PRP@CERIC: Scientific Seminar Series
The studies on structure and mechanism of action of Antimicrobial Peptides (AMPs) are carried out using some tools, such as computational analysis, peptide synthesizer and spectroscopic techniques. Here, we report our approach adopted on the study of primate cathelicidins.
Antimicrobial peptides are an important component of innate immunity that act as a first line of defence against the occurrence of infections. Among these natural antibiotics, those of the cathelicidin family, which includes LL-37 in humans and RL-37 in the primate Macaca mulatta, are intensively studied because of their diverse properties.
For example, LL -37 is capable of adopting an amphipathic helical structure in physiological solutions and then oligomerizing; RL-37, on the other hand, remains monomeric and disordered under the same conditions.
The occurrence of intramolecular salt bridges could play an important role in determining the particular structure which is adopted. These important structural aspects are highlighted by predictive applications, allowing us to identify a new stabilized analogue of RL-37 or destabilized analogues of LL -37 to probe positional effects in their sequences underlying their structural behavior.
We were able to evaluate the effect on structural stability by monitoring thermal denaturation in plasma mimetic buffer, using circular dichroism assays. These data were compared with functional assays of efficacy against bacterial cells or cytotoxicity to host immune cells.
Selected analogues were also evaluated for the mechanism of antimicrobial action monitoring permeabilization of bacterial membranes to fluorescent probes and other roles in immunity, such as cytotoxicity towards, or triggering of proinflammatory M1 macrophages.
These studies have shown a direct correlation between the structure and behavior of the peptides in terms of their direct antimicrobial and host-mediated activity.
Speaker: Andrea Caporale, CNR – IC
Facilities for genomic and epigenomic research can be extremely useful in the fight against emerging diseases.
Scientists can identify the genes and proteins of infections by sequencing their genomes; these genes and proteins can subsequently be used as targets for vaccinations and medications.
Studies on the genome and epigenome can also help researchers better understand how pathogens change over time and adapt, which can be used to create ways to stop them from developing drug resistance.
This session describes the most current projects carried out by Area Science Park Genomics and Epigenomics lab.
Speaker: Danilo Licastro, Genomics and Epigenomics Laboratory (LAGE) – Area Science Park
All atom simulations allow uncovering the molecular mechanism of complex biological molecules, supporting and expanding experimental data.
In this talk I show how multiscale simulations can decipher the molecular mechanism of the (i) spliceosome, a complex protein/RNA macromolecular machinery, that removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to protein coding mRNAs and functional non-coding RNAs [1-3]; (ii) Ctr1 a transporter involved in Cu(I) internalization [4] and of (iii) the SARS-CoV-2 spike proteins and its variants of concerns as well as of the nsp1 protein [5-7].
Speaker: Alessandra Magistrato, SISSA – International School for Advanced Studies
The talk provides a brief introduction to epigenetics and epitranscriptomics, and gives a synthetic overview of the most significant RNA modifications discovered nowadays.
The aim of the talk is to inform the interested community of existing expertise at the Genomics and Epigenomics Lab, to stimulate proficient collaborations focused on the new viral epitranscriptomics field, which would add significant value to the Pathogen Readiness Platform project.
Speaker: Valentina Perrera, Area Science Park
The talk is about the sequencing using Oxford Nanopore technology (PromethION platform).
A brief summary of the advantages of nanopore based technology, is followed by the description of the major workflows for DNA and RNA seq.
Speaker: Margherita Degasperi, Genomics and Epigenomics Laboratory (LAGE) – Area Science Park
SISSI-Bio is the chemical and life science branch of the infrared beamline at Elettra.
In this presentation the most relevant features and instruments of SISSI-Bio will be introduced, focusing on the application of infrared vibrational spectroscopy on topics relevant for the PRP@CERIC project: IR cytology and IR histology for cell and tissue analysis, respectively.
The ultimate aim of the presentation is to introduce the audience to the approach for identifying common area of interest and synergic actions toward the PRP@CERIC goal.
Speaker: Lisa Vaccari, Elettra Sincrotrone Trieste
In this contribution, Ms. Rossi provides an overview of the basic principles of UV resonance Raman spectroscopy and its possible applications in the investigation of biological specimens.
A description is provided of the advantages and challenges of this technique, representing a unique label-free tool for non-invasive study of nucleic acids, proteins, organic samples and pathogens.
The portfolio of the multi-wavelengths UV Raman setups available on the IUVS beamline at Elettra Sincrotrone is presented.
Special focus is given to the instrumental upgrades planned in the framework of PRP@Ceric and Elettra 2.0.
Speaker: Barbara Rossi, Elettra Sincrotrone Trieste
Artificial Cell membrane mimetic platforms to assess extracellular vesicles/pathogens-cell interaction.
Speaker: Loredana Casalis, Elettra Sincrotrone Trieste
The seminar presents the application of an integrative structural biology approach to the field of neurotrophins.
The interaction of ATP with both mature NGF and its precursor was investigated with solution NMR and a set of complementary biophysical and computational methodologies.
The used methods are briefly presented, as well as the scientific results.
From these data, it was possible to identify the role of ATP in modulating the neurotrophin biology and this can explain some features of neurodegeneration.
Speaker: Francesca Paoletti, Institute of Crystallography – CNR
Over the last 20 years the emphasis in structural biology has shifted from the technique (crystallography, NMR, etc..) to biological issues.
Due to a number of technical advances in both biology and structural analysis, the size and complexity of the macromolecular targets have systematically increased.
In a number of cases, this has required the combination of multiple techniques, to be used in an integrated approach, to fully understand the structure, function and dynamics of the biological complex.
This is particularly true for protein-nucleic acid complexes, which often show a degree of polymorphism, multiple conformations, presence of disordered regions, a multiplicity of alternative substrates, and so on.
Mrs. Onesti’s research is focused on a number of proteins involved in basic genetic processes, including DNA replication, DNA repair, transcription and translation.
In particular, she has focused on helicases, which are molecular motors able to unwind a variety of nucleic acid substrates (DNA, RNA, G-quadruplexes, R-loops, etc..); being essential in nucleic acid metabolism they are becoming novel targets for anti-viral, anti-bacterial and anti-tumor drugs.
The talk covers some of the recent projects, focusing on the use of a combination of macromolecular crystallography and single particle electron microscopy to understand the structure and function of a number of DNA and RNA helicases involved in replication and repair, and thus involved in genetic diseases, cancer development and progression and aging.
Speaker: Silvia Onesti, Elettra Sincrotrone Trieste
Prevention of virus infection can be performed following different strategies, from the development of effective vaccines to the reduction of the vector in the case of insects-borne viral infection.
All these strategies rely on a deep knowledge of the biology of the virus.
For instance, development of new vaccines requires the characterization of the structure that the viral proteins assume during the different steps of the viral cycle.
Also, antiviral molecules can be used not only as a cure but also as prevention tools when directly expressed in insect vectors.
Speaker: Giuditta De Lorenzo, RIT – Area Science Park
In Elettra’s Structural Biology Laboratory, a protein production platform has been active for almost 10 years, acting as a facility supporting external users from academic and industrial labs in producing and characterizing proteins for structural biology applications.
The talk presents the rationale behind the establishment of the Facility, describing how it evolved and its present organization and capabilities.
The most significative results are presented, focusing on structural based drug discovery projects, including drug targets as kinases, SARS-CoV2 proteases, and less standard ones, as glycogen targeting protein.
Future developments and instruments’ implementation planned within the PRP@CERIC project are presented to the partner community.
The aim of the talk is to inform the interested community of existing competences at the Protein Facility to stimulate proficient collaborations.
Speaker: Paola Storici, Elettra Sincrotrone Trieste