Thermodynamics of β-Sheet Formation in Polyglutamine

Abstract

The role of beta-sheets in the early stages of protein aggregation, specifically amyloid formation, remains unclear. Interpretations of kinetic data have led to a specific model for the role of beta-sheets in polyglutamine aggregation. According to this model, monomeric polyglutamine, which is intrinsically disordered, goes through a rare conversion into an ordered, metastable, beta-sheeted state that nucleates aggregation. It has also been proposed that the probability of forming the critical nucleus, a specific beta-sheet conformation for the monomer, increases with increasing chain length. Here, we test this model using molecular simulations. We quantified free energy profiles in terms of beta-content for monomeric polyglutamine as a function of chain length. In accord with estimates from experimental data, the free energy penalties for forming beta-rich states are in the 10-20 kcal/mol range. However, the length dependence of these free energy penalties does not mirror interpretations of kinetic data. In addition, although homodimerization of disordered molecules is spontaneous, the imposition of conformational restraints on polyglutamine molecules does not enhance the spontaneity of intermolecular associations. Our data lead to the proposal that beta-sheet formation is an attribute of peptide-rich phases such as high molecular weight aggregates rather than monomers or oligomers.

Dynamic Imaging by Fluorescence Correlation Spectroscopy Identifies Diverse Populations of Polyglutamine Oligomers Formed in Vivo

“…While some in vitro studies have suggested a predominant oligomer species (30,71,72), others indicate the appearance of a heterogeneous distribution of oligomers (63,73,74). Furthermore, recently both simulations and models have also predicted a heterogeneity of oligomer and aggregate species (75,76). Studies on Htt aggregation in cells have also described an oligomer population reaching an equilibrium, suggesting that oligomers are the rate-limiting event in inclusion body formation (73,77).…”

Overexpression of Q-rich prion-like proteins suppresses polyQ cytotoxicity and alters the polyQ interactome

“…Further evidence for direct interactions between the QA-repeat region of Gts1p and the polyQ tract of Htt was obtained by performing atomistic Monte Carlo simulations using the CAMPARI simulation engine (campari.sourceforge.net) and ABSINTH implicit solvation model and forcefield paradigm (45). This approach has recently been used to generate accurate insights regarding the early, nonspecific steps that lead to polyQ aggregation (46,47) and their modulation by sequences flanking the polyQ tract within Htt (48).…”

“…The choice of a 35 residue polyQ molecule was made because this allows for simulations that afford reliable and reproducible statistics, and as shown in previous studies, the simulation results are unlikely to vary by increasing or decreasing the polyQ length by five residues vis-à-vis 35Q (46,47).…”

Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy

“…In vivo, polyQ tracts occur embedded within larger proteins, such as the huntingtin protein. Full length proteins are impractical for detailed structural studies, and so isolated polyQ sequences are often used instead in experiments and simulations (3)(4)(5). Although isolated polyQ sequences may not aggregate in precisely the same manner as they would in fulllength proteins (3,6,7), it has been established that such models yield data that are relevant to some, if not all, polyQ pathologies (8).…”