Biocrystal Facility
Academic collaboration, Facility, Industrial collaboration, Skill
The Biocrystal facility, a large multidisciplinary laboratory established at the Institute of Molecular Biology and Pathology (IBPM) of CNR, in collaboration with the Biochemistry Department of Sapienza University aims at supporting the Italian scientists and the pharmaceutical companies in the research to find new drug and vaccine against the endemic and epidemic diseases through structure-based drug design. The Biocrystal facility is part of the ITACA.SB INFRASTRUCTURE financed by the Mission 4 / Education and Research Component 2: from research to business, Investment 3.1: Fund for the realisation of an integrated system of research and innovation infrastructures. The main Biocrystal Facility...
Computational Modelling, HPC Linux cluster, Modelling software, computational biophysics, academic collaborations, industrial collaborations
Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill
Computational Modelling: The main research directions developed in the lab are in silico drug discovery and modelling of basic biomolecular mechanisms on protein targets. Prediction of structure-function relationships is carried out by using all-atom computational modelling and Molecular Dynamics and by developing specific analysis methods based on statistical mechanics and AI. Computational drug discovery projects are enhanced by machine learning and strongly rely on in silico virtual screening and molecular docking. Starting from a protein target of interest, this approach leads to designing candidate hits as well as predicting their biological activity and pharmacokinetic parameters. Within SCITEC, our work relies...
Cryo-electron microscopy , IOM cryo-EM facility (CMF), Electron Microscope
Academic collaboration, Facility, Industrial collaboration, Skill
Cryo-Electron Microscopy (Cryo-EM) is an advanced imaging technique used to determine the three-dimensional (3D) structure of biological molecules and complexes at near-atomic resolution. In this method, the sample is rapidly frozen at temperatures below -150 °C, encapsulating it in vitreous ice. The specimen is then imaged from various angles using an electron microscope, where a beam of electrons passes through the sample, producing a series of two-dimensional (2D) projections. Advanced computational algorithms are employed to reconstruct a 3D model of the sample from these projections. The CMF is equipped with the necessary instruments to conduct cryo-electron microscopy studies, including single-particle...
CUBE Computational Unit for Biological Exploration
Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill, Software
Background and skills: Recent years have seen ground-breaking achievements of deep-learning methods applied to the 3D structure predictions of biomacromolecules, with the phenomenal success of AlphaFold software in obtaining protein structures at an unprecedented level of accuracy. The availability of huge data on predicted protein structures is revolutionizing the field of experimental structural biology (based on classical X-ray, NMR and Cry-EM methods) making the frontier between experimental and computational approaches more and more blurred. In this context, it is increasingly important to integrate the outcomes from the different techniques in order to favour the mutual exchange, validation, enhancement of experimental...
Glycomics, Bottom-up proteomics, Structural analysis of Glycoconjugates. Gglycoproteomics and MS laboratories
Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill
Glycomics: sample preparation from biological fluids, cells and tissues, permethylation analysis, Rapifluor derivatization, HILIC separation, MS detection, MSMS analysis in healthy and pathological conditions (CDGs, neurodegenerations, inflammatory diseases) Proteomics: enzymatic digestions, peptide separation (multi-dimensional), MALDI LC-MS/MSMS, ESI LC-MS/MSMS. Glycoconjugate characterization: LipoPolysaccharides, Lipid-A, core OS, LPS characterization by MALDI MS. Immunopurification of targeted glycobiomarkers. Instrumentation: -MALDI 4800 AB Sciex -MALDI UltraflExtreme Bruker -Exactive Orbitrap Thermo Scientific -Fortis TSQ Thermo Scientific -Exploris 120 Orbitrap Thermo Scientific
Integrative approaches of structural biology by multi-scale imaging applied to single protein for “in vitro” and “in vivo” pre-clinical screening of bioactive compounds. NeuroChemistry and Cell Signaling Lab (CristinoLab)/ Cryostat; Utramicrotome; INCUCYTE SYSTEM; LIVE CELL MICROSCOPY” WORKSTATION; ZOOM/AIVIA/MetaMorph Software.
Academic collaboration, Facility, Industrial collaboration, Research field/topic, Skill
How do molecular machines work, interact, and harmonize their activities to create a fully functional cell? How are these processes regulated in physiological conditions or deregulated in pathological ones like those in human disease? The Structural Biology approach of the Cristino Lab aims to answer these questions by gaining precise knowledge of the spatial identity and distribution of macromolecules and macromolecular complexes within cellular compartments (lysosomes, mitochondria, rough endoplasmic reticulum, Golgi apparatus, membranes, and nucleus), tissues, and anatomically well-defined structures (brain, synapses, choroid plexus, gut barrier, blood-brain barrier, tight junctions, exosomes, nanovesicles, neurovascular unit, neuromuscular junction, retina). The Cristino Lab's...
Spontaneous Raman Microspectroscopy, Scanning Probe Microscopy, Machine Learning and Deep Learning
Academic collaboration, Facility, Industrial collaboration, Skill
My group is focused on the application of Raman spectroscopy to cancer tissues for a complete grading of variuos type of cancers. For such topics we emply machine learing and deep learing techniques for managing large datasets. In addition, we use Raman spectroscopy for a characterization of biological samples, such as cells, etc. Another activity of our group is the synthesis of nanocomposites for antiviral application, making use of electrospinning techniques and drug delivery, nanoparticles etc., making use of microfluidic device. In turn, we are active on quantum biology.