A5015294553- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Monoclonal and Polyclonal Antibodies Research
- vaccines and immunoinformatics approaches
- Influenza Virus Research Studies
- interferon and immune responses
- Amyotrophic Lateral Sclerosis Research
- Circadian rhythm and melatonin
- Lipid Membrane Structure and Behavior
- Lepidoptera: Biology and Taxonomy
- Mass Spectrometry Techniques and Applications
- Spectroscopy and Quantum Chemical Studies
- Genetics, Aging, and Longevity in Model Organisms
- Microbial Metabolic Engineering and Bioproduction
- Neurobiology and Insect Physiology Research
- Bacteriophages and microbial interactions
- Protein purification and stability
- Animal Virus Infections Studies
- Evolutionary Algorithms and Applications
- Phytoplasmas and Hemiptera pathogens
- RNA Research and Splicing
- Infant Nutrition and Health
Sapienza University of Rome
2016-2025
Italian Institute of Technology
2018-2025
University of Rome Tor Vergata
2022
University of Puerto Rico at Río Piedras
2022
Center for Nano Science and Technology
2022
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 Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content >2000 coronaviruses and computed >100 000 human protein with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees conservation. SARS-CoV-2 domain encompassing nucleotides 22 500–23 is conserved both at sequence structural level. upstream downstream, however, vary significantly. This part...
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...
Heliconius butterflies, a speciose genus of Müllerian mimics, represent classic example an adaptive radiation that includes range derived dietary, life history, physiological and neural traits. However, key lineages within the genus, across broader Heliconiini tribe, lack genomic resources, limiting our understanding how neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous assemblies for nine Heliconiini, 29 additional reference-assembled...
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...
Abstract Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but often difficult design. Here, we exploited the cat RAPID algorithm generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On pathway forming insoluble inclusions, TDP-43 adopts heterogeneous population of assemblies, many smaller than diffraction-limit light. We...
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...
Lactoferrins and lactoferrin-derived peptides display numerous functions linked to innate immunity in mammalians, spanning from antimicrobial anti-inflammatory immunomodulatory actions, even demonstrate antitumor properties. To date, the proposed mechanisms for their biological actions are varied, although molecular basis that governs lactoferrin interactions with targets has been clarified only a limited number of specific cases. However, key silico methods have recently moved topic fore,...
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...
A wide range of higher-order structures, including dense, liquid-like assemblies, serve as key components cellular matter. The molecular language how protein sequences encode the formation and biophysical properties biomolecular condensates, however, is not completely understood. Recent notion on scale invariance cluster sizes below critical concentration for phase separation suggests a universal mechanism, which can operate from oligomers to non-stoichiometric assemblies. Here, we propose...
Monoclonal antibodies are essential tools in the contemporary therapeutic armory. Understanding how these recognize their antigen is a fundamental step rational design and engineering. The rising amount of publicly available data catalyzing development computational approaches able to offer valuable, faster cheaper alternatives classical experimental methodologies used for study antibody-antigen complexes.Here, we present proABC-2, an update original random-forest antibody paratope...
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...
Abstract Chemosensory receptors play a crucial role in distinguishing the wide range of volatile/soluble molecules by binding them with high accuracy. Chemosensation is main sensory modality organisms lacking long-range mechanisms like vision/hearing. Despite its low number neurons, nematode Caenorhabditis elegans possesses several chemosensory receptors, allowing it to detect about as many odorants mammals. Here, we show that C. displays attraction towards urine samples women breast cancer,...