Proteins and RNA Modeling

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

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

Codes: NAMD, VMD

Related publications:

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

Example of a 3D predicted structure for an exon of a long non coding RNA

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).