Proline/arginine dipeptide repeat polymers derail protein folding in amyotrophic lateral sclerosis

Abstract

Amyotrophic lateral sclerosis and frontotemporal dementia are two neurodegenerative diseases with overlapping clinical features and the pathological hallmark of cytoplasmic deposits of misfolded proteins. The most frequent cause of familial forms of these diseases is a hexanucleotide repeat expansion in the non-coding region of the C9ORF72 gene that is translated into dipeptide repeat polymers. Here we show that proline/arginine repeat polymers derail protein folding by sequestering molecular chaperones. We demonstrate that proline/arginine repeat polymers inhibit the folding catalyst activity of PPIA, an abundant molecular chaperone and prolyl isomerase in the brain that is altered in amyotrophic lateral sclerosis. NMR spectroscopy reveals that proline/arginine repeat polymers bind to the active site of PPIA. X-ray crystallography determines the atomic structure of a proline/arginine repeat polymer in complex with the prolyl isomerase and defines the molecular basis for the specificity of disease-associated proline/arginine polymer interactions. The combined data establish a toxic mechanism that is specific for proline/arginine dipeptide repeat polymers and leads to derailed protein homeostasis in C9orf72-associated neurodegenerative diseases.

Peptidyl Prolyl Isomerase A Modulates the Liquid–Liquid Phase Separation of Proline-Rich IDPs

“…PR dipeptide repeat proteins are abnormally expressed in the brain of patients with C9-ALS/FTD . The toxicity of PR dipeptide repeat proteins in C9-ALS/FTD is linked to their incorporation into membrane-less compartments, thus changing their properties. , Previous studies demonstrated that the dipeptide repeat protein PR20 interacts with PPIA in vitro and in cells. , …”

“…To gain single-residue resolution insight into the interaction of PPIA with the dipeptide repeat protein PR20, we used NMR spectroscopy. In agreement with previous results, PR20 induced strong signal broadening of selected PPIA residues. The cross peak of Arg55, the PPIA residue that is crucial for its catalytic activity, was broadened beyond detection (Figure S1a).…”

“…In addition, several other residues in the active site of PPIA were perturbed (Figures a, S1a). In the crystal structure of the PPIA/PR20 complex, Arg55 forms a hydrogen bond with the carbonyl group of a proline–arginine peptide of PR20 . The binding affinity of this interaction, as determined from the intensity perturbations of Arg55 and Asn102, is 23 μM (Figure S1c).…”

Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations

“…The coordinates of CD147 were derived from the cryo-EM structure (PDB: 6LZ0 23 ), which was determined at 3.30 Å resolution. CypA was performed using its crystal structure (PDB: 7ABT 33 ). CD147-CypA complexes were obtained using the general used Zdock and Rdock programs, 34,35 with the contact residue constraint from the NMR analysis.…”

CRISPR and iPSCs: Recent Developments and Future Perspectives in Neurodegenerative Disease Modelling, Research, and Therapeutics

“…A hexanucleotide (GGGGCC) repeat expansion in the first intron of the C9ORF72 gene is a well-established cause for ALS (Braems et al 2020 ). The mutation results in the expression of glycine-arginine and proline-arginine dipeptide repeat proteins, which tend to bind to a large number of intracellular proteins, thereby promoting aggregate formation and consequently DNA damage (Babu et al 2021 ). A study aiming to better understand the mechanism of dipeptide repeat protein-mediated DNA damage using a CRISPR/iPSC-based C9ORF72 disease model revealed that dipeptide repeat proteins such as proline-arginine repeat proteins compromise the proper functioning DNA double-strand repair pathways by inhibiting the action of key proteins such as nucleophosmin (Andrade et al 2020 ).…”