Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171IPAKTPPAPK180 Using Molecular Dynamic Simulation and the Markov State Model.

The formation of neurofibrillary tangles (NFT) with ß-sheet-rich structure caused by abnormal aggregation of misfolded microtubule-associated protein Tau is a hallmark of tauopathies, including Alzheimer's Disease. It has been reported that acetylation, especially K174 located in the proline-rich region, can largely promote Tau aggregation. So far, the mechanism of the abnormal acetylation of Tau that affects its misfolding and aggregation is still unclear. Therefore, revealing the effect of acetylation on Tau aggregation could help elucidate the pathogenic mechanism of tauopathies. In this study, molecular dynamics simulation combined with multiple computational analytical methods were performed to reveal the effect of K174 acetylation on the spontaneous aggregation of Tau peptide 171IPAKTPPAPK180, and the dimerization mechanism as an early stage of the spontaneous aggregation was further specifically analyzed by Markov state model (MSM) analysis. The results showed that both the actual acetylation and the mutation mimicking the acetylated state at K174 induced the aggregation of the studied Tau fragment; however, the effect of actual acetylation on the aggregation was more pronounced. In addition, acetylated K174 plays a major contributing role in forming and stabilizing the antiparallel ß-sheet dimer by forming several hydrogen bonds and side chain van der Waals interactions with residues I171, P172, A173 and T175 of the corresponding chain. In brief, this study uncovered the underlying mechanism of Tau peptide aggregation in response to the lysine K174 acetylation, which can deepen our understanding on the pathogenesis of tauopathies.

The misfolding mechanism of the key fragment R3 of tau protein: a combined molecular dynamics simulation and Markov state model study.

The formation of neurofibrillary tangles (NFT) by abnormal aggregation of misfolded microtubule-associated protein tau is a hallmark of tauopathies, including Alzheimer's disease. However, it remains unclear how tau monomers undergo conformational changes and further lead to the abnormal aggregation. In this work, molecular dynamics simulation combined with the Markov state model (MSM) analysis was used to uncover the misfolding progress and structural characteristics of the key R3 fragment of tau protein at the atomic level. The simulation results show that R3 exists in disordered structures mainly, which is consistent with the experimental results. The MSM analysis identified multiple ß-sheet conformations of R3. The residues involved in the ß-sheet structure formation are mainly located in three regions: PHF6 at the N-terminal, S324 to N327 at the middle of R3, and K331 to G334 at the C-terminal. In addition, the path analysis of the formation of the ß-sheet structure by transition path theory (TPT) revealed that there are multiple paths to form ß-sheet structures from the disordered state, and the timescales are at the millisecond level, indicating that a large number of structural rearrangements occur during the formation of ß-sheet structures. It is interesting to note that S19 is a critical intermediate state for the formation of two target ß-sheet structures, S23 and S4. In S19, three regions of V306 to K311, C322 to G326, and K331 to G334 form a turn structure, the regions that form the ß-sheet structure in target states S23 and S4, indicating that the formation of a turn structure is necessary to form a ß-sheet structure and then the turn structure will eventually transform into the ß-sheet structure through key hydrogen bonding interactions. These findings can provide insights into the kinetics of tau protein misfolding.

Disclosing the Mechanism of Spontaneous Aggregation and Template-Induced Misfolding of the Key Hexapeptide (PHF6) of Tau Protein Based on Molecular Dynamics Simulation.

The microtubule-associated protein tau is critical for the development and maintenance of the nervous system. Tau dysfunction is associated with a variety of neurodegenerative diseases called tauopathies, which are characterized by neurofibrillary tangles formed by abnormally aggregated tau protein. Studying the aggregation mechanism of tau protein is of great significance for elucidating the etiology of tauopathies. The hexapeptide 306VQIVYK311 (PHF6) of R3 has been shown to play a vital role in promoting tau aggregation. In this study, long-term all-atom molecular dynamics simulations in explicit solvent were performed to investigate the mechanisms of spontaneous aggregation and template-induced misfolding of PHF6, and the dimerization at the early stage of nucleation was further specifically analyzed by the Markov state model (MSM). Our results show that PHF6 can spontaneously aggregate to form multimers enriched with ß-sheet structure and the ß-sheets in multimers prefer to exist in a parallel way. It is observed that PHF6 monomer can be induced to form a ß-sheet structure on either side of the template but in a different way. In detail, the ß-sheet structure is easier to form on the left side but does not extend well, but on the right side, the monomer can form the extended ß-sheet structure. Furthermore, MSM analysis shows that the formation of dimer mainly occurs in three steps. First, the separated monomers collide with each other at random orientations, and then a dimer with short ß-sheet structure at the N-terminal forms; finally, ß-sheets elongate to form an extended parallel ß-sheet dimer. During these processes, multiple intermediate states are identified and multiple paths can form a parallel ß-sheet dimer from the disordered coil structure. Moreover, the residues I308, V309, and Y310 play an essential role in the dimerization. In a word, our results uncover the aggregation and misfolding mechanism of PHF6 from the atomic level, which can provide useful theoretical guidance for rational design of effective therapeutic drugs against tauopathies.