Nuclear Magnetic Resonance (NMR) spectroscopy in solution can effectively recognize and characterize protein state heterogeneity and can simultaneously probe the structures and dynamics of proteins and their complexes with atomic resolution. It can also detect sparsely populated, high-energy conformational states of proteins with population fractions close to 1% and lifetimes from µs to ms....
Small Angle X-ray Scattering (SAXS) is widely used in the study of biomolecules, providing valuable insights into their structural properties and behavior in solution. SAXS is particularly suitable for investigating biomolecules' overall shape, size, conformation, and flexibility, including proteins, nucleic acids, and complexes. In the case of proteins, SAXS can provide information about...
Computer simulations are becoming an inevitable tool for describing the dynamics and function of biological macromolecules at various levels of resolution, in particular at the atomistic level. Among motions particularly important are those related to the transport processes. The complex topology of macromolecular channels and the transient nature of the penetrant passage pose difficulties in...
Non-tubercolous mycobacteria (NTM) encompass a diverse group of 172 species with distinct virulence features, that differentiate from the M. tuberculosis complex. NTM are widely distributed in the environment and affect individuals with chronic pulmonary diseases like cystic fibrosis (CF), leading to severe infections.
Among NTM, M. abscessus is emerging as one of the most virulent pathogens,...
The interplay between pathogens and their targets is the focus of research in our department. We are particularly interested in the molecular interactions and molecular mechanisms of action that lead to various pathological conditions in humans, animals or plants. Plants are vital and an essential resource for food, water, medicine, oxygen, habitat, climate and more. But plants also get sick....
In recent decades the extracellular matrix (ECM) has aroused growing interest in biomedical and regenerative fields. It is a complex network made by different macromolecules, in which the main component is the type I collagen, a fibril-forming protein characterized by a tissue-specific morphology. Its hierarchical structure, with specific functional domains, supplies bio-physical support to...
The field of cryo-electron microscopy (cryo-EM) has seen rapid development and significant technical improvements in the last decade. Perhaps most important have been the advances in sample preparation, direct electron detectors and data analysis for which the Nobel Prize in Chemistry was awarded in 2017. Cryo-EM has become an important tool for gaining structural insights into cells,...
We present DeLA-Drug,(1) a recurrent neural network (RNN) model composed of two Long Short-Term Memory (LSTM) layers and conceived for data-driven generation of drug-like compounds. DeLA-Drug captures the syntax of SMILES strings of more than 1 million molecules belonging to the ChEMBL28 database and generates analogues starting from a single user-defined query compound by employing a new...
Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks for the de novo design of polyhedral protein nanostructures, using topological design principles distinct from natural globular proteins. While the CCPO strategy has proven successful in designing various protein topologies, obtaining high-resolution structural information has remained challenging due to the small size...
Neurodegenerative disorders (NDs) such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and prion diseases are some of the most common forms of age-related diseases. Even if pathogenesis of these neurodegenerative diseases remains unclear, increasing evidence point out a common critical molecular process involving the assembly of various aggregated proteins with a β-sheet conformation,...
