Biomolecular NMR: structural and interaction studies of biological macromolecules and drug discovery applications
Academic collaboration, Facility, Research field/topic, Skill
-Instrumentation Our team is provided with a cutting-edge Bruker Avance 500 MHz NMR spectrometer equipped with a nitrogen-cooled cryogenic probe. The advanced technology of this NMR instrument allows us to acquire mono and multi-dimensional NMR spectra of small molecules and macromolecules at low concentrations, due to its high sensitivity. The NMR spectrometer is optimized to study the solution structure and dynamics of proteins and nucleic acids and their interactions with peptides, and small compounds for drug-discovery applications. We can analyze samples under different buffer and temperature conditions and even in the cellular environment. The main components of the NMR spectrometer...
Cellular and Molecular Drug Profiling in Disease Models, ICB facility
Facility, Research field/topic, Skill
Cellular and Molecular Drug Profiling in Disease Models: Cell-based platforms to study drug effects in cancer and neuroinflammation models. Techniques include cell proliferation and survival assays, autophagy analysis, invasion and migration studies, and EMT-stemness profiling. Expertise includes analysis of inflammatory pathways through cytokine/chemokine assessment, immune cell polarization, and FACS-based cell surface marker characterization.
Computational Biology, Computational Enzymology, Drug Discovery, Molecular recognition, Protein-Protein-peptide interaction, Peptide design and synthesis, High Performance Computing, Surface Plasmon Resonance, ELISA, Antibody characterization
Academic collaboration, Facility, Research field/topic, Skill, Software
The Structural Biology Group at CNR-ICCOM focuses on exploring the relationship between the structure, dynamics, and function of biomolecules using a combination of computational biology tools, synthetic chemistry, and biomolecular recognition techniques. Computational Laboratory The group employs advanced methods such as molecular dynamics simulations, docking, drug discovery, and bioinformatics (from quantum to empirical force-fields) to investigate and design biological systems, ranging from small molecules and peptides to proteins and nucleic acids. Key research areas include: 1. Molecular Effects of Sequence-Structure Perturbations: Investigating the impact of binding events and mutations on the activity and interactions of proteins involved in critical biological...
Computational Chemistry and Cheminformatics, StOrMoDB platform, EHBAS platform
Facility, Research field/topic, Skill, Software
The main computational chemistry skills in the ICB Computational Chemistry and Cheminformatics group (ICB-CCC) cover the fields of homology modelling, molecular docking and molecular dynamics simulations of biomolecular systems and quantum chemistry calculations on isolated molecules or their complexes with representative protein fragments. These skills are mainly aimed at studying the driving forces at molecular level of ligand-protein interactions, the molecular bases of receptor selectivity, and the conformational transitions associated to the modulation of receptor activities. As for the main application areas of these techniques and approaches, ICB-CCC devotes a special attention to the characterization of nuclear receptors, GPCRs and...
Computational Chemistry, HPC Clusters, simulation software
Academic collaboration, Facility, Research field/topic, Skill, Software
Computational chemistry and molecular modeling. Both quantum chemistry calculations and classical reactive/non-reactive molecular dynamics simulation methods are employed. These are creatively used to investigate the conformational and physicochemical properties, dynamics, and reactivity of oligopeptides, proteins, enzymes, DNA/RNA/PNA, lipids, micelles, membranes, cellulose-based materials, polymers, small molecules, etc., in the gas phase, in solution (explicit molecules or a continuum medium), and contact with various types of inorganic interfaces (hybrid complexes). The structure and dynamics of metal and metal oxide nanoparticles (various morphologies and sizes) functionalized with different types of molecules are simulated with appropriately parametrized reactive force fields (ReaxFF - missing parameters...
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...
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...
Design, Synthesis and Characterization of Natural-Like Phenols and Hydroxylated Biphenyls with Potential Biological Activity
Facility, Research field/topic, Skill
The research activity aims to optimize the use of industrially accessible natural resources on a large scale to enhance the value of their compounds in the service of sustainable development and technological innovation. These actions require expertise and basic research, often challenging to develop within a company or industry for economic and structural reasons. A computational protein-ligand study on specific receptors is used to predict the structure of the target molecule, which guides the synthesis design. The activity focuses on chemical synthesis oriented toward the molecular diversity of small collections of phenols and hydroxylated biphenyls with natural reminiscence to identify...
DEVELOPMENT ON MOLECULAR BASIS OF SELECTIVE BIOACTIVE MOLECULES FOR THE DIAGNOSIS AND TREATMENT OF DISEASES WITH HIGH SOCIAL IMPACT
Facility, Research field/topic, Skill
The research activity is part of the development of new molecules for diagnostic and therapeutic applications with molecular approaches based on the study of the relationships between structure and biological activity aimed at the design and/or identification of selective molecules for the diagnosis and treatment of diseases with high social impact with particular reference to diseases neurodegenerative and oncological diseases with a higher incidence (Alzheimer's and Parkinson's disease, prostate cancer, colon cancer), as well as inflammatory and bacterial infectious diseases. In particular, the topics covered are: a) study of protein/protein and protein/oligonucleotide complexes; b) synthetic systems recognizable by biological targets;...
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
GPCR Drug Discovery and Pharmacological Profiling Platform, ICB facility, b-counter, multi-detection plate reader
Facility, Research field/topic, Skill
GPCR Drug Discovery and Pharmacological Profiling Platform: Screening of compound libraries to evaluate binding affinity and functional responses on GPCR targets. Expertise includes pharmacological profiling, mechanism of action studies, and preclinical evaluation of drug candidates across in vitro, in vivo, and ex vivo models, targeting therapeutic applications in cancer and neuroinflammation.
In silico structural biology to solve biological mechanisms and guide drug discovery
Academic collaboration, Facility, Patent, Research field/topic, Skill, Software
The Laboratory of Molecular Modeling and Virtual Screening (MMVS_Lab) at SCITEC-Rome integrates diverse computational expertise to investigate biological structures and processes: -Computational Chemistry: molecular dynamics simulations of biological molecules; quantum mechanical methods to analyze molecular properties; molecular docking to predict ligand-protein and protein-protein binding interactions. -Molecular Modeling: structural homology; fold recognition; conformational analysis. -Computer Science and Data Science: use of supercomputers/high-performance computing (HPC) facilities at European computing centers for complex simulations; application of machine learning and artificial intelligence (AI) to predict molecular structures and behaviors. -Bioinformatics: Sequence analysis for the prediction of functional domains and structural features of proteins. -Drug...
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...
Membrane protein structure/function relationships
Academic collaboration, Research field/topic, Skill, Software
Study of structure/function relationships of membrane proteins by combining in silico approahces with recombinant protein production, site directed mutagenesis and in vitro activity assay
Mitochondrial Bioenergetics and Oxidative Stress Analysis, ICB facility, high-resolution respirometer (Oroboros)
Facility, Research field/topic, Skill
Mitochondrial Bioenergetics and Oxidative Stress Analysis: Mitochondrial function study using high-resolution respirometry (Oroboros) for precision OXPHOS analysis. Expertise includes investigating oxidative stress via mtROS assays, bioenergetic pathway analysis, and studying metabolic shifts in intact cells, isolated mitochondria, and freshly isolated tissues. Capabilities extend to linking mitochondrial function with cellular metabolism and survival in disease contexts.
MolBD3: Molecular Bases of Diseases and Drug Design
Academic collaboration, Facility, Research field/topic, Skill
Skills in Structural Biology and Protein Biochemistry/Biophysics Experimental Techniques Protein Expression and Purification Production of recombinant proteins in bacterial, insect, yeast, and mammalian systems. Expression of isotopically labeled proteins (¹H, ¹⁵N, ¹⁵N/¹³C). X-ray Crystallography Protein crystallization. Data collection and processing. Structure determination and refinement. Cryo-Electron Microscopy (Cryo-EM) Single-particle reconstruction. Atomic model building. Small Angle X-ray Scattering (SAXS) Solution-based structural analysis. Data modeling and shape reconstruction. Bioinformatics and Computational Tools Protein Structure Modeling Homology modeling. De novo structure prediction. Docking Studies Protein-ligand docking. Protein-protein and protein-DNA/small molecule interaction modeling. Molecular Dynamics Simulations Simulation setup and execution. Analysis of trajectories. Structure Visualization...
Molecular Biology, Structural Biology, Protein-binding studies. Facility: XRD1 beamline, Cryo-EM (late 2025), Binding studies platform. Instruments: FPLCs, shakers, centrifuges, Spark (Tecan), GCI Wave-delta (Malvern), Helix+ (Bruker), ITCs (Malvern), UPLC-MS (mid 2025)
Academic collaboration, Facility, Research field/topic, Skill
Skills - Molecular Biology. The IC-Ts laboratory is deeply involved in structural biology, in this respect the laboratory has a long and important experience in molecular biology, proteins expression and purification. Structural Biology: Among the techniques used in Structural Biology at IC-Ts' laboratory, we have been using X-ray Crystallography, SAXS and NMR. Furthermore, we have recently upgraded the laboratory devoted to Protein-ligand interaction studies. Facility: IC-Ts is strongly involved in synchrotron radiation, we share at 50% XRD1 diffraction beamline with Elettra – Sincrotrone Trieste and we have a facilitated access to the XRD2 beamline. We are part of the PNRR...
Molecular dynamics, modeling, AI-based protein design.
Research field/topic, Skill, Software
Molecular Dynamics (MD): We simulate proteins to study the physical movements of atoms and molecules over time. By applying classical or biased mechanics, MD provides insights into the dynamic behavior of molecular systems, including stability, effect of mutations, binding sites. AI-Based Protein Design: We apply cutting-edge approaches that use machine learning algorithms to create, optimize, or predict the structure of proteins.
Production and characterization of soluble and membrane proteins involved in riboflavin homeostasis and related diseases
Academic collaboration, Facility, Research field/topic, Skill, Software
The laboratory of DBBA of the University of Bari (Convenzione operativa tra IBIOM e Università di Bari, prot n. 0174808 del 24/05/2024) is equipped with a Gilson HPLC system with a FP-2020 Plus Jasco fluorescence detector and Unipoint system software; a spectrophotometer; a FP-3800 spectrofluorometer; and laboratory equipment for molecular biology. At DBBA modern laboratory rooms are organised as multidisciplinary technological core consisting of different platforms: 1) proteomics 2) genomics 3) cellular engineering and biology 4) sub-cellular biochemistry and biophysics 5) Imaging facilities. DBBA also has an animal house and rooms for culturing mammalian cells and bacteria, yeasts and invertebrates...
Protein chemistry
Academic collaboration, Research field/topic, Skill
Protein chemistry, enzymology, rare diseases, drug discovery, pharmacological chaperone, Thermal Shift Assay, Cellular Thermal Shift Assay, enzymatic assay (any kind, spectrophotometric, fluorimetric, etc. assay including 31P-NMR-based assay), purification of native and recombinant proteins; expression of proteins; indirect structural studies (by CD, fluorescence, and biochemical approaches such as limited proteolysis and others). Small basic instruments are available in the lab (spectrophotometer, fluorimeter, electrophoresis, chromatography and others). Structural in silico studies are performed in collaboration with prof MV Cubellis dept Biology UNINA
Protein interactions and dynamics by solution NMR – Istrumentation: NMR spectrometers for solution studies – Advanced NMR techniques for mechanistic investigation of disease related protein systems
Academic collaboration, Facility, Research field/topic, Skill
*SKILLS: - NMR based drug design and optimization - NMR detection for protein-protein and protein/ligand interactions - Time-resolved NMR to follow misfolding and aggregation phenomena - NMR Diffusion methods for interaction and aggregation phenomena characterization - Data driven docking approaches *FACILITY INSTRUMENTATION: SCITEC-CNR has a well-established NMR Facility with 3 solution-state NMR spectrometers operating at 600 MHz, 500 MHz, 400 MHz. 600 MHz Avance Neo Bruker is equipped with triple resonance (1H, 15N, 13C) Prodigy CryoProbe ensuring the sensitivity gain necessary to fully characterize proteins interactions and dynamics employing low protein concentrations 500 MHz spectrometer is equipped with a triple...
Single Particle Anaysis, ElectronTomography, Cryo Electron Microscopy
Academic collaboration, Facility, Patent, Research field/topic, Skill, Software
The Cryo Electron Microscopy (Cryo-EM) laboratory at ISASI Naples (EYELAB) offers advanced facilities and expertise for identifying, visualizing, and characterizing biological macromolecules in their native states. It supports a comprehensive approach to studying the structure and function of proteins, nucleic acids, and other macromolecules, as well as their interactions within cells and tissues. The laboratory offers high-resolution structural analysis through Single Particle Analysis (SPA) and Electron Tomography (ET). SPA reveals the 3D structures of proteins, enzymes, and complexes in their hydrated states, providing unprecedented detail on their architecture and function. ET enables 3D visualization of cellular structures, and tissues, shedding...
Structural and Dynamic Insights into Oligopeptides through NMR and EPR
Academic collaboration, Facility, Research field/topic, Skill
My recent research focuses on the coordination of copper in oligomers of amyloid-β peptides and in peptides involved in angiogenesis, employing magnetic resonance techniques such as EPR, solution NMR, and fast field cycling NMR. Additionally, I have extensive experience investigating the internal motions of peptides and the conformational propensity of single amino acid residues using solution NMR. At CNR-ICCOM-Pisa, my group operates a fully equipped laboratory dedicated to fast field cycling NMR. I also have access to a state-of-the-art solid-state NMR facility at the Chemistry Department of Pisa University. Furthermore, I have experience in utilizing the EPR facility at the...
Structural Characterization of Biologically Relevant Molecules Across Varied Complexity Levels: Method Development, Software Implementation and Applications
Research field/topic, Skill, Software
The IC-CRYST team is a multidisciplinary group internationally recognized for advancing biomolecu-lar crystallography, from small compounds to macromolecules, and developing innovative software such as SIR for single-crystal and EXPO for powder diffraction data. Collaborating with academic and industrial partners, including pharmaceutical companies, the team excels in solving complex cases, determining protein structures, and characterizing drug compounds. Their strength lies in tai-loring in-house crystallographic tools to address the unique challenges of each case. Key Competencies in Bio-Crystallography: Structural Determination of Biological Macromolecules - Ab Initio Approaches Effective phasing strategies, utilizing SIR software, for accurate ab initio structural analysis of complex biological...
Vibrational spectroscopy FTIR/Raman/Raman SERS for protein analysis
Academic collaboration, Facility, Research field/topic, Skill, Software
Vibrational spectroscopy FTIR/Raman/Raman SERS for biomolecule analysis ICCOM Pisa has instrumentation and consolidated skills in the field of biomacromolecule identification in biological complex systems (tissues and cells) by FTIR, Raman and Raman-SERS (Bramanti, Legnaioli, Campanella), and conformational analysis of proteins (Bramanti), including skills for extracting information from spectroscopic data using advanced chemometric tools (Campanella). ICCOM team has also a facilities and skills for the characterization of proteins by UV spectroscopy, Fluorescence spectroscopy, and liquid chromatography and for study of surface tension and viscosity of proteins by a home made dynamic surface tension detector (DSTD). These facilities allow strict collaborations with...