CV

Education

• PhD Computational Chemistry, University of Southampton, UK (2024-2028)
• BSc Chemistry with Medicinal Chemistry and a Year in Industry, Imperial College London, UK (2020-2024)
• International A-levels A* A* A* A A in Chemistry, Maths, Further Maths, Physics and Biology, Yuet Wah College and Chan Sui Ki Perpetual Help College, Macau SAR China (2014-2020)
• IGCSE A* A* A* in Chemistry, Maths and Physics.

Work experience

• Computational Chemistry internship - AstraZeneca UK (July 2024 - Sep 2024)
  • Based in the new HQ The Discovery Centre (DISC) in Cambridge.
  • Computational modelling on antibody-drug-conjugate.
• Multi-Disciplinary Computational Biology industrial placement - UKRI STFC (Aug 2023 - Jul 2024)
  • Supervisors: Jas Kalayan (MD), James Gebbie-Rayet (HPC) and Joel Greer (EM)
  • Research project developing protocols for MD-based synthetic micrographs pipeline developed by STFC, Rosalind Franklin institute and TU Delft to improve protein heterogeneous reconstruction in cryoEM.
  • Bi-weekly update meeting with direct supervisors, and with project advisors Martyn Winn and Tom Burnley (CCP-EM).
• Computational Structural Biology (2022 - 2024)
  • Supervisors: Sarah Rouse
  • Parasite GAC protein project, co-supervised by Steve Matthews and Marc Morgan (ICL Life Sciences). Protein modelling with coarse-grained MD (CG-MD); steered MD coupled to SAXS; x-ray density refinement using CCP4i2 and COOT.
  • Mitochondrial protein TgMAF1 and TOM70 project, in collaboration with Lena Pernas (MPI Cologne). Transmembrane protein modelling and dynamics using MODELLER and CG-MD to obtain insight into parasite membrane tethering.
  • Class B1 GPCRs project, in collaboration with Alejandra Tomas (ICL Medicine). Using CG-MD to study lipid modulations by membrane environment, and using AT-MD to obtain insight into SUMOylation and palmitoylation in GLP-1R.
  • B1AR GPCR project, in collaboration with Carol Robinson (Oxford Chemistry). Modelling of ICL3 loop and using CG-MD and AT-MD to investigate the effect of ICL3 on MiniGas orientation.
• Experimental Structural Biology (Aug 2022 - June 2023)
  • CryoEM shadowing (supervised by PDRA Joe Barritt, Rouse lab) – theories and operation of the two microscopes in the department; cryoEM processing using RELION.
  • Protein purification shadowing (supervised by PDRA Grace Wu, Matthews lab) – recombinant protein expression and purification process from transformation, incubation, affinity purification, size exclusion chromatography.

Summer research

• Computational Biochemistry UROP (summer 2022)
  • Primary supervisor: Sarah Rouse. Secondary supervisor: Ed Tate Project title: “Rational design of synthetic cardiolipin analogues” A blue-skies, collaborative project, aimed at generating preliminary data. Keywords: CG-MD, cardiolipin analogue. This project exposed me to biomolecular simulations.
• Computational Biology UROP (summer 2021)
  • Supervised by Sarah Rouse. Project title: Towards building a mitochondrial interactome knowledge graph (KG). Keywords: Vaticle TypeDB and TypeQL coding, python, uniprot Contributed to a collaboration with the US company Vector Space Biosciences. Featured in this news.
• Digital Chemistry UROP (summer 2021)
  • Digital Chemistry summer project based Imperial College Advanced Hackspace in White City. Keywords: soldering, wiring, circuit design, Arduino IDE, python, Fusion360, laser cutting, 3D printing. Featuered in this blog post.

Publications

Human class B1 GPCR modulation by plasma membrane lipids

(6)Chao, K. W.; Wong, L.; Oqua, A. I.; Kalayan, J.; Manchanda, Y.; Gebbie-Rayet, J.; Hedger, G.; Tomas, A.; Rouse, S. L. Human Class B1 GPCR Modulation by Plasma Membrane Lipids. 2024. https://doi.org/10.1101/2024.12.19.629375.

Coupling and Activation of the β1 Adrenergic Receptor-The Role of the Third Intracellular Loop

(5)Qiu, X.; Chao, K.; Song, S.; Wang, Y.-Q.; Chen, Y.-A.; Rouse, S. L.; Yen, H.-Y.; Robinson, C. V. Coupling and Activation of the β1 Adrenergic Receptor - the Role of the Third Intracellular Loop. Journal of the American Chemical Society 2024. https://doi.org/10.1021/jacs.4c11250.

Coarse-Grained Simulations of Adeno-Associated Virus and Its Receptor Reveal Influences on Membrane Lipid Organization and Curvature

(4)Nichakorn Pipatpadungsin; Chao, K.; Rouse, S. L. Coarse-Grained Simulations of Adeno-Associated Virus and Its Receptor Reveal Influences on Membrane Lipid Organization and Curvature. The Journal of Physical Chemistry B 2024. https://doi.org/10.1021/acs.jpcb.4c03087.

Molecular mapping and functional validation of GLP-1R cholesterol binding sites in pancreatic beta cells

(3)Oqua, A. I.; Chao, K.; Eid, L. E.; Casteller, L.; Miguéns, A.; Barg, S.; Jones, B.; Bernadino, J.; Rouse, S. L.; Tomas, A. Molecular Mapping and Functional Validation of GLP-1R Cholesterol Binding Sites in Pancreatic Beta Cells. bioRxiv (Cold Spring Harbor Laboratory) 2024. https://doi.org/10.7554/elife.101011.1.

Modulation of class B GPCRs by their lipid environment

(2)Chao, K.; Affiong Oqua; Tomas, A.; Rouse, S. L. Modulation of Class B GPCRs by Their Lipid Environment. Biophysical Journal 2024, 123 (3), 152a152a. https://doi.org/10.1016/j.bpj.2023.11.1043.

Structural and regulatory insights into the glideosome-associated connector from Toxoplasma gondii

(1)Kumar, A.; Vadas, O.; Dos, N.; Zhang, X.; Chao, K.; Darvill, N.; Rasmussen, H. H.; Xu, Y.; Gloria Meng-Hsuan Lin; Stylianou, F.; Jan Skov Pedersen; Rouse, S. L.; Morgan; Soldati‐Favre, D.; Matthews, S. Structural and Regulatory Insights into the Glideosome-Associated Connector from Toxoplasma Gondii. eLife 2023, 12. https://doi.org/10.7554/elife.86049.

Talks and Poster Presentations

Modulation of Class B1 GPCRs by the Plasma Membrane Environment

July 04, 2024

15-minute talk at Dame Margaret Barbour Building, Newcastle University

Molecular Dynamics (MD) Simulations to Address Challenges in Structural Biology

December 11, 2023

15-minute talk and poster presentation at Department of Biochemistry, University of Oxford

A multiscale simulation approach to characterise the glidesome-associated connector (GAC) from Toxoplasma gondii

April 04, 2023

Poster presentation at Hotel Brooklyn, Manchester

Characterising protein-membrane interactions by molecular dynamics (MD) simulations

October 18, 2022

Poster presentation at Department of Chemistry, Imperial College London