Proteins Modeling
We work at the modeling of membrane proteins, in particular nicotinic receptors, to investigate the relationship between structure and function.
The most intriguing part of the investigation is the understanding of the open-to-close gating transition.
We use standard and advanced sampling statistical mechanics methods, based on molecular dynamics simulations.
Snapshot from an all-atom molecular dynamics simulation of the alpha7 nicotinic receptor embedded in the cellular lipidic membrane
Collaborators: G. Cottone, L. Maragliano, T.E. Maillavin, M. Lauricella.
Codes: NAMD, VMD
Related publications:
Guardiani, F. Cecconi, L. Chiodo, G. Cottone, P. Malgaretti, L. Maragliano, M. L. Barabash, G. Camisasca, M. Ceccarelli, B. Corry, R. Roth, A. Giacomello, B. Roux, “Computational methods and theory for ion channel research”, Advances in Physics: X 7, 2080587 (2022).
Lauricella, L. Chiodo, F. Bonaccorso, M. Durve, A. Montessori, A. Tiribocchi, A. Loppini, S. Filippi, S. Succi, “Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling”, Communications in Computational Physics (2022).
Cottone, L. Chiodo, L. Maragliano, M.-R. Popoff, C. Razetti-Escargueil, E. Lemichez, T.E. Malliavin, “In silico conformational features of botulinum toxins A1 and E1 according to intraluminal acidification”, Toxins (2022).
L. Chiodo, T. E. Malliavin, S. Giuffrida, L. Maragliano, G. Cottone, “Closed-locked and apo-resting state structures of the human α7 nicotinic receptor: a computational study”, J Chem Inf Model 58, 2278 (2018).
L. Chiodo, T. E. Malliavin, L. Maragliano, G. Cottone, “A possible desensitized state conformation of the human α7 nicotinic receptor: a molecular dynamics study”, Biophys. Chem. 229, 99-109 (2017).
L. Chiodo, T. E. Malliavin, L. Maragliano, G. Cottone, G. Ciccotti, “A structural model of the human α7 nicotinic receptor in an open conformation”, Plos One 10 (7), e0133011 (2015).
RNA Modeling
We work at the modeling of RNA – proteins interaction. In particular, we investigate the role of secondary and tertiary structure of long non coding RNAs in their interaction with proteins.
Collaborators: G. Cottone, F. Guerrieri, M. Levrero
Codes: ITasser, DotKnot, catRAPID, NPDock, HEX, HADDOCK
Example of a 3D predicted structure for an exon of a long non coding RNA
Related publications:
A. G. Matarrese, A. Loppini, M. Nicoletti, S. Filippi, L. Chiodo, “Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective”, Journal of Biomolecular Structure & Dynamics (2022).
D. Salerno, L. Chiodo, V. Alfano,et al., “Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription”, Gut (2020).
