References: Glycosphingolipids, Lipid Rafts and Structural Biology
Simons, K. & Ikonen, E. Functional rafts in the plasma membrane. Nature 387, 569–572 (1997).
Simons, K. & Toomre, D. Lipid rafts and signal transduction. Nature Reviews Molecular Cell Biology 1, 31–39 (2000).
Hakomori, S. Glycosphingolipids in cell interactions, differentiation and carcinogenesis. Annual Review of Biochemistry 50, 733–764 (1981).
Kasahara, K. & Sanai, Y. Functional roles of glycosphingolipids in signal transduction via lipid rafts. Glycoconjugate Journal 17, 153–162 (2000).
Merrill, A. H. Jr. Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics. Chemical Reviews 111, 6387–6422 (2011).
Hannun, Y. A. & Obeid, L. M. Sphingolipids and their metabolism in physiology and disease. Nature Reviews Molecular Cell Biology 19, 175–191 (2018).
Platt, F. M. Emptying the stores: lysosomal diseases and therapeutic strategies. Nature Reviews Drug Discovery 17, 133–150 (2018).
Platt, F. M. Sphingolipid lysosomal storage disorders. Nature 510, 68–75 (2014).
Ichikawa, S., Sakiyama, H., Suzuki, G., Hidari, K. I. & Hirabayashi, Y. Expression cloning of human ceramide glucosyltransferase, which catalyzes the first glycosylation step of glycosphingolipid synthesis. Proceedings of the National Academy of Sciences of the United States of America 93, 12654–12658 (1996).
Ichikawa, S. & Hirabayashi, Y. Glucosylceramide synthase and glycosphingolipid synthesis. Trends in Cell Biology 8, 198–202 (1998).
Grabowski, G. A. Phenotype, diagnosis and treatment of Gaucher disease. The Lancet 372, 1263–1271 (2008).
Germain, D. P. Fabry disease. Orphanet Journal of Rare Diseases 5, 30 (2010).
Sidransky, E. et al. Multicenter analysis of glucocerebrosidase mutations in Parkinson’s disease. New England Journal of Medicine 361, 1651–1661 (2009).
Mazzulli, J. R. et al. Gaucher disease glucocerebrosidase and α-synuclein form a bidirectional pathogenic loop in synucleinopathies. Cell 146, 37–52 (2011).
Zunke, F. et al. Reversible conformational conversion of α-synuclein into toxic assemblies by glucosylceramide. Neuron 97, 92–107 (2018).
Cox, T. M. et al. Comparison of eliglustat and imiglucerase in patients with type 1 Gaucher disease stabilized on enzyme replacement therapy. The Lancet 385, 2355–2362 (2015).
Mistry, P. K. et al. Effect of oral eliglustat on splenomegaly in patients with type 1 Gaucher disease: the ENGAGE randomized clinical trial. JAMA 313, 695–706 (2015).
Butters, T. D., Dwek, R. A. & Platt, F. M. Iminosugar inhibitors for treating lysosomal glycosphingolipidoses. Glycobiology 15, 43R–52R (2005).
Marks, D. L. et al. Oligomerization and topology of the Golgi membrane protein glucosylceramide synthase. Journal of Biological Chemistry 274, 451–456 (1999).
Lairson, L. L., Henrissat, B., Davies, G. J. & Withers, S. G. Glycosyltransferases: structures, functions and mechanisms. Annual Review of Biochemistry 77, 521–555 (2008).
Breton, C., Snajdrová, L., Jeanneau, C., Koca, J. & Imberty, A. Structures and mechanisms of glycosyltransferases. Glycobiology 16, 29R–37R (2006).
Basu, S., Kaufman, B. & Roseman, S. Enzymatic synthesis of glucocerebroside by glucosyltransferase from embryonic chicken brain. Journal of Biological Chemistry 248, 1388–1394 (1973).
Peterschmitt, M. J. et al. Pharmacokinetics, pharmacodynamics, safety and tolerability of oral venglustat in healthy volunteers. Clinical Pharmacology in Drug Development 10, 86–98 (2021).
Platt, F. M., Neises, G. R., Dwek, R. A. & Butters, T. D. N-Butyldeoxynojirimycin is a novel inhibitor of glycolipid biosynthesis. Journal of Biological Chemistry 269, 8362–8365 (1994).
Wild, R. et al. The structure of the yeast oligosaccharyltransferase complex provides insight into eukaryotic N-glycosylation. Science 359, 545–550 (2018).
Van Kempen, M. et al. Fast and accurate protein structure searches using Foldseek. Nature Biotechnology 42, 243–246 (2024).
Maloney, F. P. et al. Structure, substrate recognition and initiation of hyaluronan synthase. Nature 604, 195–201 (2022).
Coutinho, P. M., Deleury, E., Davies, G. J. & Henrissat, B. An evolving hierarchical family classification for glycosyltransferases. Journal of Molecular Biology 328, 307–317 (2003).
Finstermeier, K. et al. A mitogenomic phylogeny of living primates. PLoS ONE 8, e69504 (2013).
Steiper, M. E. & Young, N. M. Primate molecular divergence dates. Molecular Phylogenetics and Evolution 41, 384–394 (2006).
Andersson, U. et al. Improved outcome of N-butyldeoxygalactonojirimycin-mediated substrate reduction therapy in a mouse model of Sandhoff disease. Neurobiology of Disease 16, 506–515 (2004).
Cai, H. et al. An improved fluorescent tag and its nanobodies for membrane-protein expression, stability assays and purification. Communications Biology 3, 753 (2020).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods 14, 290–296 (2017).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods 16, 1153–1160 (2019).
Abramson, J. et al. Accurate structural prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators and developers. Protein Science 30, 70–82 (2021).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallographica Section D Biological Crystallography 66, 486–501 (2010).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D Biological Crystallography 66, 213–221 (2010).
O’Leary, N. A. et al. The NCBI Reference Sequence database: current status, taxonomic expansion and functional annotation. Nucleic Acids Research 44, D733–D745 (2016).
UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Research 51, D523–D531 (2023).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797 (2004).
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. Journal of Computational Chemistry 29, 1859–1865 (2008).
Abraham, M. J. et al. GROMACS: high-performance molecular simulations through multilevel parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A. & Moreno, E. gmx_MMPBSA: a new tool to perform end-state free-energy calculations with GROMACS. Journal of Chemical Theory and Computation 17, 6281–6291 (2021).
Wu, C. & Jin, S. Simulation files for UGCG. Zenodo (2026).
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