A5004111266- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- SARS-CoV-2 and COVID-19 Research
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Influenza Virus Research Studies
- Machine Learning in Materials Science
- Monoclonal and Polyclonal Antibodies Research
- Amyotrophic Lateral Sclerosis Research
- Receptor Mechanisms and Signaling
- Molecular spectroscopy and chirality
- vaccines and immunoinformatics approaches
- Protein purification and stability
- Prion Diseases and Protein Misfolding
- Infant Nutrition and Health
- Biochemical Acid Research Studies
- Metal-Organic Frameworks: Synthesis and Applications
- Bacteriophages and microbial interactions
- Asthma and respiratory diseases
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Glycosylation and Glycoproteins Research
- Fungal and yeast genetics research
- Magnetism in coordination complexes
- Spectroscopy and Quantum Chemical Studies
Italian Institute of Technology
2020-2025
Center for Nano Science and Technology
2022
Sapienza University of Rome
2017-2020
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions proteins surfaces. This innovative general procedure, based on representation molecular iso-electron density surface in terms 2D Zernike polynomials, allows rapid quantitative assessment geometrical shape interacting proteins, that was unfeasible with previous methods. first tested large dataset known protein complexes obtaining an overall area under ROC...
Abstract Motivation Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing temperature at which proteins are stable has important theoretical implications, intimately linked with properties native fold, and wide range potential applications from drug design to optimization enzyme activity. Results Here, we present novel graph-theoretical framework assess based on structure without any priori information. In this approach describe as...
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions protein surfaces. This innovative general procedure, based on representation molecular iso-electron density surface in terms 2D Zernike polynomials, allows rapid quantitative assessment geometrical shape interacting proteins, that was unfeasible with previous methods. first tested large dataset known complexes obtaining an overall area under ROC curve 0.76...
Despite the huge effort to contain infection, novel SARS-CoV-2 coronavirus has rapidly become pandemic, mainly due its extremely high human-to-human transmission capability, and a surprisingly viral charge of symptom-less people. While seek for vaccine is still ongoing, promising results have been obtained with antiviral compounds. In particular, lactoferrin regarded beneficial effects both in preventing soothing infection. Here, we explore possible molecular mechanisms which interferes cell...
Abstract What are the molecular determinants of protein–protein binding affinity and whether they similar to those regulating fold stability two major questions biology, whose answers bring important implications both from a theoretical applicative point view. Here, we analyze chemical physical features on large dataset complexes with reliable experimental data compare them set monomeric proteins for which melting temperature was available. In particular, probed spatial organization protein...
Abstract Motivation Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic protein-protein binding regions, and it critical in influencing stability complex. Measuring such great importance for number theoretical practical implications, however, only limited tools are currently available to efficiently rapidly assess it. Results Here, we introduce Zepyros-ISC, webserver fast measuring shape between two given complex using structural information....
Among the many aspects that characterize COVID-19 pandemic, two seem particularly challenging to understand: (i) great geographical differences in degree of virus contagiousness and lethality which were found different phases epidemic progression, (ii) potential role infected people's blood type both infectivity progression disease. A recent hypothesis could shed some light on aspects. Specifically, it has been proposed subject-to-subject transfer SARS-CoV-2 conserves its capsid...
Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields computational biology, such as drug design, biomolecular interaction, folding prediction. Over past decades, descriptors were devised to evaluate hydrophobicity side chains. In this field, recently we likewise have developed method, based on molecular dynamics data, for investigation hydrophilicity features 20 natural amino acids, analyzing changes occurring hydrogen bond...
Understanding the mechanisms driving bio-molecules binding and determining resulting complexes' stability is fundamental for prediction of regions, which starting point drug-ability design. Characteristics like preferentially hydrophobic composition interfaces, role van der Waals interactions, consequent shape complementarity between interacting molecular surfaces are well established. However, no consensus has yet been reached on electrostatic. Here, we perform extensive analyses a large...
It is not well understood why severe acute respiratory syndrome (SARS)-CoV-2 spreads much faster than other β-coronaviruses such as SARS-CoV and Middle East (MERS)-CoV. In a previous publication, we predicted the binding of N-terminal domain (NTD) SARS-CoV-2 spike to sialic acids (SAs). Here, experimentally validate this interaction present simulations that reveal second possible between SAs protein via site located in receptor-binding (RBD). The predictions from molecular-dynamics...
Recent experimental evidence demonstrated the capability of SARS-CoV-2 Spike protein to bind sialic acid molecules, which was a trait not present in SARS-CoV and could shed light on molecular mechanism used by virus for cell invasion. This peculiar feature has been successfully predicted in-silico studies comparing sequence structural characteristics that shares with other acid-binding viruses, like MERS-CoV. Even if region binding identified N-terminal domain protein, so far no...
Abstract As the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic continues to spread, several variants of virus, with mutations distributed all over viral genome, are emerging. While most present having little no effects at phenotypic level, some these spreading a rate that suggests they may selective advantage. In particular, rapidly specific on spike protein. These observations call for an urgent need characterize variants’ phenotype features like contagiousness and...
The development of methods able to modulate the binding affinity between proteins and peptides is paramount biotechnological interest in view a vast range applications that imply designed polypeptides capable impair or favour Protein-Protein Interactions. Here, we applied peptide design algorithm based on shape complementarity optimization electrostatic compatibility provided first experimental vitro proof efficacy algorithm. Focusing interaction SARS-CoV-2 Spike Receptor-Binding Domain...
In this study, we focused on the computational analysis of a selected single-point mutation identified by NGS screening panel in TET2 enzyme classified as “variant uncertain clinical significance.” The mutation, namely Q1084P, occurs at interface between TET2, an important epigenetic regulator, and NANOG, transcription factor fundamental for hematopoietic cells differentiation. Notably, protein region distant from active site; moreover, experimental structures interacting both proteins are...
Predicting interactions between proteins is fundamental for understanding the mechanisms underlying cellular processes, since protein–protein complexes are crucial in physiological conditions but also many diseases, example by seeding aggregates formation. Despite advancements made so far, performance of docking protocols deeply dependent on their capability to identify binding regions. From this, importance developing low-cost and computationally efficient methods this field. We present an...
We present a method for efficiently and effectively assessing whether where two proteins can interact with each other to form complex. This is still largely an open problem, even those relatively few cases the 3D structure of both known. In fact, if much information about interaction encoded in chemical geometric features structures, set possible contact patches their relative orientations are too large be computationally affordable reasonable time, thus preventing compilation reliable...
The present investigation focuses on the analysis of interactions among human lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) receptor in order to assess possible mutual that could provide a molecular basis reported preventative effect against CoV-2 infection. In particular, kinetic thermodynamic parameters for pairwise three proteins were measured via two independent techniques, biolayer interferometry latex nanoparticle-enhanced...
Thermal properties of proteins are great importance for a number theoretical and practical implications. Predicting the thermal stability protein is difficult still scarcely addressed task.Here, we introduce Thermometer, webserver to assess using structural information. Thermometer implemented as publicly available, user-friendly interface.Our server can be found at following link (all major browser supported): http://service.tartaglialab.com/new_submission/thermometer_file.Supplementary...
Mutations in the superoxide dismutase 1 (SOD1) gene are second most common known cause of ALS. SOD1 variants express high phenotypic variability and over 200 have been reported people with It was previously proposed that can be broadly classified two groups, 'wild-type like' (WTL) 'metal binding region' (MBR) variants, based on their structural location biophysical properties. MBR but not WTL were associated a reduction enzymatic activity. In this study we used molecular dynamics large...
Abstract Coordination polymers (CPs), including metal–organic frameworks (MOFs), are crystalline materials with promising applications in electronics, magnetism, catalysis, and gas storage/separation. However, the mechanisms pathways underlying their formation remain largely undisclosed. Herein, we demonstrate that diffusion‐controlled mixing of reagents at very early stages crystallization process (i.e., within ≈40 ms), achieved by using continuous‐flow microfluidic devices, can be used to...
Abstract Studying the binding processes of G protein-coupled receptors (GPCRs) proteins is particular interest both to better understand molecular mechanisms that regulate signaling between extracellular and intracellular environment for drug design purposes. In this study, we propose a new computational approach identification site specific ligand on GPCR. The method based Zernike polynomials performs ligand-GPCR association through shape complementarity analysis local surfaces....
Abstract We describe here a superposition free method for comparing the surfaces of antibody binding sites based on Zernike moments and show that they can be used to quickly compare cluster sets antibodies. The clusters provide information about nature bound antigen that, when combined with predicting number direct contacts, allows discrimination between protein non-protein antibodies an accuracy 76%. This is relevance in several aspects science, example select framework combinatorial library.