@article {69730, title = {How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer{\textquoteright}s disease brain by a strain-relief mechanismAbstractBackgroundMethodResultConclusion}, journal = {Alzheimer{\textquoteright}s \& Dementia}, volume = {20}, year = {2024}, month = {01/2025}, abstract = {

Background

Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer{\textquoteright}s disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC fragments tau fibrils from AD brains (AD-tau) into benign segments, whereas its six-residue analog D-TLKIVW cannot. However, the underlying fragmentation mechanism remains unknown, preventing the further development of this type of drug candidate for AD.

Method

To understand the necessity of the cysteine residue of D-TLKIVWC in fragmenting AD-tau, we designed a series of peptides of sequence D-TLKIVWX varying only at the seventh residue, X. To better understand the fragmentation process of AD-tau, we conducted a time-course dot blot and EM experiment. We determined the structures of D-TLKIVWX amyloid-like fibrils by atomic force microscopy and cryo-electron microscopy. We studied the complexes of D-TLKIVWX (X = I, S, R) with AD-tau by cryo-electron microscopy and confirmed the binding site between D-TLKIVWX and Tau through NMR.

Result

These D-TLKIVWX candidates showed various efficacies in fragmenting AD-tau in vitro, in which X = Ile was the best performer. From electron microscopy, we discovered that D-TLKIVWX peptides form amyloid-like fibrils themselves, and from atomic force microscopy we learned that these fibrils have a right-handed helical twist, in contrast to the left-handed helical twist of AD-tau. From cryo-EM we learned that D-TLKIVWX protofilaments bind to tau fibrils of opposing twist.

Conclusion

We find that the amyloid-like, fibril-forming property of D-TLKIVWX contributes to the fragmentation of AD-tau fibrils. We propose the strain-relief mechanism of fragmentation and believe the fragmentation of AD-tau fibrils is driven by the release of torsion in D-TLKIVWX protofilaments.

}, issn = {1552-5260}, doi = {10.1002/alz.v20.S610.1002/alz.085001}, url = {https://alz-journals.onlinelibrary.wiley.com/toc/15525279/20/S6https://alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.085001}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Dolinsky, Joshua L. and Yang, Yuan and Jiang, Yi Xiao and Lutter, Liisa and Boyer, David and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S.} } @article {69688, title = {Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, and found that nucleosomes have a nearly random orientation distribution in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

}, doi = {10.1101/2024.12.01.626131}, url = {https://doi.org/10.1101/2024.12.01.626131}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K. and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K.} } @article {65869, title = {Cryo-EM structure of the inhibited (10S) form of myosin II.}, journal = {Nature}, volume = {588}, year = {2020}, month = {2020 Dec 02}, pages = {521-25}, abstract = {

Myosin II is the motor protein that enables muscle cells to contract and nonmuscle cells to move and change shape. The molecule has two identical heads attached to an elongated tail, and can exist in two conformations: 10S and 6S, named for their sedimentation coefficients. The 6S conformation has an extended tail and assembles into polymeric filaments, which pull on actin filaments to generate force and motion. In 10S myosin, the tail is folded into three segments and the heads bend back and interact with each other and the tail, creating a compact conformation in which ATPase activity, actin activation and filament assembly are all highly inhibited. This switched-off structure appears to function as a key energy-conserving storage molecule in muscle and nonmuscle cells, which can be activated to form functional filaments as needed-but the mechanism of its inhibition is not understood. Here we have solved the structure of smooth muscle 10S myosin by cryo-electron microscopy with sufficient resolution to enable improved understanding of the function of the head and tail regions of the molecule and of the key intramolecular contacts that cause inhibition. Our results suggest an atomic model for\ the off state of myosin II, for its activation and unfolding by phosphorylation, and for understanding the clustering of disease-causing mutations near sites of intramolecular interaction.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-3007-0}, author = {Yang, Shixin and Tiwari, Prince and Lee, Kyoung Hwan and Sato, Osamu and Ikebe, Mitsuo and Padr{\'o}n, Ra{\'u}l and Craig, Roger} }