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      O-GlcNAc transferase modulates the cellular endocytosis machinery by controlling the formation of clathrin-coated pits

      research-article
      1 , 2 , 1 , 1 , 1 , 2 , 3 , , 1 , 2 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      metabolism, O-GlcNAc transferase, clathrin mediated endocytosis, O-GlcNAc, AP-2 associated kinase, traffic, PICALM, EPSIN, hexosamine biosynthetic pathway, epidermal growth factor receptor, AAK1, AP2-associated kinase-1, AMPK, AMP-activated protein kinase, BSA, bovine serum albumin, CCP, clathrin-coated pit, CLS, clathrin-labeled structure, CME, clathrin-mediated endocytosis, DMEM, Dulbecco's modified Eagle's medium, EGFR, EGF Receptor, GBP, GFP-binding protein, O-GlcNAc, O-linked β-GlcNAc, sCLS, subthreshold clathrin-labeled structure, TfR, Transferrin Receptor, TIRF, total internal reflection fluorescence, TIRFM, TIRF microscopy, TMG, Thiamet G, WGA, wheat germ agglutinin

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          Abstract

          Clathrin-mediated endocytosis (CME) controls the internalization and function of a wide range of cell surface proteins. CME occurs by the assembly of clathrin and many other proteins on the inner leaflet of the plasma membrane into clathrin-coated pits (CCPs). These structures recruit specific cargo destined for internalization, generate membrane curvature, and in many cases undergo scission from the plasma membrane to yield intracellular vesicles. The diversity of functions of cell surface proteins controlled via internalization by CME may suggest that regulation of CCP formation could be effective to allow cellular adaptation under different contexts. Of interest is how cues derived from cellular metabolism may regulate CME, given the reciprocal role of CME in controlling cellular metabolism. The modification of proteins with O-linked β-GlcNAc (O-GlcNAc) is sensitive to nutrient availability and may allow cellular adaptation to different metabolic conditions. Here, we examined how the modification of proteins with O-GlcNAc may control CCP formation and thus CME. We used perturbation of key enzymes responsible for protein O-GlcNAc modification, as well as specific mutants of the endocytic regulator AAK1 predicted to be impaired for O-GlcNAc modification. We identify that CCP initiation and the assembly of clathrin and other proteins within CCPs are controlled by O-GlcNAc protein modification. This reveals a new dimension of regulation of CME and highlights the important reciprocal regulation of cellular metabolism and endocytosis.

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          Highly accurate protein structure prediction with AlphaFold

          Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1 – 4 , the structures of around 100,000 unique proteins have been determined 5 , but this represents a small fraction of the billions of known protein sequences 6 , 7 . Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’ 8 —has been an important open research problem for more than 50 years 9 . Despite recent progress 10 – 14 , existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14) 15 , demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.
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            UCSF ChimeraX : Structure visualization for researchers, educators, and developers

            UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
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              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

              The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk ) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.
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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                31 January 2023
                March 2023
                31 January 2023
                : 299
                : 3
                : 102963
                Affiliations
                [1 ]Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
                [2 ]Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
                [3 ]Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
                Author notes
                []For correspondence: Warren W. Wakarchuk; Costin N. Antonescu wakarchu@ 123456ualberta.ca cantonescu@ 123456torontomu.ca
                Article
                S0021-9258(23)00095-9 102963
                10.1016/j.jbc.2023.102963
                9999237
                36731797
                48169d18-5cae-4218-8c1e-72a4a58284bb
                © 2023 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 17 June 2022
                : 16 January 2023
                Categories
                Research Article

                Biochemistry
                metabolism,o-glcnac transferase,clathrin mediated endocytosis,o-glcnac,ap-2 associated kinase,traffic,picalm,epsin,hexosamine biosynthetic pathway,epidermal growth factor receptor,aak1, ap2-associated kinase-1,ampk, amp-activated protein kinase,bsa, bovine serum albumin,ccp, clathrin-coated pit,cls, clathrin-labeled structure,cme, clathrin-mediated endocytosis,dmem, dulbecco's modified eagle's medium,egfr, egf receptor,gbp, gfp-binding protein,o-glcnac, o-linked β-glcnac,scls, subthreshold clathrin-labeled structure,tfr, transferrin receptor,tirf, total internal reflection fluorescence,tirfm, tirf microscopy,tmg, thiamet g,wga, wheat germ agglutinin

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