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1. Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy

   https://doi.org/10.1186/s12859-023-05389-8  

   Guerler, Aysam; Baker, Dannon; van den Beek, Marius; Gruening, Bjoern; Bouvier, Dave; Coraor, Nate; Shank, Stephen D.; Zehr, Jordan D.; Schatz, Michael C.; Nekrutenko, Anton (December 2023, BMC Bioinformatics)

   Abstract BackgroundProtein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein–protein interactions and produce high-quality multimeric structural models. ResultsApplication of our method to the Human and Yeast genomes yield protein–protein interaction networks similar in quality to common experimental methods. We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2’s non-structural protein 3. We also produced models of SARS-CoV2’s spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor and dipeptidyl peptidase-4. ConclusionsThe presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation. The interactome modeling pipeline is available at usegalaxy.org and usegalaxy.eu. 

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2. The vacuolar protein sorting genes in insects: A comparative genome view

   https://doi.org/10.1016/j.ibmb.2014.11.007  

   Li, Zhaofei; Blissard, Gary (July 2015, Insect Biochemistry and Molecular Biology)
3. Genome organization and interaction with capsid protein in a multipartite RNA virus

   https://doi.org/10.1073/pnas.1915078117  

   Beren, Christian; Cui, Yanxiang; Chakravarty, Antara; Yang, Xue; Rao, A. L. N.; Knobler, Charles M.; Zhou, Z. Hong; Gelbart, William M. (May 2020, Proceedings of the National Academy of Sciences)

   We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content—specifically, RNAs 3 and 4—assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific “packaging signals” throughout the viral RNA to package their monopartite genomes. 

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4. Differential nuclear import sets the timing of protein access to the embryonic genome

   https://doi.org/10.1038/s41467-022-33429-z  

   Nguyen, Thao; Costa, Eli J.; Deibert, Tim; Reyes, Jose; Keber, Felix C.; Tomschik, Miroslav; Stadlmeier, Michael; Gupta, Meera; Kumar, Chirag K.; Cruz, Edward R.; et al (October 2022, Nature Communications)

   Abstract The development of a fertilized egg to an embryo requires the proper temporal control of gene expression. During cell differentiation, timing is often controlled via cascades of transcription factors (TFs). However, in early development, transcription is often inactive, and many TF levels stay constant, suggesting that alternative mechanisms govern the observed rapid and ordered onset of gene expression. Here, we find that in early embryonic development access of maternally deposited nuclear proteins to the genome is temporally ordered via importin affinities, thereby timing the expression of downstream targets. We quantify changes in the nuclear proteome during early development and find that nuclear proteins, such as TFs and RNA polymerases, enter the nucleus sequentially. Moreover, we find that the timing of nuclear proteins’ access to the genome corresponds to the timing of downstream gene activation. We show that the affinity of proteins to importin is a major determinant in the timing of protein entry into embryonic nuclei. Thus, we propose a mechanism by which embryos encode the timing of gene expression in early development via biochemical affinities. This process could be critical for embryos to organize themselves before deploying the regulatory cascades that control cell identities. 

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5. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate

   https://doi.org/10.1038/s41589-021-00776-9  

   Weiss, Ryan J.; Spahn, Philipp N.; Chiang, Austin W.; Liu, Qing; Li, Jing; Hamill, Kristina M.; Rother, Sandra; Clausen, Thomas M.; Hoeksema, Marten A.; Timm, Bryce M.; et al (June 2021, Nature Chemical Biology)

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