I have experience in the development and application of computational algorithms in the field of proteins in aqueous solution. Since my PhD, I have been programming many different codes in Fortran, C++ or bash for the description of the structural dynamics of proteins. In collaboration with Prof.Laio (SISSA, Italy), I have developed the algorithm for the design of nanobodies as binders of protein targets. My background in chemistry, computational chemistry and biophysics applied to protein systems offers me the unique opportunity to cover a wide range of problems and applications in the research field of proteins. My research goes through the study of vibrational relaxation of peptides (Murcia), the protein folding (Lisbon), and protein-protein interaction (Italy). Therefore, my expertise is often required in my work for disentangle this intriguing triangular relationship among dynamics-structure-function that regulates the biological role of proteins. In the present, I am carrying on new projects in Genova, always in the field of protein biophysics and medicine, while I continue my collaboration in the protein design field. On one hand, I am working in a project for the development of broad-spectrum vaccines for Dengue and Zika in collaboration with Dr. Burrone (ICGEB) based on the in silico design of anti-idiotypic antibodies, which has been awarded in the 19th PRACE call. Moreover, I am currently broadening my knowledge in computational structural biology within the project in collaboration with the Institute of Cancer Research (UK) focused on the study of mechanisms for the regulation of the activity of protein cancer targets.
Design of anti-idiotypic antibody fragments as vaccines.
In this project we exploit the PRACE HPC resources awarded this year 2019 with our recently developed evolutionary algorithm of binder design to produce immuno-agents with the capability of being employed as broad-spectrum vaccines for Zika (ZIKV) and all serotypes of Dengue virus (DENV). Thus, we propose a protocol of in silico mutagenesis coupled to affinity and selectivity screening in order to test the anti-idiotypic antibody hypothesis, i.e. the capability of an antibody directed against the binding regions of another antibody (anti-A) to mimic the molecular features of the original antigen A. Our group in collaboration with our experimental partner, the Laboratory of Molecular Immunology of ICGEB in Trieste, led by Prof. Oscar Burrone, already identified a preliminary molecular construct, at present under experimental testing, exposing 2 out of the 4 main epitopes responsible for the binding of EDE with the EDE1-C8 antibody.
Recently awarded with PRACE 2019 Call (19,700,000 core hours, W. Rocchia and M.A. Soler).
Current collaborators include: Oscar Burrone (ICGEB, Italy), Ario DeMarco (University of Nova Gorica,
Slovenia).
Enhanced sampling MD simulations for studying protein functionality
Most interesting molecular phenomena in proteins often occur on a timescale which is out of reach for conventional "brute force" Molecular Dynamics (MD) simulation. Enhanced Sampling techniques act so as to achieve a statistically significant sampling of relevant regions of the conformational space, allowing the study of the mechanisms that control the biological role of proteins and the development of strategies for the modulation of the protein activity. For instance, we currently collaborate with the group of Computational Structural Biology in the Institute of Cancer Research Institute (UK) to discover cryptic allosteric epitopes for the regulation of protein cancer targets.
Current external collaborators include: Bissan Al-Lazikani, Patrizio Di Micco (ICR, UK).
Nanobody design
Different computational protocols for evaluating with more accuracy and more efficiently the binding affinity of protein-protein complexes have been developed during the last period, as well as new approaches to predict the stability of the engineered nanobodies. This methodologies resulted essential for the optimal performance of the in silico design of protein binders with enhanced affinities. Nowadays, the design of nanobodies for the molecular recognition of HER2, the most famous mammalian cancer biomarker, have been performed and are being produced and analyzed for their affinity and stability in an iterative two-way transfer between empiric data and theoretical modelling. My research involves the selection of new protein targets related with diseases which allows extending the application of the designed nanobodies to the diagnosis and prognosis and to therapeutical drugs.
Recently awarded with ARDF Annual Open Grant 2019 ($39,980 US, S. Fortuna and M.A. Soler).
Current external collaborators include: Alessandro Laio (SISSA, Trieste, IT), Ario DeMarco (University of Nova Gorica, Slovenia), Loredana Casalis (Elettra, Trieste, IT) , Sara Fortuna (Univ. Trieste, IT).
L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.
IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.
Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.
Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei, 17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali
La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.
Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance). The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.
IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators, 110 researchers and technologists, 350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion is 41% female against 59% male.
In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.
So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications, 12 up start-ups and as many which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.
