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Giulio Alberini

Visiting Scientist
Neuroscience and Smart Materials
Telefono
Research center
Interests
Biografia

I am a researcher in the field of computational biophysics.

Currently, my research interests are focused on the study of structural properties of biological macromolecules. My experience is mainly based on structural modeling and molecular dynamics simulations of these systems. More generally, I use different bioinformatic methods for understanding biological data.

Project I: structural validation of structural models of paracellular channels and design of novel molecules able to modulate the paracellular permeability. 

Gene/Protein

CLDN5/Claudin 5 

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Project II:  understanding the molecular mechanisms of ion channels related to conductivity, selectivity and investigating the impact of disease associated variants. 

Gene/Protein

SCN2A/Nav1.2

KCNQ2/Kv7.2

Education

Title: Ph.D. (Dottorato di Ricerca) in Neurosciences
Institute: Università degli Studi di Genova
Location: Genova
Country: Italy
From: 2016 To: 2019

Title: M.Sc. student - M.Sc. (Laurea Magistrale) in Nuclear Engineering (ongoing)
Institute: Università degli Studi di Pisa
Location: Pisa
Country: Italy
From: 2020 To: null

Title: M.Sc. (Laurea Magistrale) in Physics
Institute: Università Cattolica del Sacro Cuore
Location: Brescia/Roma
Country: Italy
From: 2014 To: 2016

Title: M.Sc. (Laurea Magistrale) in Mathematics
Institute: Università Cattolica del Sacro Cuore
Location: Brescia
Country: Italy
From: 2012 To: 2014

Title: B.Sc. (Laurea) in Physics
Institute: Università Cattolica del Sacro Cuore
Location: Brescia
Country: Italy
From: 2008 To: 2012

Skills

Molecular modeling
- Homology protein modeling (Modeller, Swiss Model)
- Protein modeling (I-TASSER)
- Ab initio protein modeling (Quark)
- Protein modeling and refinement (Galaxy, FG-MD)

Docking (Protein-ligand | Protein-protein|Protein-peptide)
- Autodock vina | ClusPro, Rosetta | FlexPepDock, Piper-FlexPepDock

Molecular dynamics
- All-atom molecular dynamics simulations (NAMD, GROMACS, CHARMM)

Enhanced sampling molecular dynamics
- Temperature accelerated molecular dynamics, TAMD (NAMD)
- Adaptive biasing force calculations, ABF (NAMD)
- Steered molecular dynamics, SMD (NAMD)

Thermodynamic calculations
- Temperature accelerated molecular dynamics, TAMD (NAMD)
- Umbrella sampling, US (NAMD, GROMACS)
- Metadynamics (NAMD, GROMACS)
- Adaptive biasing force calculations, ABF (NAMD)

Kinetic calculations
- Milestoning (NAMD)

Force fields
- CHARMM
- AMBER

Interactive visualization and analysis
- UCSF Chimera
- ChimeraX
- VMD

UNIX operating systems

Peptide design

Functional annotation of voltage gated ion channels

All Publications
2023
Berselli A., Alberini G., Benfenati F., Maragliano L.
The impact of pathogenic and artificial mutations on Claudin-5 selectivity from molecular dynamics simulations
Computational and Structural Biotechnology Journal, vol. 21, pp. 2640-2653
2023
Franchi F., Marte A., Corradi B., Sterlini B., Alberini G., Romei A., De Fusco A., Vogel A., Maragliano L., Baldelli P., Corradi A., Valente P., Benfenati F.
The intramembrane COOH-terminal domain of PRRT2 regulates voltage-dependent Na+ channels
Journal of Biological Chemistry, vol. 299, (no. 5)
Article Journal
2022
Berselli A., Alberini G., Benfenati F., Maragliano L.
Computational Assessment of Different Structural Models for Claudin-5 Complexes in Blood-Brain Barrier Tight Junctions
ACS Chemical Neuroscience, vol. 13, (no. 14), pp. 2140-2153
2022
Berselli A., Alberini G., Benfenati F., Maragliano L.
Computational study of ion permeation through claudin-4 paracellular channels
Annals of the New York Academy of Sciences, vol. 1516, (no. 1), pp. 162-174
2022
Alberini G., Alexis Paz S., Corradi B., Abrams C.F., Benfenati F., Maragliano L.
Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels
Journal of Chemical Theory and Computation