Cyan Ching

Cyan Ching

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

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Pages

Posts

Future Blog Post

less than 1 minute read

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Blog Post number 4

less than 1 minute read

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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 3

less than 1 minute read

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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 2

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 1

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

portfolio

European Forum Alpbach

Granted full scholarship to attend the European Forum Alpbach 2024 in Alpbach, Austria. The European Forum Alpbach is a yearly event since 1945 that brings together global leaders from science, politics, business, civil society, arts, and culture, alongside young scholarship holders from around the world to generate ideas and spark actions to create a better future for Europe. Completed European Space Policy Institute’s Inaugural Space Policy Bootcamp, titled “The Unfolding Space Revolution: Space for Prosperity, Peace & Future Generations”. I am also a founding member of the AI startup Lawgic with fellow scholarship holders: Adrianna Czechowska and Artur Willonski. Lawgic was selected by Alpbach IDEAS 2024, and won Red Bull Basement Poland, 2024.

Guided tour at the Curie Museum

Providing guided tours of the Curie Museum for visiting academics and students in 2022-2024. Content of the tour includes the general history of radioactivity research, the scientific, and societal significance of discoveries and innovations made by the Curie family, explanations of working mechanisms of the exhibits, and their associated anecdotes, etc. Provided tours to high school students from Lycée Louis-le-Grand in Paris, France, Horsens Gymnasium in Horsens, Denmark, and to bachelor students from St. Norbert College, Wisconsin, the US up til May 2024.

Science communication at French high schools

Volunteered as a science communicator of Déclics (12 2022 & 11 2023), a French non-profit initiative that organises meetings between high school students and researchers to spark and encourage scientific interests in the young generation. Visited and exchanged with high school students at Lycée Victor Hugo, Lycée Stanislas, and Lycée Pierre-Gilles de Gennes - ENCPB.

Twitter paper bot

Set up and have been maintaining a Twitter bot (@Pha_Tran_Papers) that posts the latest papers on the topic of biomolecular phase transition since 2020. More than 3k followers up until July, 2023. The code for Scitify, a custom tool I developed to automatically retrieve the latest scientific publications based on specified research interests, is now open source and supports my bot.

Science Spreaders

Board member (2018-2019) of the Science Spreaders, a student-led non-profit group at Heidelberg University that organised educational events to engage university students and the general public in keeping up with the latest socially relevant science and technology. As an example, a public symposium featuring the past, present, and the future of artificial intelligence.

UAEM

Board member (2018-2020) of the Heidelberg University chapter of Universities Allied for Essential Medicines (UAEM), a global student-led non-governmental organisation that aims to improve access and affordability of essential medicines around the world. In particular, UAEM strives to increase research and development of medicines for neglected diseases. Organised public lecture series to raise awareness of access to medicine/medical care crisis for wide-spread diseases such as tuberculosis and snake bite.

MedCo

PR manager for the medicine committee of University College Utrecht, 2017-2018. MedCo specialised in organising activities to equip students with essential education of basic medical skills by combining cure and care. E.g., first aid courses, the basic suturing workshop, lecture on the importance of keeping a healthy circadian rhythm, etc.

Liberal Academics Society

A platform for university students to share their knowledge, ideas, and skills to peers and beyond. Founder of the Liberal Academics Society in 2016 at University College Utrecht, an honours college of Utrecht University. With two generations of board members, we organised public interactive lecture sessions for undergraduate students to share their academic as well as non-academic knowledge, ideas, and skills. E.g., quantum mechanics: fiction versus reality, misconceptions about crocodiles, convert mental health struggles into growth, songwriting from the heart with the help of a loop panel, etc.

publications

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

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

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

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

talks

teaching

Master internship student supervison

Master year 1 internship, the Physical Chemistry Curie Lab, Institut Curie, 2022

Assisted supervision of the following master year 1 students from the Master Biologie Moléculaire et Cellulaire programme at Sorbonne University in membrane protein purification (theory & practice): Kailun Liu (currently a research intern at Johns Hopkins University in Baltimore, the US) & Hugo Bost (currently a PhD student at the Architecture et Fonction des Macromolécules Biologiques Laboratory in Marseilles, France). Both Kailun and Hugo spent 2 months working in our team.

Image Processing for Electron Microscopy – Tomography course trainer

Practical course, Institut Pasteur, 2023

Trainer of the one-week (6-10th of November, 2023) practical course: Image Processing for Electron Microscopy focused on (Cryo-)Tomography (IPEMtomo). This course aims to inform basic concepts in image processing for cryo-electron tomography, and help students gain practical experience in tomographic reconstruction (e.g., processing of low-dose tilt series with and without fiducials for 3D volume annotation or subtomogram averaging). An introduction to subtomogram averaging and initial model generation steps will also be covered. We welcome PhD students, post-doctoral fellows, engineers, and researchers to register by the 30th of September. A maximum of 12 participants will be selected. Applicants who already have tilt-series for processing will be prioritized.