineering toward improved developability.…”
Section: Introductionmentioning
confidence: 99%