Our Skills
The Operating Unit “PSM” collects the legacy of the former Biopolymers and Structural Proteomics, of the Structural Biology and of the Bioinformatics Units. Therefore its actual research lines are many and different.
In particular, the competences of the Unit include:
The Operating Unit “PSM” collects the legacy of the former Biopolymers and Structural Proteomics, of the Structural Biology and of the Bioinformatics Units. Therefore its actual research lines are many and different.
In particular, the competences of the Unit include:
- Cellular, Molecular and Structural Biology
- MTT Assay applied to in-vitro toxicological evaluation of compounds and / or drugs.
- Proteins / protein complex interaction identification and characterization through Tandem Affinity Purification).
- Cloning, expression, purification and crystallization of biological proteins and macromolecules.
- Three-dimensional identification of proteins- and nucleic acids- ligand complexes using X-Ray Diffraction by Macromolecules.
- Biomolecules characterization through Multi-Angle static Light Scattering (MALS) and Dynamic Light Scattering (DLS) techniques. Analyzes are carried out thanks to the collaboration with SOLEIL Synchrotron (Gif-sur-Yvette, France), and their Small-angle X-ray scattering (SAXS). Most of these techniques are coupled online with HPLC.
- Bioinformatics
- Computational Mass Spectrometry: Development of innovative algorithms and software for the management mass spectra.
- Data Mining: Development of innovative algorithms and software for significant signals extraction, and comparative analysis for prognostic/diagnostic signature identification.
- Data Integration: innovative databases development for the syntactic and semantic integration of biomedical data.
- Automation of data analysis processes: Development of automatic workflows for biomedical data integration and analysis.
- Mass spectrometry
- Protein-based biomarkers research and identification of new therapeutic targets using MALDI-MS, LC-MS or LC-MS / MS approach.
- Pharmacokinetic research using SRM / MRM quantitative analysis.
- Proteomic analysis by fingerprinting or MS / MS.
- Characterization of new molecules for Guided Drug Development.
- Evaluation of metabolic profiles.
- Isotope coded affinity tag (ICAT)
- Stable isotope labeling by/with amino acids in cell culture (SILAC)
- Isobaric tags for relative and absolute quantitation (iTRAQ)
- Molecular Modeling
- US-SOMO software suit development and maintenance. The software applications include simulations using hydrodynamic and SAXS data (University of Montana, USA collaboration).
- Three-dimensional Modeling applied to biological macromolecules with unknown structure through X-ray scattering, Cryo-EM or NMR techniques.
- Multi-resolution modeling, using the techniques mentioned above.
- Molecular dynamics simulations
- Drug design and Drug Delivery
- Lead compound guided identification based on analyses of biological targets’ 3D structures.
- Study and characterization of molecules for the Oncology field
- Study and characterization of new vaccines adjuvants used in the Oncology field
- Reposition of existing drugs through molecular docking simulations
- Study of new vectors for active or passive drug transport
- Study of fibrin gels as vehicles for local drug delivery
Clinical relevance
As an Operative Unit with different preclinical/translational research lines, the medium and long-term impact of our activities is significative for the Italian Health System. For topics as identification of tumor biomarkers for diagnostics, drugs repositioning and local release of drugs via fibrin gel, the relapse can be considered as short-term.
Laboratory and computational activities
- PCR
- Expression and purification of recombinant proteins
- Crystallization of proteins and other biological macromolecules
- 3D-structure determination of biological macromolecules by X-ray diffraction
- Electrophoretic analysis
- MALS and DLS light diffusion techniques
- Cell cultures
- Modeling of biological “in silico” macromolecules
- In-silico rational drug design
- Vector designo for drug transport based on:
- Dendrimers
- Polymers
- Macrocycles
- HydroGel and Fibrin Gel
- Apoptosis and cell cycle analysis
- Toxicological assessments (MTT test)
- Software development in LAMP environment (Linux, Apache, MySql, PHP)
- Implementation of databases and websites for research
- Qualitative Mass Spectrometry (molecular identification and characterization)
- Quantitative mass spectrometry (dosing of molecules in biological matrices)
- Chromatographic techniques (analytical and preparative)
