Atomistic Insights into the Inhibitory Mechanism of Tyrosine Phosphorylation against the Aggregation of Human Tau Fragment PHF6

Abstract

Abnormal aggregation of the microtubule-associated protein tau into intracellular fibrillary inclusions is characterized as the hallmark of tauopathies, including Alzheimer’s disease and chronic traumatic encephalopathy. The hexapeptide 306VQIVYK311 (PHF6) of R3 plays an important role in the aggregation of tau. Recent experimental studies reported that phosphorylation of residue tyrosine 310 (Y310) could decrease the propensity of PHF6 to form fibrils and inhibit tau aggregation. However, the underlying inhibitory mechanism is not well understood. In this work, we systematically investigated the influences of phosphorylation on the conformational ensembles and oligomerization dynamics of PHF6 by performing extensive all-atom molecular dynamics (MD) simulations. Our replica exchange MD simulations demonstrate that Y310 phosphorylation could effectively suppress the formation of β-structure and shift PHF6 oligomers toward coil-rich aggregates. The interaction analyses show that hydrogen bonding and hydrophobic interactions among PHF6 peptides, as well as Y310–Y310 π–π stacking and I308–Y310 CH−π interactions, are weakened by phosphorylation. Additional microsecond MD simulations show that Y310 phosphorylation could inhibit the oligomerization of PHF6 by preventing the formation of large β-sheet oligomers and multi-layer β-sheet aggregates. This study provides mechanistic insights into the phosphorylation-inhibited tau aggregation, which may be helpful for the in-depth understanding of the pathogenesis of tauopathies.

Deciphering the Inhibitory Mechanism of Naphthoquinone–Dopamine on the Aggregation of Tau Core Fragments PHF6* and PHF6

“…A number of computational and experimental studies have manifested the crucial role of Y310 in the tau aggregation, as Y310 could form CH−π interactions with residue I308 and display π−π interaction with itself. 39,41,45,46 Therefore, we further examined whether NQDA interferes with these CH−π and π−π interactions. The PDFs of intra-chain and inter-chain CH−π distance between the atom Cγ of I308 and the benzene ring of Y310 are shown in Figure S8.…”

“…H-bonding interactions are considered to be crucial to the fibrillization of tau peptide fragments. ,, Therefore, we calculated the PDFs of the total H-bond number of PHF6* and PHF6 in four systems. As seen in Figure a, the PDF curve of the H-bond number presents the peak at the number of 56 in the PHF6* system, and the notable peak shift toward a small number is observed in the NQDA-PHF6* system.…”

“…For the PHF6 peptides, as shown in Figure d, NQDA displays the highest contact number with aromatic residue Y310, significantly larger than the second one (I308), indicative of strong binding between NQDA and Y310. A number of computational and experimental studies have manifested the crucial role of Y310 in the tau aggregation, as Y310 could form CH−π interactions with residue I308 and display π–π interaction with itself. ,,, Therefore, we further examined whether NQDA interferes with these CH−π and π–π interactions. The PDFs of intra-chain and inter-chain CH−π distance between the atom Cγ of I308 and the benzene ring of Y310 are shown in Figure S8.…”

“…Four 500 ns REMD simulations were performed in the isothermal-isobaric (NPT) ensemble using 48 replicas at temperatures ranging from 308 to 414 K. All the initial structures of PHF6* and PHF6 peptides used in our REMD simulations were in fully extended coil states, in accordance with our previous studies. 39,56,57 Twelve peptide chains were randomly placed in the simulation box, and the minimum distances between any two chains or between NQDA and any chains were larger than 1.2 nm. The PHF6*/PHF6:NQDA molar ratio was 1:5.…”

Effect of Cosolutes on the Aggregation of a Tau Fragment: A Combined Experimental and Simulation Approach

“…Moreover, fragments of the Tau protein containing R3 may be originated within the human brain by endopeptidase cleavage and these fragments may be crucial in amyloid core formation. Specifically, the hexapeptide VQIVYK (paired helical filament 6, PHF6), located in R3, is considered crucial for Tau fibrillation. − Cryo-EM analysis of Tau filaments isolated from Alzheimer’s patients has revealed that the PHF6 sequence constitutes the first β-strand of the filament core . Cross-linking mass spectrometry, recombinant protein and synthetic peptide systems, in silico modeling and cell models have additionally shown that the PHF6 motif forms metastable compact structures with its upstream sequence that modulate aggregation propensity …”