Ubiquitination driving ER protein complexation

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Last Updated: Tuesday, 06 June 2023 09:05
The computational cell biology group of Ramachandra Bhaskara has used MARTINI models of Ubiquitinated RHD proteins to show volume exclusion and non-specific Ub-Ub interactions driving the formation of homomeric and heteromeric complexes on ER membranes boosting selective-ER phagy. The computation-based findings are supported by super-resolution imaging and in vitro membrane remodeling assays apart from cell biology experiments. Published in TWO (!) Nature papers:
 

González, A., Covarrubias-Pinto, A., Bhaskara, R. M., Glogger, M., Kuncha, S. K., Xavier, A., Seemann, E., Misra, M., Hoffmann, M. E., Bräuning, B., Balakrishnan, A., Qualmann, B., Dötsch, V., Schulman, B. A., Kessels, M. M., Hübner, C. A., Heilemann, M., Hummer, G., & Dikić, I. (2023). Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, 1-8. https://doi.org/10.1038/s41586-023-06089-2

Foronda, H., Fu, Y., Covarrubias-Pinto, A., Bocker, H. T., González, A., Seemann, E., Franzka, P., Bock, A., Bhaskara, R. M., Liebmann, L., Hoffmann, M. E., Katona, I., Koch, N., Weis, J., Kurth, I., Gleeson, J. G., Reggiori, F., Hummer, G., Kessels, M. M., Qualmann, B., . . . Hübner, C. A. (2023). Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature, 1-9.https://doi.org/10.1038/s41586-023-06090-9 

Martini in OpenMM

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Last Updated: Thursday, 13 April 2023 10:59

The group of Tieleman has completed an implementation of Martini 2 and Martini 3 in the OpenMM molecular dynamics software package. OpenMM is a flexible molecular dynamics package widely used for methods development and is competitive in speed on GPUs with other commonly used packages. OpenMM has facilities to easily implement new force field terms, external forces and fields, and other non-standard features, which were used to implement all force field terms of Martini 2 and Martini 3. This allows OpenMM simulations, starting with GROMACS topology files that are processed by custom scripts, with all the added flexibility of OpenMM. For details, see the paper of MacCallum et al., Biophys J., 2023.

Martini MOF

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Last Updated: Wednesday, 24 May 2023 06:03

Martini keeps expanding its application horizon - see the birth of Martini models for a zeolite MOF: https://doi.org/10.1063/5.0145924

SARS-COV-2 envelope

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Last Updated: Friday, 07 April 2023 06:13

cover-structure-SARC-Cov.jpg 

Finally our integrative model of SARS-Cov-2 is published, representing the most realistic model of this viral envelope to date, with interesting pattern formation of the M-dimers.

For details, see Pezeshkian et al., Structure (2023).

Technical difficulties

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Last Updated: Tuesday, 14 March 2023 15:34

Dear users,

Over the past week we have experienced technical difficulties, due to which new users did not receive their registration emails. In case you tried to create an account on this website within the past 10 days, please resubmit the registration application. Apologies for the inconvenience.

Optimized cholesterol

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Last Updated: Thursday, 23 February 2023 14:23

Now available: optimized Martini 2 cholesterol model which remedies the artificial  temperature gradients using loose LINCS settings. See https://doi.org/10.1021/acs.jctc.2c01032 for details. Nice work from Fábián, Thallmair, and Hummer !