Charge and Hydrophobicity Patterning Along The Sequence Predicts The Folding Mechanism and Aggregation of Proteins:  A Computational Approach

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Protein Folding, Protein Aggregation, Recurrence Quantification Analysis, Charge/hydrophobicity Patterning, Partially Folded Intermediate.

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The presence of partially folded intermediates along the folding funnel of proteins has been suggested to be a signature of potentially aggregating systems. Many studies have concluded that metastable, highly flexible intermediates are the basic elements of the aggregation process. In a previous paper, we demonstrated how the choice between aggregation and folding behavior was influenced by hydrophobicity distribution patterning along the sequence, as quantified by recurrence quantification analysis (RQA) of the Myiazawa−Jernigan coded primary structures. In the present paper, we tried to unify the “partially folded intermediate” and “hydrophobicity/charge” models of protein aggregation verifying the ability of an empirical relation, developed for rationalizing the effect of different mutations on aggregation propensity of acyl-phosphatase and based on the combination of hydrophobicity RQA and charge descriptors, to discriminate in a statistically significant way two different protein populations:  (a) proteins that fold by a process passing by partially folded intermediates and (b) proteins that do not present partially folded intermediates.

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Journal of Proteome Research, v. 3, issue 6, p. 1243-1253