Cyan Ching

Cyan Ching

PhD graduate at the Physical Chemistry Curie Lab working in cryo-EM image processing.

Publications

Galactocerebroside Lipid Nanotubes, a Model Membrane System for Studying Membrane-Associated Proteins on a Molecular Scale

Published in Intracellular Lipid Transport: Methods and Protocols, 2024

Galactocerebroside lipid nanotubes are membrane-mimicking systems for studying the function and structure of proteins involved in membrane shape remodeling, such as in intracellular trafficking, cell division, and migration or involved in the formation of membrane contact sites. They exhibit a constant and small diameter of 30 nm and a length of up to 2 μm. They can be functionalized with lipid ligands, providing a large binding surface for protein without membrane shape remodeling. These features make it possible to study protein assemblies on membranes different from those accessible with vesicular systems. This chapter describes the process of galactocerebroside nanotube formation, the incorporation of different lipid ligands, factors influencing protein binding, and the experimental conditions for their use in flotation assay and imaging by transmission electron and cryo-electron microscopy

Recommended citation: Di Cicco, A., Manzi, J., Maufront, J., Cheng, X., Dezi, M., & Lévy, D. (2024). Galactocerebroside Lipid Nanotubes, a Model Membrane System for Studying Membrane-Associated Proteins on a Molecular Scale. In Intracellular Lipid Transport: Methods and Protocols (pp. 237-248). New York, NY: Springer US. https://journals.sagepub.com/doi/full/10.1177/25152564241231364

Cool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components

Published in Contact, 2024

Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.

Recommended citation: Ching, C., Maufront, J., di Cicco, A., Lévy, D., & Dezi, M. (2024). Cool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components. Contact, 7, 25152564241231364. https://journals.sagepub.com/doi/full/10.1177/25152564241231364

Molecular mechanisms of stress-induced reactivation in mumps virus condensates

Published in Cell, 2023

Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.

Recommended citation: Zhang, X., Sridharan, S., Zagoriy, I., Eugster Oegema, C., Ching, C., Pflaesterer, T., Fung, H. K. H., Becher, I., Poser, I., Müller, C. W., Hyman, A. A., Savitski, M. M., & Mahamid, J. (2023). Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell, 186(9), 1877-1894.e27. https://www.sciencedirect.com/science/article/pii/S0092867423002763

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

Published in The Journal of Chemical Physics, 2020

The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular dynamics (MD) simulation. Consequently, to explore ligand egress mechanisms and compute dissociation rates, it is necessary to enhance the sampling of ligand unbinding. Random Acceleration MD (RAMD) is a simple method to enhance ligand egress from a macromolecular binding site, which enables the exploration of ligand egress routes without prior knowledge of the reaction coordinates. Furthermore, the τRAMD procedure can be used to compute the relative residence times of ligands. When combined with a machine-learning analysis of protein–ligand interaction fingerprints (IFPs), molecular features that affect ligand unbinding kinetics can be identified. Here, we describe the implementation of RAMD in GROMACS 2020, which provides significantly improved computational performance, with scaling to large molecular systems. For the automated analysis of RAMD results, we developed MD-IFP, a set of tools for the generation of IFPs along unbinding trajectories and for their use in the exploration of ligand dynamics. We demonstrate that the analysis of ligand dissociation trajectories by mapping them onto the IFP space enables the characterization of ligand dissociation routes and metastable states. The combined implementation of RAMD and MD-IFP provides a computationally efficient and freely available workflow that can be applied to hundreds of compounds in a reasonable computational time and will facilitate the use of τRAMD in drug design.

Recommended citation: Kokh, D. B., Doser, B., Richter, S., Ormersbach, F., Cheng, X. (Ching, C.), & Wade, R. C. (2020). A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories. The Journal of Chemical Physics, 153(12), 125102. https://pubs.aip.org/aip/jcp/article-abstract/153/12/125102/1062851/A-workflow-for-exploring-ligand-dissociation-from?redirectedFrom=fulltext