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Giulio Alberini

Visiting Scientist
Neuroscience and Smart Materials
Telefono
Research center
Interests
Informazioni su

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
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
Article Journal
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
Article Book Series
2022
Berselli A., Benfenati F., Maragliano L., Alberini G.
Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces
Computational and Structural Biotechnology Journal, vol. 20, pp. 5984-6010
Review Journal
2021
Alberini G., Benfenati F., Maragliano L.
Structural Mechanism of ω-Currents in a mutated Kv7.2 voltage sensor domain from molecular dynamics simulations
Journal of Chemical Information and Modeling
Article in Press Journal
2020
Malerba F., Alberini G., Balagura G., Marchese F., Amadori E., Riva A., Vari M. S., Gennaro E., Madia F., Salpietro V., Angriman M., Giordano L., Accorsi P., Trivisano M., Specchio N., Russo A., Gobbi G., Raviglione F., Pisano T., Marini C., Mancardi M. M., Nobili L., Freri E., Castellotti B., Capovilla G., Coppola A., Verrotti A., Martelli P., Miceli F., Maragliano L., Benfenati F., Cilio M. R., Johannesen K. M., Møller R. S., Ceulemans B., Minetti C., Weckhuysen S., Zara F., Taglialatela M., Striano P.
Genotype-phenotype correlations in patients with de novo KCNQ2 pathogenic variants
Neurology: Genetics