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Dipartimento di Fisica e Scienze della Terra

 

Welcome to the web pages of the Biophysics section at the Department of Physics and Earth Sciences.

Our research activities are focused on structural and dynamical properties of biological macromolecules.

Detailed descriptions can be found in the personal web pages linked in the left column.

Development of photochromic proteins for superresolution microscopy

 

The development of genetically encoded photoswitchable fluorescent proteins is of greatest interest to expand the toolkit of fluorescent reporters suitable for super-resolution microscopy applications based on random activation of single molecules.
We are exploiting YtvA, a photochromicblue light photoreceptor from Bacillus subtilis, as a fluorescent probe for superresolution microscopy. Current efforst include novel GAF domains.


 

Protein based nanocarriers for applications in photodynamic therapy

We exploit proteins as nanosized carriers for photosensitizers. The nanostructured materials are inherently theranostic devices, with built in terapeutic (photosensitized production of singlet oxygen) and diagnostic (through their fluorescence emission) capabilities.

 

 

 


 

Ligand migration in hemeproteins

 

The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. Through an integrated approach using quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations we try to gain insight into the migration mechanism of ligands.


 

 

Protein-solvent interactions

 

Water molecules play an active role in biomolecular recognition due to the partial desolvation of the ligand as well as of the region of the receptor involved in the ligand recognition process, involving rearrangement of water molecules close to the active site. Association processes between biomolecules immersed in an aqueous solvent, require water reorganization in the contact surface. Reorganization in the solvation structure of the two binding partners leads to subtle changes in the water hydrogen-bonding network that may have direct consequences over the whole binding process, especially when water molecules are embedded in a ligand-recognition cavity.

Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process.


 

Structure and dynamics of proteins by means of computational methods