Dr Manish S Kushwah
Supervisor Details
Research Interests
Research Fellow at Aston University, within AIME.
Research Groups
In three words or phrases: open, in-depth, collaborative.
Provision of Training
I believe in working together with the student to give them best theoretical and technical training, followed by regular discussions to maintain the course of work.
Progression Monitoring and Management
At the start of the project, I would like to have regular discussions to ensure the work progression and the understanding of the field. As the student gains experience and expertise, I expect them to design the experiments to take the work forward, discuss the experimental plan and get back to me with updates. At this stage, it is paramount that student reach out to me if they are facing insurmountable problems. Every project comes with an uncertainty of direction, both I and student must be practical and change direction if the project appears stalled. My expectation from the students is that they should become the expert in the field of their work, and I will try my best to provide the support that is needed to achieve this goal.
Communication
I don’t expect my students to spend their entire time at work, having said that, I know it is important that they are supported as much as possible. For this reason, I am available at all reasonable hours. All my students can reach out to me at all normal hours through official channels. For emergencies, you have access to my personal contact information. I am open to discuss queries, concerns, scientific and non-scientific discussions. If you need help with personal matters that are affecting your professional life, I am open to discussions and help you find out possible avenues for help.
PhD Students can expect scheduled meetings with me:
| In a group meeting | In year 1 of PhD study | In year 2 of PhD study | In year 3 of PhD study |
|---|---|---|---|
| At least once per fortnight | At least once per fortnight |
At least once per month |
At least once per month |
These meetings will be a mixture of face to face and via video chat or telephone, and I am usually contactable for an instant response on every working day.
Working Pattern
Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team.
Notice Period for Feedback
I need at least 2 weeks' notice to provide feedback on written work of up to 5000 words.
MIBTP Project Details
Current Projects (2025-26)
Primary supervisor for:
See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.
Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).
Mass photometry enabled Mechanistic Understanding of ESCRT-III complex polymerisation and membrane remodelling in Health and Disease
Secondary Supervisor(s): Professor Roslyn Bill
University of Registration: Aston University
BBSRC Research Themes: Understanding the Rules of Life (Immunology, Neuroscience and Behaviour, Stem Cells, Structural Biology)
Project Outline
ESCRT III (E-III) is a complex of membrane binding proteins that catalyse membrane remodelling and fission in a range of cellular functions such as including multivesicular bodies (MVB) biogenesis, cilia formation, neuronal pruning, wound repair, exosome biogenesis, nuclear pore maintenance, and cell division, 1–4, and is targeted in the range of diseases1,2,5–8.
Existing methods to study the mechanisms of membrane remodelling by E-III proteins2,9,10, are limited to the fully assembled polymer and provide little to no information on the early steps of polymer assembly, moreover, these techniques are unable to account for the effect of protein interactions on E-III polymerisation.
Mass photometry (MP), is a label-free microscopy technique that allows dynamics of protein-protein interaction and the affinities for purified proteins in solution 11–15 and simultaneous tracking of mass and diffusion of protein oligomers on supported bilayers (SLB), termed as Dynamic MP (DMP)16. DMP is placed perfectly to study the early stages of E-III polymerisation on membranes.
In this project, we will develop a platform which combines quantitative information on protein-protein interaction with MP with theory and functional reconstitution to understand the membrane remodelling by E-III.
This framework will be divided into following sub-projects:
- Quantitative model of E-III protein polymerisation on SLBs – Using dynamic MP, we will reconstitute E-III proteins, SNF7/CHMP4A and CHMP1B polymerisation on supported bilayers to study early steps of polymerisation and the effect of growing polymer bilayer dynamics (protein-membrane dynamics). By collaborating with experts on modelling protein-catalysed membrane deformation, we will gain theoretical understanding of E-III protein-membrane dynamics on membrane remodelling.
- Functional reconstitution of E-III membrane remodelling and fission – Using surface stabilised tubes, we will establish the reconstitution system to study the membrane remodelling and fission by E-III and incorporate the understanding from modelling to obtain fine-tuned models for E-III catalysed membrane remodelling.
- E-III protein interaction partners change in health and disease – Using SNF7/ CHMP1B as bait proteins, we will catalogue the interacting partners in heathy and diseased cells via pulldown and proteomics studies. Using dynamic MP and use protein specific nanobodies to determine the stoichiometric nature of SNF7/ CHMP1B-protein complexes.
- E-III complex function reconstitution in the presence of partner proteins – Reconstitution of SNF7/CHMP1A polymerisation in the presence of lysate of healthy or diseased cells, and using nanobodies specific to partner proteins, we will catalogue how different interacting partners recruit and modify SNF7/CMHP1B assembly and function.
References
1. Migliano, S. M., Wenzel, E. M. & Stenmark, H. Biophysical and molecular mechanisms of ESCRT functions, and their implications for disease. Curr. Opin. Cell Biol. 75, 102062 (2022).
2. McCullough, J. et al. Structure and membrane remodeling activity of ESCRT-III helical polymers. Science 350, 1548–1551 (2015).
3. Adell, M. A. Y. & Teis, D. Assembly and disassembly of the ESCRT-III membrane scission complex. FEBS Lett. 585, 3191–3196 (2011).
4. Babst, M. MVB vesicle formation: ESCRT-dependent, ESCRT-independent and everything in between. Curr. Opin. Cell Biol. 23, 452–457 (2011).
5. Gingras, M.-C., Kazan, J. M. & Pause, A. Role of ESCRT component HD-PTP/ PTPN23 in cancer. Biochem. Soc. Trans. 45, 845–854 (2017).
6. Stuffers, S., Brech, A. & Stenmark, H. ESCRT proteins in physiology and disease. Exp. Cell Res. 315, 1619–1626 (2009).
7. Gregor, L., Stock, S. & Kobold, S. ESCRT machinery: role of membrane repair mechanisms in escaping cell death. Signal Transduct. Target. Ther. 7, 238 (2022).
8. Liu, J., Kang, R. & Tang, D. ESCRT-III-mediated membrane repair in cell death and tumor resistance. Cancer Gene Ther. 28, 1–4 (2021).
9. Jukic, N., Perrino, A. P., Humbert, F., Roux, A. & Scheuring, S. Snf7 spirals sense and alter membrane curvature. Nat. Commun. 13, 2174 (2022).
10. McCullough, J., Frost, A. & Sundquist, W. I. Structures, Functions, and Dynamics of ESCRT-III/Vps4 Membrane Remodeling and Fission Complexes. Annu. Rev. Cell Dev. Biol. 34, 85–109 (2018).
11. Soltermann, F. et al. Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew. Chem. 132, 10866–10871 (2020).
12. Soltermann, F., Struwe, W. B. & Kukura, P. Label-free methods for optical in vitro characterization of protein–protein interactions. Phys. Chem. Chem. Phys. 23, 16488–16500 (2021).
13. Asor, R. et al. Cooperativity and Induced Oligomerisation Control the Interaction of SARS-CoV-2 with Its Cellular Receptor and Patient-Derived Antibodies. http://biorxiv.org/lookup/doi/10.1101/2023.09.14.557399 (2023) doi:10.1101/2023.09.14.557399.
14. Fineberg, A., Surrey, T. & Kukura, P. Quantifying the Monomer–Dimer Equilibrium of Tubulin with Mass Photometry. J. Mol. Biol. 432, 6168–6172 (2020).
15. Olerinyova, A. et al. Mass Photometry of Membrane Proteins. Chem 7, 224–236 (2021).
16. Foley, E. D. B., Kushwah, M. S., Young, G. & Kukura, P. Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers. Nat. Methods 18, 1247–1252 (2021).