11 papers · ranked by Valyu relevance
Sanjarbek Hudaiberdiev, Ivan Ovcharenko
Enhancers and promoters are classically considered to be bound by a small set of TFs in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with often no…
Sabrina Ninck, Thomas Klaus, Tatiana V. Kochetkova, Sarah P. Esser + 7 more
Microbial communities are significant drivers of global biogeochemical cycles, yet accurate function prediction of their proteome and discerning their activity in situ for bioprospecting remains challenging. Here, we present environmental activity-based protein profiling (eABPP) as a novel proteomics-based approach…
Megan Leander, Zhuang Liu, Qiang Cui, Srivatsan Raman
A fundamental question in protein science is where allosteric hotspots – residues critical for allosteric signaling – are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allosteric transcription factors (aTF) to identify hotspots and built a…
Ya-Ting Tai, Wei-Chou Lin, Duncan Yi-Te Wang, Jieru Ye + 3 more
OCCC has high incidence in Asia with frequent occurrence at early stage but without sufficient data on molecular stratification for high-risk patients. Recently, immune-hot features have been proposed as an indicator for poor prognosis for early-stage OCCC. Specific patterns of intra-tumoral heterogeneity (ITH)…
Parvathy Jayadevan, Yazhini Arangasamy, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
Hotspots are interfacial residues in protein-protein complexes that contribute significantly to complex stability. Methods for identifying interfacial residues in protein-protein complexes are based on two approaches, namely, (a) distance-based methods, which identify residues that form direct interactions with the…
Jiaxing Chen, Leslie A. Kuhn, Sebastian Raschka
With machine learning now transforming the sciences, successful prediction of biological structure or activity is mainly limited by the extent and quality of data available for training, the astute choice of features for prediction, and thorough assessment of the robustness of prediction on a variety of new cases. Here…
Nils Kurzawa, Matthias Stahl, Isabelle Leo, Elena Kunold + 7 more
The complexity of the functional proteome extends significantly beyond the protein coding genome resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases, but challenging to perform systematically. Here…
Alexa R. Heaton, Nathaniel J. Burkard, Anqi Gao, Anna Hoefges + 13 more
Immunotherapy has potential for impactful cancer cures by empowering patients’ own immune cells. We developed a radio-immunotherapy regimen that can cure large immunologically hot and cold murine tumors. Here, we explored the divergent role of CD8 T cells during this radio-immunotherapy in contrasting hot colon…
Johannes F. Hevler, Mirat Sojitra, Tomislav Caval, Michael Schoof + 2 more
Protein glycosylation regulates essential cellular processes including protein folding, stability, and cell-cell interactions; however, how aberrant glycosylation impacts protein function and interaction networks remains poorly understood. Here we combine mass spectrometry-based proteomics, chemical glycobiology, and…
Xuepei Zhang, Bohdana Sokolova, Zhaowei Meng, Hassan Gharibi + 4 more
Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational changes but are limited…
Carina Groh, Per Haberkant, Frank Stein, Sebastian Filbeck + 4 more
Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger the mitoprotein-induced stress response. To dissect the effects of…