TBA

Data inizio

20/06/2024 13:00

Data fine

20/06/2024 15:00

Luogo

Dipartimento di Fisica - A501

Relatori

Alessio Bartocci
Università di Trento

The association of ligands to proteins is regulated by interactions between the molecule and protein residues at the binding site, which can be located in a binding pocket or on the protein surface.
Such interactions can directly modulate protein functions and conformations, with possible implications for biophysical processes such as protein co-crystallisation [1-3] or selective molecular design [4].
Computational methods to study these systems, as molecular dynamics simulations (MDs) which can range from atomistic to coarse-grained resolution [5,6], provide insights into the mechanisms, kinetics and thermodynamics underlying protein-ligand complex formation.

Here, it will be discussed how these supramolecular structures may be described by these approaches, highlighting characteristic fingerprints and key models for interactions.

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[2] Bartocci, A., Pereira, G.P., Cecchini, M., Dumont, E. JCIM 62, 6739-6748 (2022)
[3] Bartocci, A., Dumont, E. J. Chem. Phys. 160, 105101 (2024)
[4] Heinzelmann, G., Henriksen, N.M., Gilson, M.K. JCTC 13, 3260-3275 (2017)
[5] Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H. J. Phys. Chem. B 111, 7812-7824 (2007)
[6] Souza, P.C.T., Thallmair, S., Conflitti, Ramírez-Palacios, P.C., Alessandri, R., Raniolo, S., Limongelli, V., Marrink, S.J. Nat. Comm. 11, 1-11 (2020)