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Project C7

Structural bases of proton dynamics in viroporins by multiscale modelling and simulation

Principal Investigator: Prof. Dr. Cecilia Clementi  (FUB)

This project focuses on the development and application of methods for the characterization of the long timescale conformational transitions coupled with protonation dynamics in proteins. By combining statistical mechanics, machine learning and molecular dynamic simulations, we will design coarse-grained and multiscale models to study the global structural changes coupled with deprotonation/reprotonation events in phytochromes, and the structural bases underlying proton conductance of a set of newly discovered viral proton channels (viroporins).

Publications

2021 - 2024

Glielmo, A., Husic, B.E., Rodriguez, A., Clementi, C., Noé, F., and Laio, A. (2021). Unsupervised Learning Methods for Molecular Simulation Data. Chem Rev, 121, 16, 9722–9758. doi: 10.1021/acs.chemrev.0c01195.

Lin, X., George, J.T., Schafer, N.P., Chau, K.N., Birnbaum, M.E., Clementi, C., Onuchic, J.N. and Levine, H. (2021). Rapid assessment of T-cell receptor specificity of the immune repertoire. Nat Comput Sci 1, 362–373. doi: 10.1038/s43588-021-00076-1.

Wang, J., Charron, N., Husic, B., Olsson, S., Noé, F., and Clementi, C. (2021). Multi-body effects in a coarse-grained protein force field. J Chem Phys, 154, 164113. doi: 10.1063/5.0041022.