Data for Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase.
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Rotation of ATP synthase c-ring
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Rotation of ATP synthase c-ring from MD simulations
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Thermodynamic bases of thermogenesis by quantum chemistry and kinetic modelling
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| Type | Research Internship |
|---|---|
| Level | Master’s student |
| Duration | 6 months |
| Start | January 2025 earliest |
| Salary | ~ 500€/month |
| Location | ISA, Lyon, France |
| Contact | Dr Florian Blanc (florian.blanc_at_isa-lyon.fr), Prof. Christophe Morell (christophe.morell_at_univ-lyon1.fr) |
publications
Myosin MyTH4-FERM Structures Highlight Important Principles of Convergent Evolution
Proceedings of the National Academy of Sciences, 2016
Crystallography, binding affinity assays and MD simulations reveal “molecular tinkering” at play in the evolution of microtubule-binding domains in myosin tails.
Vicente José Planelles‑Herrero, Florian Blanc, Serena Sirigu, Helena Sirkia, Jeffrey Clause, Yannick Sourigues, Daniel O. Johnsrud, Béatrice Amigues, Marco Cecchini, Susan P. Gilbert, Anne Houdusse, and Margaret A. Titus (2016). "Myosin MyTH4-FERM Structures Highlight Important Principles of Convergent Evolution." Proceedings of the National Academy of Sciences. 11321. https://doi.org/10.1073/pnas.1600736113
The Myosin X Motor Is Optimized for Movement on Actin Bundles
Nature Communications, 2016
Crystallography, single-molecule studies and implicit solvent simulations reveal how myosin X is optimised to walk fast on F-actin bundles.
Virginie Ropars*, Zhaohui Yang*, Tatiana Isabet*, Florian Blanc, Kaifeng Zhou, Tianming Lin, Xiaoyan Liu, Pascale Hissier,Frédéric Samazan, Béatrice Amigues, Eric D. Yang, Hyokeun Park, Olena Pylypenko, Marco Cecchini, Charles Sindelar, H. Lee Sweeney and Anne Houdusse (2016). "The Myosin X Motor Is Optimized for Movement on Actin Bundles." Nature Communications. https://doi.org/10.1038/ncomms12456
An Intermediate Along the Recovery Stroke of Myosin VI Revealed by X-ray Crystallography and Molecular Dynamics
Proceedings of the National Academy of Sciences, 2018
With crystallography, conventional MD and ABF, we characterise a structural state of the myosin motor domain which suggests a “ratchet-like” mechanism in which lever-arm repriming precedes active site closure and is not strongly coupled to it.
Florian Blanc, Tatiana Isabet, Hannah Benisty, H. Lee Sweeney, Marco Cecchini, Anne Houdusse (2018). "An Intermediate Along the Recovery Stroke of Myosin VI Revealed by X-ray Crystallography and Molecular Dynamics." Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1711512115
In Situ Structural Analysis of SARS-CoV-2 Spike Reveals Flexibility Mediated by Three Hinges
Science, 2020
In situ cryo-ET and molecular modelling reveal the hinges of the SARS-CoV-2 a few months into the pandemic.
Turoňová*, B., Sikora*, M., Schürmann*, C., Hagen, W.J.H., Welsch, S., Blanc, F.E.C., von Bülow, S., Gecht, M., Bagola, K., Hörner, C., van Zandbergen, G., Landry, J., Trevisan Doimo de Azevedo N., Mosalaganti, S., Schwarz, A., Covino, R., Mühlebach, M.D., Hummer, G., Locker, J.K., Beck, M. (2020). "In Situ Structural Analysis of SARS-CoV-2 Spike Reveals Flexibility Mediated by Three Hinges." Science. Volume(Number). https://doi.org/10.1126/science.abd5223
An Asymmetric Mechanism in a Symmetric Molecular Machine
The Journal of Physical Chemistry Letters, 2021
We combine ABF and the string method to look at how a synthetic molecular muscle contracts, and show that an asymmetric pathway in which subunits bend and rearrange sequentially dominates despite the symmetry of the supra-molecule.
Florian Blanc, Marco Cecchini (2021). "An Asymmetric Mechanism in a Symmetric Molecular Machine." The Journal of Physical Chemistry Letters. 1213. https://doi.org/10.1021/acs.jpclett.1c00404
Computational Epitope Map of SARS-CoV-2 Spike Protein
PLOS Computational Biology, 2021
We build one of the first complete models of the SARS-CoV-2 spike protein, simulate a viral membrane patch with 4 spike copies for 2.5 microseconds, and devise a machine learning approach to predict immunogenic sites from the simulation.
Sikora, M.*, von Bülow, S.*, Blanc, F.E.C.*, Gecht, M.*, Covino, R.*, Hummer, G. (2021). "Computational Epitope Map of SARS-CoV-2 Spike Protein." PLOS Computational Biology. 174. https://doi.org/10.1371/journal.pcbi.1008790
Antibody Accessibility Determines Location of Spike Surface Mutations in SARS-CoV-2 Variants
PLOS Computational Biology, 2023
Using data from the early days of the pandemic, we show that surface accessibility to antibodies -estimated using a simple computational protocol- is a predictor of mutation sites found in later variants of concern.
von Bülow, S., Sikora, M., Blanc, F.E.C., Covino, R., Hummer, G. (2023). "Antibody Accessibility Determines Location of Spike Surface Mutations in SARS-CoV-2 Variants." PLOS Computational Biology. 191. https://doi.org/10.1371/journal.pcbi.1010822
Molecular Mechanisms of Inorganic-Phosphate Release from the Core and Barbed End of Actin Filaments
Nature Structural & Molecular Biology, 2023
We combine cryo-EM, enhanced sampling MD simulations, machine learning, and in vivo and in vitro reconstitution to reveal the mechanism and pathway for Pi release from F-actin, both from filament interior and barbed end.
W. Oosterheert*, F.E.C. Blanc*, A. Roy, A. Belyy, O. Hofnagel, G. Hummer, P. Bieling, S. Raunser (2023). "Molecular Mechanisms of Inorganic-Phosphate Release from the Core and Barbed End of Actin Filaments." Nature Structural & Molecular Biology. https://doi.org/10.1038/s41594-023-01101-9
Mechanism of Proton-Powered c-Ring Rotation in a Mitochondrial ATP Synthase
Proceedings of the National Academy of Sciences, 2024
With extensive eABF calculations, we reveal the mechanism of the 36 deg rotation step of the ATP synthase rotor, clarifying the water-mediated proton transfer pathway and the role of experimentally-detected intermediates.
Blanc, Florian E. C. and Hummer, Gerhard (2024). "Mechanism of Proton-Powered c-Ring Rotation in a Mitochondrial ATP Synthase." Proceedings of the National Academy of Sciences. 12111. https://doi.org/10.1073/pnas.2314199121
A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis
PLOS Computational Biology, 2024
With eABF and the string method, we find that the recovery stroke of myosin VI is initiated by lever-arm re-priming with only weak coupling to ATPase activation.
Florian E.C. Blanc*, Anne Houdusse, Marco Cecchini* (2024). "A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis" https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012005
teaching
Traitement stochastique du signal biomédical
Graduate course, Institut Supérieur des BioSciences (ISBS), 2014
- Spectral analysis: Fourier transform, wavelet transform
- Machine learning: principal component analysis, support vector machines
Biologie Structurale et Modélisation
Graduate course, Université de Strasbourg, 2016
- Introduction to statistical mechanics (microcanonical ensemble, canonical ensemble, free energy, chemical potential).
- Normal mode analysis of protein dynamics (practical session)
Méthodologie Scientifique
Undergraduate course, Université de Strasbourg, 2017
Elementary calculus, linear algebra, Euclidean geometry, trigonometry, probabilities and statistics.
Computational drug discovery
Graduate course, Goethe University Frankfurt, 2021
- Introduction to MD simulations of proteins and small drug-like molecules.
- Statistical-mechanical theory of binding affinity.
- Binding free energy calculations.
- Kinetic perspectives on binding affinity estimation.