Merge pull request #46 from bioshape-analysis/AliFeleParanj

nefinal report added

posts/cryo_ET/.ipynb_checkpoints/references-checkpoint.bib

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+@article{Shi2023,
+author={Shi, Wei
+and Cai, Yongfei
+and Zhu, Haisun
+and Peng, Hanqin
+and Voyer, Jewel
+and Rits-Volloch, Sophia
+and Cao, Hong
+and Mayer, Megan L.
+and Song, Kangkang
+and Xu, Chen
+and Lu, Jianming
+and Zhang, Jun
+and Chen, Bing},
+title={Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane},
+journal={Nature},
+year={2023},
+month={Jul},
+day={01},
+volume={619},
+number={7969},
+pages={403-409},
+abstract={The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.},
+issn={1476-4687},
+doi={10.1038/s41586-023-06273-4},
+url={https://doi.org/10.1038/s41586-023-06273-4}
+}
+
+@article{mepsi2022,
+title = {MEPSi: A tool for simulating tomograms of membrane-embedded proteins},
+journal = {Journal of Structural Biology},
+volume = {214},
+number = {4},
+pages = {107921},
+year = {2022},
+issn = {1047-8477},
+doi = {https://doi.org/10.1016/j.jsb.2022.107921},
+url = {https://www.sciencedirect.com/science/article/pii/S1047847722000910},
+author = {Borja {Rodríguez de Francisco} and Armel Bezault and Xiao-Ping Xu and Dorit Hanein and Niels Volkmann},
+keywords = {Simulations, tomographic reconstruction, Image processing, Quality metrics, cryo-EM},
+abstract = {The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.}
+}