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作者：Xing, Zhichao; Cai, Xiaoying; He, Ting; Li, Peiheng; He, Jun; Qiu, Yuxuan; Li, Na; Mi, Li; Li, Ruixi; Zhu, Jingqiang; Li, Zhihui; Su, Anping; Ye, Haoyu; Wu, Wenshuang
作者单位：Sichuan University; Sichuan University; Sichuan University; Sichuan University; Sichuan University; Sichuan University; Westlake University
摘要：DNA damage repair (DDR) is essential for cancer cell survival and treatment resistance, making it a critical target for tumor therapy. The eukaryotic AAA+ adenosine triphosphatase valosin-containing protein (VCP), which is transported from the cytoplasm into the nucleus, plays a critical role in the DDR process. However, the nuclear translocation and molecular mechanism of VCP for DDR remain elusive. Here, we define VCP as a KPNB1 interacting protein through a combination of chemical and immun...
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作者：Yang, Wei; Feng, Xi; Chen, Huahui; Liman, Geraldy Lie Stefanus; Santangelo, Thomas J.; Zhang, Changyi; Zeng, Zhirui
作者单位：Southern University of Science & Technology; Colorado State University System; Colorado State University Fort Collins; University of Illinois System; University of Illinois Urbana-Champaign
摘要：Enhancement of the cyclization of membrane lipids GDGTs (glycerol dialkyl glycerol tetraethers) is a critical strategy for archaea to adapt to various environmental stresses. However, the physiological function of membrane lipid cyclization remains unclear. Here, we reported that the GDGT ring synthases mutant, deficient in GDGT cyclization, inhibited archaellum formation and reduced cell motility in thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. This inhibition was caused by decrea...
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作者：Banerjee, Anupam; Bogetti, Anthony T.; Bahar, Ivet
作者单位：State University of New York (SUNY) System; Stony Brook University; State University of New York (SUNY) System; Stony Brook University; Stony Brook University Hospital
摘要：Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here Rhapsody-2, a machine learning tool for discriminating pathogenic and neutral SAVs, significantly expanding on a precursor limited by the availability of structural data. With the advent of AlphaFold2 as a powerful tool for structure prediction, Rhapsody-2 is trained on a...
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作者：Gong, Mengsha; Ashok, Minakshi; Helou, Ariane; Goentoro, Lea
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作者：Wang, Xinyao; Xie, Chen; Shen, Ke; Li, Dubai; Xie, Xiaoliang Sunney
作者单位：Peking University; Peking University; Changping Laboratory; Peking University
摘要：In eukaryotes, the expression of specific genes is regulated by a combination of transcription factors (TFs) bound on regulatory regions of the genomic DNA (promoters and enhancers). Recent advances in genomic sequencing technology have enabled the measurements of TFs' footprints and binding affinities on DNA at the single-molecule level, facilitating the probing of binding cooperativity among adjacent TFs. This necessitates quantitative descriptions of TFs' binding cooperativity and understan...
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作者：Ferrada, Evandro
作者单位：Universidad de Valparaiso; Universidad de Valparaiso
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作者：Gu, Jinge; Zhou, Xiaoming; Sutherland, Lillian; Liszczak, Glen; Mcknight, Steven L.
作者单位：University of Texas System; University of Texas Southwestern Medical Center; Westlake University
摘要：Protein domains of low sequence complexity are unable to fold into stable, three-dimensional structures. In test tube studies, these unusual polypeptide regions can self-associate in a manner causing phase separation from aqueous solution. This form of protein:protein interaction has been implicated in numerous examples of dynamic morphological organization within eukaryotic cells. In several cases, the basis for low complexity domain (LCD) self-association and phase separation has been traced...
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作者：Matalon, Nadav; Weinreb, Eyal; Freche, Dominik; Volk, Erez; Biron, Tirza; Moses, Elisha; Biron, David
作者单位：Weizmann Institute of Science; Hebrew University of Jerusalem; Weizmann Institute of Science; University of Chicago; University of Chicago
摘要：Prosody, the musical facet of speech, is pivotal in human communication, and its structure and meaning remain subjects of ongoing research. In this study, we introduce a data-driven model for English prosody, based on large-scale analysis of spontaneous conversations. As a first step, we identify approximately 200 discernible prosodic patterns-which we view as building blocks of the prosodic vocabulary-and outline their properties and range of meanings. Next, we reveal a Markovian logic, akin ...
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作者：Guo, Liangyue; Yu, Qilin; Wang, Di; Wu, Xiaoyu; Wolynes, Peter G.; Chen, Mingchen
作者单位：Changping Laboratory; Rice University; Rice University; Rice University; Rice University
摘要：The concept that proteins are selected to fold into a well-defined native state has been effectively addressed within the framework of energy landscapes, underpinning the recent successes of structure prediction tools like AlphaFold. The amyloid fold, however, does not represent a unique minimum for a given single sequence. While the cross-/3 hydrogen-bonding pattern is common to all amyloids, other aspects of amyloid fiber structures are sensitive not only to the sequence of the aggregating p...
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作者：Iwasaki, Kenichi; Neuhauser, Charles; Stokes, Chris; Rayshubskiy, Aleksandr
作者单位：Harvard University; Harvard University
摘要：Engineering small autonomous agents capable of operating in the microscale environment remains a key challenge, with current systems still evolving. Our study explores the fruit fly, Drosophila melanogaster, a classic model system in biology and a species adept at microscale interaction, as a biological platform for microrobotics. Initially, we focus on remotely directing the walking paths of fruit flies in an experimental arena. We accomplish this through two distinct approaches: harnessing t...
