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.
Collaborators: G. Cottone, L. Maragliano, T.E. Maillavin
Codes: NAMD, VMD
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).
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
Related publications: 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).