PARTNER / COORDINATOR
SAPIENZA
Università degli Studi di Roma
Department: Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Website: dsb.uniroma1.it
Piazzale Aldo Moro 5
00185 Rome – Italy
READ EXPERTISE
Sapienza has relevant expertise in crystallography, and it has recently developed a research line on membrane proteins structure. Both access to Synchrotron facilities and robot equipment for protein crystallization are available. Notably, Sapienza has pioneered time resolved crystallography and wide-angle X-ray scattering2,3, which could be exploited for the analysis of membrane protein dynamics, relevant to detect transient states to be addressed for inhibitor binding. Moreover, in the context of the X-Probe MSCA ITN (B. Vallone, coordinator), XFEL time and expertise could be available for serial crystallography, in case only micro-crystals were obtained.
Sapienza and ITQBE together provide an arsenal of advanced methodologies for protein functional characterization, a mandatory step for the characterization and design of bioactive molecules.
A wide variety of biophysical and biochemical methods are available to complement structural characterization. This know-how is essential to ensure the correct folding, stability and activity of the recombinant/expressed proteins, as well as to analyse protein-ligand interactions and affinity, essential for drug development.
The equipment and methods include stopped-flow for steady state and pre-steady state kinetics, time-resolved spectroscopy, CD, IR, mass-spectrometry, gas spectrometry, VP-DSC Calorimeter, Dynamic Light Scattering, Isothermal Titration Calorimetry, Differential scanning calorimetry, advanced chromatographic techniques, N-terminal protein and peptide sequencing analysis, Seahorse XF Analyzers in anaerobiosis, Surface Plasmon Resonance, NMR facility (including 800 MHz NMR spectrometers), small molecule analysis (by HPLC, GC and elemental analysis), Fluorescence spectrophotometers and bioimaging (light and fluorescence microscopy).
Structure determination. (Crystallography, SAXS, and Cryo-EM)
GROUP LEADER
Professor Beatrice Vallone
E-Mail: beatrice.vallone@uniroma1.it
Website: Vallone Lab
SECONDEES
GABRIELE CERUTTI
Gabriele Cerutti obtained his Master’s Degree in Chemistry of Biological Systems in 2016 and his PhD in Biochemistry in 2019, both from Sapienza University of Rome.
During his PhD he carried out the structural and functional characterization of fungal FAD-dependent enzymes involved in lignin degradation, by means of X-ray crystallography and spectrophotometric methods.
In 2019 he spent six months at COMPPÅ, New York City, where he worked on the biochemical characterization of membrane proteins involved in androgen metabolism.
He is currently a Postodoc at Columbia University, New York City, where he is using cryo-EM to investigate the structure of viral fusion proteins and adhesion proteins.
IDA FREDA
Ida Freda obtained a B.S. in Biotechnology at Tor Vergata University and a M.S. in Medical Biotechnology at Sapienza University.
As an undergraduate intern, she focused on the structure-function relationship of heme proteins by means of protein engineering, X-ray crystallography and spectroscopic techniques.
In 2018 she became a fellow at the PhD course in Biochemistry at Dept. of Biochemical Sciences of Sapienza University, where she is currently working on the structural characterization by single particle cryo-electron microscopy of a ternary complex that mediate hemoglobin scavenging and clearance.
Another research project focuses on the structural and functional characterization of a membrane enzyme family involved in steroid metabolism, carried out in collaboration with Columbia University of New York.
BEATRICE VALLONE
Beatrice Vallone is Full Professor of Biochemistry at the Dept. of Biochemical Sciences of the Sapienza University of Rome (Italy).
The work of the group is focused on structural biology and enzymology of proteins, the main methodologies used are crystallography and single-particle CryoEM and biophysical and spectroscopic methods for activity and stability analysis.
SAPIENZA
Università degli Studi di Roma
Department: Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”
Website: dsb.uniroma1.it
Piazzale Aldo Moro 5
00185 Rome – Italy
READ EXPERTISE
Sapienza has relevant expertise in crystallography, and it has recently developed a research line on membrane proteins structure. Both access to Synchrotron facilities and robot equipment for protein crystallization are available. Notably, Sapienza has pioneered time resolved crystallography and wide-angle X-ray scattering2,3, which could be exploited for the analysis of membrane protein dynamics, relevant to detect transient states to be addressed for inhibitor binding. Moreover, in the context of the X-Probe MSCA ITN (B. Vallone, coordinator), XFEL time and expertise could be available for serial crystallography, in case only micro-crystals were obtained.
Sapienza and ITQBE together provide an arsenal of advanced methodologies for protein functional characterization, a mandatory step for the characterization and design of bioactive molecules.
A wide variety of biophysical and biochemical methods are available to complement structural characterization. This know-how is essential to ensure the correct folding, stability and activity of the recombinant/expressed proteins, as well as to analyse protein-ligand interactions and affinity, essential for drug development.
The equipment and methods include stopped-flow for steady state and pre-steady state kinetics, time-resolved spectroscopy, CD, IR, mass-spectrometry, gas spectrometry, VP-DSC Calorimeter, Dynamic Light Scattering, Isothermal Titration Calorimetry, Differential scanning calorimetry, advanced chromatographic techniques, N-terminal protein and peptide sequencing analysis, Seahorse XF Analyzers in anaerobiosis, Surface Plasmon Resonance, NMR facility (including 800 MHz NMR spectrometers), small molecule analysis (by HPLC, GC and elemental analysis), Fluorescence spectrophotometers and bioimaging (light and fluorescence microscopy).
Structure determination. (Crystallography, SAXS, and Cryo-EM)
GROUP LEADER
Professor Beatrice Vallone
E-Mail: beatrice.vallone@uniroma1.it
Website: Vallone Lab
SECONDEES
GABRIELE CERUTTI
Gabriele Cerutti obtained his Master’s Degree in Chemistry of Biological Systems in 2016 and his PhD in Biochemistry in 2019, both from Sapienza University of Rome.
During his PhD he carried out the structural and functional characterization of fungal FAD-dependent enzymes involved in lignin degradation, by means of X-ray crystallography and spectrophotometric methods.
In 2019 he spent six months at COMPPÅ, New York City, where he worked on the biochemical characterization of membrane proteins involved in androgen metabolism.
He is currently a Postodoc at Columbia University, New York City, where he is using cryo-EM to investigate the structure of viral fusion proteins and adhesion proteins.
IDA FREDA
Ida Freda obtained a B.S. in Biotechnology at Tor Vergata University and a M.S. in Medical Biotechnology at Sapienza University.
As an undergraduate intern, she focused on the structure-function relationship of heme proteins by means of protein engineering, X-ray crystallography and spectroscopic techniques.
In 2018 she became a fellow at the PhD course in Biochemistry at Dept. of Biochemical Sciences of Sapienza University, where she is currently working on the structural characterization by single particle cryo-electron microscopy of a ternary complex that mediate hemoglobin scavenging and clearance.
Another research project focuses on the structural and functional characterization of a membrane enzyme family involved in steroid metabolism, carried out in collaboration with Columbia University of New York.
BEATRICE VALLONE
Beatrice Vallone is Full Professor of Biochemistry at the Dept. of Biochemical Sciences of the Sapienza University of Rome (Italy).
The work of the group is focused on structural biology and enzymology of proteins, the main methodologies used are crystallography and single-particle CryoEM and biophysical and spectroscopic methods for activity and stability analysis.
PARTNERS
ITQB
Instituto de Tecnologia Química e Biológica António Xavier Nova
Department: Biological Chemistry Division
Website: itqb.unl.pt
Avenida da Republica-Estação Agronómica Nacional
2780-157 Oeiras – Portugal
READ EXPERTISE
The Membrane Protein Crystallography Group at ITQB aims at the structure determination of membrane proteins using X-ray crystallography (MX) along with their functional characterization. In addition to the in-house X-ray diffractometer, periodic access is available to various European Synchrotrons facilities, such as ESRF, PETRA III and Diamond allowing for extensive screen of crystals and data. More recently, the combined approach of cryo-EM and/or SAXS with MX has been implemented. Crystallization robots and other state-of-art-equipment for growth and handling of protein crystal are available.
Sapienza and ITQBE together provide an arsenal of advanced methodologies for protein functional characterization, a mandatory step for the characterization and design of bioactive molecules.
A wide variety of biophysical and biochemical methods are available to complement structural characterization. This know-how is essential to ensure the correct folding, stability and activity of the recombinant/expressed proteins, as well as to analyse protein-ligand interactions and affinity, essential for drug development.
The equipment and methods include stopped-flow for steady state and pre-steady state kinetics, time-resolved spectroscopy, CD, IR, mass-spectrometry, gas spectrometry, VP-DSC Calorimeter, Dynamic Light Scattering, Isothermal Titration Calorimetry, Differential scanning calorimetry, advanced chromatographic techniques, N-terminal protein and peptide sequencing analysis, Seahorse XF Analyzers in anaerobiosis, Surface Plasmon Resonance, NMR facility (including 800 MHz NMR spectrometers), small molecule analysis (by HPLC, GC and elemental analysis), Fluorescence spectrophotometers and bioimaging (light and fluorescence microscopy).
Structure determination. (Crystallography, SAXS, and Cryo-EM)
GROUP LEADER
Professor Margarida Archer
E-Mail: archer@itqb.unl.pt
Website: Margarida Archer Lab
SECONDEES
JOSÉ RODRIGUES
FEDERICO ISSOGLIO
Federico Issoglio obtained his Chemistry degree at Universidad Nacional de Córdoba (Argentina). He completed the PhD in 2014 at the Departamento de Química Biológica (UNC). During this period he focused on biochemical, biophysical and structural analysis of enzymes involved in proteoglycogen biosynthesis.
In 2015 started a Postdoc position at Facultad de Ciencias Exactas, Universidad de Buenos Aires. From 2015 to 2019 He studied proteins using computational tools, acquiring expertise in quantum chemistry, molecular dynamics simulations, molecular docking and free energy calculations.
Currently, he holds a postdoc position at Universidade Nova de Lisboa (ITQB). He is studying membrane proteins form Mycobacterium tuberculosis, by determining the 3D structure using X-ray crystallography and/or cryo-electron microscopy, exploring the reactivity and thus unraveling the mechanisms underlying its catalysis.
UNIVPM
Università Politecnica delle Marche
Department: Dipartimento di Scienze della Vita e dell’Ambiente
Website: disva.univpm.it
Via Brecce Bianche
60131 Ancona – Italy
READ EXPERTISE
UNIVPM has considerable expertise in small-angle X-ray scattering (SAXS), a robust technique for the structural characterizations of macromolecules and macromolecular complexes in solution. SAXS is a low-resolution technique, but it can be applied to a wide variety of solution conditions, temperatures, particle sizes and composition, as well as in time-resolved conditions (few-tens millisecond.
SAXS experiments at synchrotron facilities (UNIVPM scientists are frequent users at ESRF, PETRA III, Diamond, Elettra) can bridge information in protein structure refinement with NMR, Crystallography and SPCryoEM providing a reliable, high-throughput characterization of macromolecular complexes under physiological/working conditions.
Moreover UNIVPM has also expertise in protein crystallography (Prof. M. Cianci). Indeed Prof. Cianci has contributed to the construction of a state-of-the-art beamline at PetraIII, and is involved in the development of new methods for structure determination from microcrystals, a crucial issue with membrane proteins.
MaSBiC (Marche Structural Biology Center) is a High-Throughput Protein Production Facility established at the Università Politecnica delle Marche (UNIVPM) by the Departments of Life and Environmental Sciences (DiSVA) and of Agricolture, Agronomy and Environment (D3A) and the Faculty of Medicine and inside a partnership with COMPPÅ. The MaSBiC facility has been operative for two years and provides robotically-assisted, high-throughput cloning, expression and purification of recombinant proteins from prokaryotic and eukaryotic cells for the Italian and European scientific community.
Several projects in the area of medicine, agrifood and marine biology are in progress, within national partnerships and in collaboration with European or extra-European research groups. MaSBiC has a close collaboration with COMPPÅ and is oriented towards innovation of HT platform for the production of G-protein coupled receptors (GPCR’s) that requires construction of special vectors and new approaches for expression in eukaryotic systems. The MaSBiC counts about 120 prokaryotic genomes, and it is enriching its genome’s bank with marine species.
GROUP LEADER
Professor Paolo Mariani
E-Mail: p.mariani@univpm.it
Website: Ma.S.Bi.C.
SECONDEES
ALESSIA SALVUCCI
Alessia Salvucci is a graduate student from the Università Politecnica delle Marche, she will work on “Cloning, expression and purification of human recombinant paraoxonase-2,
She comes from Laboratory of Enzymology and Clinical Molecular Biology (Prof. Monica Emanuelli, Faculty of Medicine) and the New York-Marche Structural Biology Center (NY-MaSBiC).
LUCREZIA SAVINI
IBET
Instituto De Biologia Experimental E Tecnologica
Department: Animal Cell Technology Unit
Website: ibet.pt
Av. República, Qta. do Marquês, EAN
2780-157 Oeiras – Portugal
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The IBET ACT Unit’s know-how in terms of biopharmaceuticals spans from the initial expression vector design and cell line establishment through all stages of process development and scale-up.
On the upstream bioprocessing, the ACT Unit is focused on devising strategies to control and optimize final product titer and quality. An array of different culture systems/platforms (mammalian, insect, transient and stable) is available, providing a landscape of possibilities for specific targets, challenges and product requirements. On the downstream bioprocessing, the ACT Unit is focused on innovative solutions, reducing manufacturing costs, increasing productivity, safety and efficacy.
The bioprocess cycle is finalized with extended expertise in (i) bioprocess monitoring tools and modelling approaches (e.g. mathematical models and 2D-fluorometry), (ii) functional genomic tools (e.g. transcriptomics, metabolomics and fluxomics), and (iii) analytical tools for product/cell characterization and quality control/assurance (e.g. mass spectrometry, tunable resistive pulse sensing and analytical size-exclusion chromatography) that can be performed at iBET’s GMP certified Analytical Services Unit and Mass Spectrometry Unit. Process scale-up can be performed from lab (250 mL to 5 L) to pre-clinical scales (2 L to 70 L scale), the latter performed at iBET’s Pilot Plant (2000 m2), an infrastructure that routinely supplies pre-clinical grade biopharmaceutical products (e.g. vaccines, mAbs and VLPs).
A crucial infrastructure of added value to Prometeus is the Protein Production Platform (PPP). The PPP main activities are recombinant protein production in several expression systems (e.g. E. coli, yeast, baculovirus-insect and mammalian cells), bioprocess development, scale-up, analytics for quality control/assurance, formulation and delivery.
IBET’s ACT Unit has been dedicating substantial effort in the development of new in vitro models for pre-clinical research (incl. toxicological assessment), the reason being the lack of efficient and cost-effective in vitro tools to predict pharmacokinetics and toxic reactions of new compounds at early stage of drug discovery. Biotransformation occurs mainly in the liver, after which hepatocyte-end products are transported to other organs, such as the brain.
ACT Unit has been working on new tools, with higher predictive power in terms of xenobiotic biotransformation than the currently available ones, using primary cultures of hepatocytes (rat and human origin) and differentiating human embryonic stem cells into functional hepatocyte-like cells. Training at ACTU and collaboration with Prometeus partners on specific/selected protein targets will be key to ensure ESRs and ERs have at the end of Prometeus project the needed skill set for membrane protein based drug design.
GROUP LEADERS
Professor Paula Alves
E-Mail: marques@ibet.pt
Professor António Roldão
E-Mail: aroldao@ibet.pt
SECONDEES
MARIA MARGARIDA RODRIGUES
Maria Margarida Rodrigues is a Junior Researcher at the Cell-Based Vaccine Development Laboratory of the Animal Cell Technology (ACT) Unit (Health & Pharma Division, iBET).
Maria Margarida Rodrigues graduated in Biological Engineering at Instituto Superior Técnico – University Lisbon in 2019. She has always followed with keen interest the fields of life sciences and biotechnology, which motivated her to carry out the research for the Master Thesis at the University of Natural Resources and Life Sciences (BOKU, Vienna, Austria), under the scope of the Erasmus programme. There, she interned at the Tissue Engineering Laboratory, whose field of research is the optimization of strategies for the cultivation of stem cells. Her thesis focused on the study and development of a device for the non-invasive monitoring of 3D cell cultures. The research experience at BOKU contributed for her eagerness to pursue a scientific research career, and led her to join the ACT Unit at iBET.
Current Research is focused on the production of relevant therapeutic products, such as viral vectors and recombinant proteins, and the study of strategies to optimize animal cell culture and improve production yields. In the next years, she intends to expand her research career and contribute to the development of novel bioprocesses for the production of vaccines against high-impact diseases.
Email: margarida.rodrigues@ibet.pt
Web pages: tca.itqb.unl.pt
RICARDO CORREIA
Ricardo Correia is currently a third year PhD student of the MIT Portugal – Bioengineering Systems doctoral program (iBET and ITQB-NOVA), working in the Vaccine Development Laboratory at the Animal Cell Technology Unit (ACT, Health & Pharma Division, iBET). Ricardo Correia holds an MSc in Biological Engineering from Instituto Superior Técnico, Universidade de Lisboa, which he graduated in 2014.
Ricardo Correia PhD’s research work focus on the development of novel bioprocess engineering approaches (development of high producing cell lines through evolutionary engineering and establishment of bioreactor production set-ups for process intensification) for the improved production of vaccine candidates (inc. VLP-based) against infectious diseases such as Influenza and malaria.
Additionally, Ricardo Correia has performed his MSc thesis work in the Department of Regenerative Medicine from the Faculty of Medicine (Ghent, Belgium) in 2014. His work focused on the reprogramming of animal (mice and human) somatic cells into pluripotent cells. Since Ricardo Correia has joined the Animal Cell Technology Unit in 2015, he has also been involved in other service driven projects focused on vaccines and protein production. As a junior researcher, he has been involved in the upstream processing of a universal Influenza vaccine candidate within the scope of the EU funded research project “EDUFLUVAC”. Recently, he has also been involved in the process development and production of a new assexual blood-stage malaria vaccine candidate, within a Japanese-funded project (GHIT Fund).
Ricardo Correia is author of 2 scientific manuscripts, over 10 poster and 1 oral communication, and has experience in co-supervision of master students (1) and other interns. His motivation focus on continuing doing research towards development of novel bioproducts and bioprocess schemes for protein and vaccine production.
Orcid: https://orcid.org/0000-0002-9434-7974
Email: rccorreia@ibet.pt
Web page: www.ibet.pt
MoLiRom
Molecular Links Rome
Contact: Dr Alessandra Bonamore
E-Mail: alessandra.bonamore@uniroma1.it
Via Ravenna, 8
00161 Rome – Italy
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MoLiRom specializes in developing protein based carriers for theranostics based on a genetically engineered thermostable globin or ferritin scaffolds.
Molirom is producing at gram scale for preclinical investigation on melanoma therapy and advanced in order to increase the photosensitive ligand load. Recombinant protein production and expression, random and site selected mutagenesis, protein immobilization on activated silicon surfaces.
Facilities comprise a fully equipped molecular biology lab, a pilot scale purification station, AFM and SEM microscopy.
Molirom brings into the Consortium advanced capabilities for protein design and engineering and conjugation with organic moieties for achieving diagnostics and therapeutics activities.
GROUP LEADER
Professor Alberto Boffi
E-Mail: a.boffi@molirom.com
SECONDEES
MARTINA PITEA
November 2018
Awarded PhD scholarship in Biochemistry (XXXIV cycle) “Sapienza” – University of Rome (Italy), “Sapienza” – University of Rome (Italy), Institute of Biology and Molecular pathology-CNR- Department of Biochemistry A. Rossi Fanelli ” Piazzale Aldo Moro 5.00185 Rome (Italy).
January 2018
Master’s degree in Medical Biotechnology, LM-9 (110/110 cum laude)
Experimental Thesis title: Engineered human ferritin for targeted transport of drugs
“Sapienza” University of Rome. Faculty of Pharmacy and Medicine; Piazzale Aldo Moro 5.00185 Rome (Italy), Institute of Biology and Molecular pathology-CNR-Department of Biochemical Sciences – A. Rossi Fanelli,
Professor: Alberto Boffi, Tutor: Pierpaolo Ceci
TECHNICAL SKILLS AND COMPETENCES
Good knowledge and expertise in the main molecular biology techniques (cloning, enzymatic digestion, bacterial transformations, plasmid DNA extraction from bacterial cultures) and cellular biology, biochemical methods (SDS-PAGE electrophoresis And on agarose gels, chromatographies such as HPLC) and spectroscopic (absorption). Experience with bacterial models (E. coli).
Correct use of the main methods and instruments present in a chemical laboratory: preparation of solutions and dilutions, application of titles and separation techniques, measurement of pH and conductivity, construction of calibration curves and Performance of UV-Visible spectrophotometric readings.
READ EXPERTISE
Extremochem is a start-up company dedicated to the development and commercialisation of new chemically synthesized compounds for protein stabilization. Extremochem main expertise is organic synthesis, such as: asymmetric synthesis of structurally diverse natural compounds and analogues, carbohydrate chemistry, solid supported synthesis, reagent development, nanoparticle synthesis, and it will provide this expertise, following the in silico evaluation of biomolecules or the design of new ones.
Extremochem compounds are a new family of stabilizers, efficient, affordable and recoverable when necessary. They are obtained exclusively by chemical synthesis. Extremochem stabilizers have important potential applications, from stabilizing proteins at laboratory scale, avoiding aggregation and degradation during purifications, to stabilizing biopharmaceuticals. These stabilizers will allow biopharmaceuticals stand several stresses, including shaking, viscosity and temperature variations, and thus transportation and storage costs will be drastically reduced. The shelf life of biopharmaceuticals will be extended.
The social and health impacts of the potential applications of these new compounds are huge, and it will be exploited for the stabilization of proteins produced within the Prometeus Consortium (membrane proteins, but also ferritin bioconjugates).
The expertise of Extremochem will therefore be very valuable, both for custom organic synthesis and for the stabilization of proteins produced in the consortium, with an alternative and innovative approach, over and above the presence of detergents.
GROUP LEADER
Dr Rita Ventura
E-Mail: rventura@itqb.unl.pt
SECONDEES
EVA LOURENÇO
Eva Lourenço obtained a Chemistry degree in 2006 and a Master in Green Chemistry in 2008, both from Faculdade de Ciências, Universidade de Lisboa.
In 2003, she received her PhD in Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.
She is responsible for synthesizing and testing new protein stabilizers.
She has experience in organic synthesis, carbohydrate chemistry and solid supported synthesis.
FRAUNHOFER
Gesellschaft zur Foerderung der Angewandten Forschung E.V.
Department: ScreeningPort
Website: ime.fraunhofer.de/en
Schnackenburgallee, 114
22525 Hamburg – Germany
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The Department ScreeningPort of the Fraunhofer Institute for Molecular Biology and Applied Ecology (IME-SP) offers industry standard small molecule drug discovery. It collaborates closely with academic institutions and pharmaceutical industry in multiple research projects.. Besides experimental screening, IME-SP offers comprehensive in silico screening capabilities including structure- and ligand-based methods (e.g. molecular docking, pharmacophore searches) using industry-standard software (e.g. MOE, GOLD, Schrödinger), 3D-Workstations and high-performance computing facilities.
The Fraunhofer-Gesellschaft is the leading organization for applied research in Europe, it employs a staff of nearly 24,000, who work with an annual research budget totaling more than 2 billion EUR.
IME-SP utilises a broad set of computational methods for the discovery of novel bioactive compounds that have been integrated into workflow tools for improving automation and data analysis. Besides molecules docking, also pharmacophore searches and combinations of both are applied.
In addition, IME-SP utilises ligand-based methods such as 3D QSAR techniques. IME-SP has developed semi-automated methods for selecting the optimal docking algorithm and scoring function for different compound classes (e.g. peptide, covalently binding molecules, fragments) thus improving the chance for finding bioactive compounds in a small molecule library.
GROUP LEADER
Dr. Björn Windshügel
SECONDEES
?
CALIXAR
Functional Membrane Proteins for Life
Website: calixar.com
60 Avenue Rockefeller
69008 Lyon – France
READ EXPERTISE
Calixar is an innovative company that provides expertise for stabilization and solubilization of membrane proteins, based on proprietary technology, and original surfactant/detergent combinations. Its “adapted chemistry” approach allows stabilization of conformation during extraction.
Training at Calixar and collaboration on the protein targets selected by high-throughput approach will prove invaluable for providing the skills demanded in membrane protein structure based drug design.
This is of the utmost importance for eukaryotic proteins, that often require a targeted and rational process of optimization to be moved from the stage of expression and purification to crystallization or Cry-EM analysis.
GROUP LEADER
Dr. Alexis Moreno
E-Mail: amoreno@calixar.com
SECONDEES
Alexis Moreno
CSI
Consorzio Sapienza Innovazione
Website: sapienzainnovazione.it
Viale Regina Elena, 291
00161 Roma – Italy
READ EXPERTISE
A key component of the training will be the acquisition by ESRs and ERs from academic partners of skills that will facilitate scientific results exploitation and of both academic and industrial components to be acquainted with the different approaches to research in the other’s environment, in order to foster synergy and cooperation, above and beyond the scopes of the scientific project and of the Prometeus Consortium.
To this purpose we have included in Prometeus the Consorzio Sapienza Innovazione (CSI) that will contribute training in skills related to patenting and partnerships and lead the WP dedicated to knowledge transfer. CSI is an independent techno-structure created by Sapienza University of Rome to provide support in exploitation of research activities by establishing new spin-off companies, promoting technology transfer and establishing and running Joint Labs for multidisciplinary public/private applied research programs aimed at providing a flow of high technology solutions for innovation processes.
CSI services are:
- Joint Labs: 17 multidisciplinary laboratories, built around the most promising technological areas and characterized by collaboration between private and public partners to support new enterprises;
- Innovative spin-off enterprises: support to 20 new entrepreneurs in the start-up and consolidation phase, with services ranging from studies of technical and economic feasibility, to finding financial support;
- Technology Transfer: promote the exploitation of research offering assistance to commercialization and licensing (e.g., licensing and intellectual property rights), and finding opportunities for licensing to the market;
- National/Regional/European Union funding opportunities: information services, specialized organizational and managerial counselling, planning and technical assistance (Project Management) for participation to calls.
GROUP LEADER
Mr. Riccardo Carelli
SECONDEES
RICCARDO CARELLI
Riccardo Carelli is currently the financial and administrative manager of projects financed by Horizon 2020 for Sapienza Innovazione.
He was external consultant of MIUR, holding the role of National Coordinator of National Contact Points (NCP) and NCP for the “Financial and legal aspects in the context of FP7; in the context of FP6 he was NCP for the “Financial and legal aspects”, for the “Specific actions for SMEs” and for the “Support for the coordination and cooperation of research and innovation activities”.
He was also a National Representative in the Expert Groups belonging to the Member and Associated States for the drafting of the “FP7 Model Grant Agreement” and Alternate Member of CREST.
He worked at the European Commission, as Project Officer responsible for projects funded under the 4th and 5th FP and at the National Research Council with the task of enhancing, disseminating and transferring the results, through licensing, to companies Italian and foreign; in the same period he participated in projects financed under the 3rd and 4th FP.
The experience makes him an expert connoisseur of European institutions and the world of Italian university research.
ITQB
Instituto de Tecnologia Química e Biológica António Xavier Nova
Department: Biological Chemistry Division
Website: itqb.unl.pt
Avenida da Republica-Estação Agronómica Nacional
2780-157 Oeiras – Portugal
READ EXPERTISE
The Membrane Protein Crystallography Group at ITQB aims at the structure determination of membrane proteins using X-ray crystallography (MX) along with their functional characterization. In addition to the in-house X-ray diffractometer, periodic access is available to various European Synchrotrons facilities, such as ESRF, PETRA III and Diamond allowing for extensive screen of crystals and data. More recently, the combined approach of cryo-EM and/or SAXS with MX has been implemented. Crystallization robots and other state-of-art-equipment for growth and handling of protein crystal are available.
Sapienza and ITQBE together provide an arsenal of advanced methodologies for protein functional characterization, a mandatory step for the characterization and design of bioactive molecules.
A wide variety of biophysical and biochemical methods are available to complement structural characterization. This know-how is essential to ensure the correct folding, stability and activity of the recombinant/expressed proteins, as well as to analyse protein-ligand interactions and affinity, essential for drug development.
The equipment and methods include stopped-flow for steady state and pre-steady state kinetics, time-resolved spectroscopy, CD, IR, mass-spectrometry, gas spectrometry, VP-DSC Calorimeter, Dynamic Light Scattering, Isothermal Titration Calorimetry, Differential scanning calorimetry, advanced chromatographic techniques, N-terminal protein and peptide sequencing analysis, Seahorse XF Analyzers in anaerobiosis, Surface Plasmon Resonance, NMR facility (including 800 MHz NMR spectrometers), small molecule analysis (by HPLC, GC and elemental analysis), Fluorescence spectrophotometers and bioimaging (light and fluorescence microscopy).
Structure determination. (Crystallography, SAXS, and Cryo-EM)
GROUP LEADER
Professor Margarida Archer
E-Mail: archer@itqb.unl.pt
Website: Margarida Archer Lab
SECONDEES
JOSÉ RODRIGUES
FEDERICO ISSOGLIO
Federico Issoglio obtained his Chemistry degree at Universidad Nacional de Córdoba (Argentina). He completed the PhD in 2014 at the Departamento de Química Biológica (UNC). During this period he focused on biochemical, biophysical and structural analysis of enzymes involved in proteoglycogen biosynthesis.
In 2015 started a Postdoc position at Facultad de Ciencias Exactas, Universidad de Buenos Aires. From 2015 to 2019 He studied proteins using computational tools, acquiring expertise in quantum chemistry, molecular dynamics simulations, molecular docking and free energy calculations.
Currently, he holds a postdoc position at Universidade Nova de Lisboa (ITQB). He is studying membrane proteins form Mycobacterium tuberculosis, by determining the 3D structure using X-ray crystallography and/or cryo-electron microscopy, exploring the reactivity and thus unraveling the mechanisms underlying its catalysis.
UNIVPM
Università Politecnica delle Marche
Department: Dipartimento di Scienze della Vita e dell’Ambiente
Website: disva.univpm.it
Via Brecce Bianche
60131 Ancona – Italy
READ EXPERTISE
UNIVPM has considerable expertise in small-angle X-ray scattering (SAXS), a robust technique for the structural characterizations of macromolecules and macromolecular complexes in solution. SAXS is a low-resolution technique, but it can be applied to a wide variety of solution conditions, temperatures, particle sizes and composition, as well as in time-resolved conditions (few-tens millisecond.
SAXS experiments at synchrotron facilities (UNIVPM scientists are frequent users at ESRF, PETRA III, Diamond, Elettra) can bridge information in protein structure refinement with NMR, Crystallography and SPCryoEM providing a reliable, high-throughput characterization of macromolecular complexes under physiological/working conditions.
Moreover UNIVPM has also expertise in protein crystallography (Prof. M. Cianci). Indeed Prof. Cianci has contributed to the construction of a state-of-the-art beamline at PetraIII, and is involved in the development of new methods for structure determination from microcrystals, a crucial issue with membrane proteins.
MaSBiC (Marche Structural Biology Center) is a High-Throughput Protein Production Facility established at the Università Politecnica delle Marche (UNIVPM) by the Departments of Life and Environmental Sciences (DiSVA) and of Agricolture, Agronomy and Environment (D3A) and the Faculty of Medicine and inside a partnership with COMPPÅ. The MaSBiC facility has been operative for two years and provides robotically-assisted, high-throughput cloning, expression and purification of recombinant proteins from prokaryotic and eukaryotic cells for the Italian and European scientific community.
Several projects in the area of medicine, agrifood and marine biology are in progress, within national partnerships and in collaboration with European or extra-European research groups. MaSBiC has a close collaboration with COMPPÅ and is oriented towards innovation of HT platform for the production of G-protein coupled receptors (GPCR’s) that requires construction of special vectors and new approaches for expression in eukaryotic systems. The MaSBiC counts about 120 prokaryotic genomes, and it is enriching its genome’s bank with marine species.
GROUP LEADER
Professor Paolo Mariani
E-Mail: p.mariani@univpm.it
Website: Ma.S.Bi.C.
SECONDEES
ALESSIA SALVUCCI
Alessia Salvucci is a graduate student from the Università Politecnica delle Marche, she will work on “Cloning, expression and purification of human recombinant paraoxonase-2,
She comes from Laboratory of Enzymology and Clinical Molecular Biology (Prof. Monica Emanuelli, Faculty of Medicine) and the New York-Marche Structural Biology Center (NY-MaSBiC).
LUCREZIA SAVINI
IBET
Instituto De Biologia Experimental E Tecnologica
Department: Animal Cell Technology Unit
Website: ibet.pt
Av. República, Qta. do Marquês, EAN
2780-157 Oeiras – Portugal
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The IBET ACT Unit’s know-how in terms of biopharmaceuticals spans from the initial expression vector design and cell line establishment through all stages of process development and scale-up.
On the upstream bioprocessing, the ACT Unit is focused on devising strategies to control and optimize final product titer and quality. An array of different culture systems/platforms (mammalian, insect, transient and stable) is available, providing a landscape of possibilities for specific targets, challenges and product requirements. On the downstream bioprocessing, the ACT Unit is focused on innovative solutions, reducing manufacturing costs, increasing productivity, safety and efficacy.
The bioprocess cycle is finalized with extended expertise in (i) bioprocess monitoring tools and modelling approaches (e.g. mathematical models and 2D-fluorometry), (ii) functional genomic tools (e.g. transcriptomics, metabolomics and fluxomics), and (iii) analytical tools for product/cell characterization and quality control/assurance (e.g. mass spectrometry, tunable resistive pulse sensing and analytical size-exclusion chromatography) that can be performed at iBET’s GMP certified Analytical Services Unit and Mass Spectrometry Unit. Process scale-up can be performed from lab (250 mL to 5 L) to pre-clinical scales (2 L to 70 L scale), the latter performed at iBET’s Pilot Plant (2000 m2), an infrastructure that routinely supplies pre-clinical grade biopharmaceutical products (e.g. vaccines, mAbs and VLPs).
A crucial infrastructure of added value to Prometeus is the Protein Production Platform (PPP). The PPP main activities are recombinant protein production in several expression systems (e.g. E. coli, yeast, baculovirus-insect and mammalian cells), bioprocess development, scale-up, analytics for quality control/assurance, formulation and delivery.
IBET’s ACT Unit has been dedicating substantial effort in the development of new in vitro models for pre-clinical research (incl. toxicological assessment), the reason being the lack of efficient and cost-effective in vitro tools to predict pharmacokinetics and toxic reactions of new compounds at early stage of drug discovery. Biotransformation occurs mainly in the liver, after which hepatocyte-end products are transported to other organs, such as the brain.
ACT Unit has been working on new tools, with higher predictive power in terms of xenobiotic biotransformation than the currently available ones, using primary cultures of hepatocytes (rat and human origin) and differentiating human embryonic stem cells into functional hepatocyte-like cells. Training at ACTU and collaboration with Prometeus partners on specific/selected protein targets will be key to ensure ESRs and ERs have at the end of Prometeus project the needed skill set for membrane protein based drug design.
GROUP LEADERS
Professor Paula Alves
E-Mail: marques@ibet.pt
Professor António Roldão
E-Mail: aroldao@ibet.pt
SECONDEES
MARIA MARGARIDA RODRIGUES
Maria Margarida Rodrigues is a Junior Researcher at the Cell-Based Vaccine Development Laboratory of the Animal Cell Technology (ACT) Unit (Health & Pharma Division, iBET).
Maria Margarida Rodrigues graduated in Biological Engineering at Instituto Superior Técnico – University Lisbon in 2019. She has always followed with keen interest the fields of life sciences and biotechnology, which motivated her to carry out the research for the Master Thesis at the University of Natural Resources and Life Sciences (BOKU, Vienna, Austria), under the scope of the Erasmus programme. There, she interned at the Tissue Engineering Laboratory, whose field of research is the optimization of strategies for the cultivation of stem cells. Her thesis focused on the study and development of a device for the non-invasive monitoring of 3D cell cultures. The research experience at BOKU contributed for her eagerness to pursue a scientific research career, and led her to join the ACT Unit at iBET.
Current Research is focused on the production of relevant therapeutic products, such as viral vectors and recombinant proteins, and the study of strategies to optimize animal cell culture and improve production yields. In the next years, she intends to expand her research career and contribute to the development of novel bioprocesses for the production of vaccines against high-impact diseases.
Email: margarida.rodrigues@ibet.pt
Web pages: tca.itqb.unl.pt
RICARDO CORREIA
Ricardo Correia is currently a third year PhD student of the MIT Portugal – Bioengineering Systems doctoral program (iBET and ITQB-NOVA), working in the Vaccine Development Laboratory at the Animal Cell Technology Unit (ACT, Health & Pharma Division, iBET). Ricardo Correia holds an MSc in Biological Engineering from Instituto Superior Técnico, Universidade de Lisboa, which he graduated in 2014.
Ricardo Correia PhD’s research work focus on the development of novel bioprocess engineering approaches (development of high producing cell lines through evolutionary engineering and establishment of bioreactor production set-ups for process intensification) for the improved production of vaccine candidates (inc. VLP-based) against infectious diseases such as Influenza and malaria.
Additionally, Ricardo Correia has performed his MSc thesis work in the Department of Regenerative Medicine from the Faculty of Medicine (Ghent, Belgium) in 2014. His work focused on the reprogramming of animal (mice and human) somatic cells into pluripotent cells. Since Ricardo Correia has joined the Animal Cell Technology Unit in 2015, he has also been involved in other service driven projects focused on vaccines and protein production. As a junior researcher, he has been involved in the upstream processing of a universal Influenza vaccine candidate within the scope of the EU funded research project “EDUFLUVAC”. Recently, he has also been involved in the process development and production of a new assexual blood-stage malaria vaccine candidate, within a Japanese-funded project (GHIT Fund).
Ricardo Correia is author of 2 scientific manuscripts, over 10 poster and 1 oral communication, and has experience in co-supervision of master students (1) and other interns. His motivation focus on continuing doing research towards development of novel bioproducts and bioprocess schemes for protein and vaccine production.
Orcid: https://orcid.org/0000-0002-9434-7974
Email: rccorreia@ibet.pt
Web page: www.ibet.pt
MoLiRom
Molecular Links Rome
Contact: Dr Alessandra Bonamore
E-Mail: alessandra.bonamore@uniroma1.it
Via Ravenna, 8
00161 Rome – Italy
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MoLiRom specializes in developing protein based carriers for theranostics based on a genetically engineered thermostable globin or ferritin scaffolds.
Molirom is producing at gram scale for preclinical investigation on melanoma therapy and advanced in order to increase the photosensitive ligand load. Recombinant protein production and expression, random and site selected mutagenesis, protein immobilization on activated silicon surfaces.
Facilities comprise a fully equipped molecular biology lab, a pilot scale purification station, AFM and SEM microscopy.
Molirom brings into the Consortium advanced capabilities for protein design and engineering and conjugation with organic moieties for achieving diagnostics and therapeutics activities.
GROUP LEADER
Professor Alberto Boffi
E-Mail: a.boffi@molirom.com
SECONDEES
MARTINA PITEA
November 2018
Awarded PhD scholarship in Biochemistry (XXXIV cycle) “Sapienza” – University of Rome (Italy), “Sapienza” – University of Rome (Italy), Institute of Biology and Molecular pathology-CNR- Department of Biochemistry A. Rossi Fanelli ” Piazzale Aldo Moro 5.00185 Rome (Italy).
January 2018
Master’s degree in Medical Biotechnology, LM-9 (110/110 cum laude)
Experimental Thesis title: Engineered human ferritin for targeted transport of drugs
“Sapienza” University of Rome. Faculty of Pharmacy and Medicine; Piazzale Aldo Moro 5.00185 Rome (Italy), Institute of Biology and Molecular pathology-CNR-Department of Biochemical Sciences – A. Rossi Fanelli,
Professor: Alberto Boffi, Tutor: Pierpaolo Ceci
TECHNICAL SKILLS AND COMPETENCES
Good knowledge and expertise in the main molecular biology techniques (cloning, enzymatic digestion, bacterial transformations, plasmid DNA extraction from bacterial cultures) and cellular biology, biochemical methods (SDS-PAGE electrophoresis And on agarose gels, chromatographies such as HPLC) and spectroscopic (absorption). Experience with bacterial models (E. coli).
Correct use of the main methods and instruments present in a chemical laboratory: preparation of solutions and dilutions, application of titles and separation techniques, measurement of pH and conductivity, construction of calibration curves and Performance of UV-Visible spectrophotometric readings.
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Extremochem is a start-up company dedicated to the development and commercialisation of new chemically synthesized compounds for protein stabilization. Extremochem main expertise is organic synthesis, such as: asymmetric synthesis of structurally diverse natural compounds and analogues, carbohydrate chemistry, solid supported synthesis, reagent development, nanoparticle synthesis, and it will provide this expertise, following the in silico evaluation of biomolecules or the design of new ones.
Extremochem compounds are a new family of stabilizers, efficient, affordable and recoverable when necessary. They are obtained exclusively by chemical synthesis. Extremochem stabilizers have important potential applications, from stabilizing proteins at laboratory scale, avoiding aggregation and degradation during purifications, to stabilizing biopharmaceuticals. These stabilizers will allow biopharmaceuticals stand several stresses, including shaking, viscosity and temperature variations, and thus transportation and storage costs will be drastically reduced. The shelf life of biopharmaceuticals will be extended.
The social and health impacts of the potential applications of these new compounds are huge, and it will be exploited for the stabilization of proteins produced within the Prometeus Consortium (membrane proteins, but also ferritin bioconjugates).
The expertise of Extremochem will therefore be very valuable, both for custom organic synthesis and for the stabilization of proteins produced in the consortium, with an alternative and innovative approach, over and above the presence of detergents.
GROUP LEADER
Dr Rita Ventura
E-Mail: rventura@itqb.unl.pt
SECONDEES
EVA LOURENÇO
Eva Lourenço obtained a Chemistry degree in 2006 and a Master in Green Chemistry in 2008, both from Faculdade de Ciências, Universidade de Lisboa.
In 2003, she received her PhD in Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.
She is responsible for synthesizing and testing new protein stabilizers.
She has experience in organic synthesis, carbohydrate chemistry and solid supported synthesis.
FRAUNHOFER
Gesellschaft zur Foerderung der Angewandten Forschung E.V.
Department: ScreeningPort
Website: ime.fraunhofer.de/en
Schnackenburgallee, 114
22525 Hamburg – Germany
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The Department ScreeningPort of the Fraunhofer Institute for Molecular Biology and Applied Ecology (IME-SP) offers industry standard small molecule drug discovery. It collaborates closely with academic institutions and pharmaceutical industry in multiple research projects.. Besides experimental screening, IME-SP offers comprehensive in silico screening capabilities including structure- and ligand-based methods (e.g. molecular docking, pharmacophore searches) using industry-standard software (e.g. MOE, GOLD, Schrödinger), 3D-Workstations and high-performance computing facilities.
The Fraunhofer-Gesellschaft is the leading organization for applied research in Europe, it employs a staff of nearly 24,000, who work with an annual research budget totaling more than 2 billion EUR.
IME-SP utilises a broad set of computational methods for the discovery of novel bioactive compounds that have been integrated into workflow tools for improving automation and data analysis. Besides molecules docking, also pharmacophore searches and combinations of both are applied.
In addition, IME-SP utilises ligand-based methods such as 3D QSAR techniques. IME-SP has developed semi-automated methods for selecting the optimal docking algorithm and scoring function for different compound classes (e.g. peptide, covalently binding molecules, fragments) thus improving the chance for finding bioactive compounds in a small molecule library.
GROUP LEADER
Dr. Björn Windshügel
SECONDEES
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CALIXAR
Functional Membrane Proteins for Life
Website: calixar.com
60 Avenue Rockefeller
69008 Lyon – France
READ EXPERTISE
Calixar is an innovative company that provides expertise for stabilization and solubilization of membrane proteins, based on proprietary technology, and original surfactant/detergent combinations. Its “adapted chemistry” approach allows stabilization of conformation during extraction.
Training at Calixar and collaboration on the protein targets selected by high-throughput approach will prove invaluable for providing the skills demanded in membrane protein structure based drug design.
This is of the utmost importance for eukaryotic proteins, that often require a targeted and rational process of optimization to be moved from the stage of expression and purification to crystallization or Cry-EM analysis.
GROUP LEADER
Dr. Alexis Moreno
E-Mail: amoreno@calixar.com
SECONDEES
Alexis Moreno
CSI
Consorzio Sapienza Innovazione
Website: sapienzainnovazione.it
Viale Regina Elena, 291
00161 Roma – Italy
READ EXPERTISE
A key component of the training will be the acquisition by ESRs and ERs from academic partners of skills that will facilitate scientific results exploitation and of both academic and industrial components to be acquainted with the different approaches to research in the other’s environment, in order to foster synergy and cooperation, above and beyond the scopes of the scientific project and of the Prometeus Consortium.
To this purpose we have included in Prometeus the Consorzio Sapienza Innovazione (CSI) that will contribute training in skills related to patenting and partnerships and lead the WP dedicated to knowledge transfer. CSI is an independent techno-structure created by Sapienza University of Rome to provide support in exploitation of research activities by establishing new spin-off companies, promoting technology transfer and establishing and running Joint Labs for multidisciplinary public/private applied research programs aimed at providing a flow of high technology solutions for innovation processes.
CSI services are:
- Joint Labs: 17 multidisciplinary laboratories, built around the most promising technological areas and characterized by collaboration between private and public partners to support new enterprises;
- Innovative spin-off enterprises: support to 20 new entrepreneurs in the start-up and consolidation phase, with services ranging from studies of technical and economic feasibility, to finding financial support;
- Technology Transfer: promote the exploitation of research offering assistance to commercialization and licensing (e.g., licensing and intellectual property rights), and finding opportunities for licensing to the market;
- National/Regional/European Union funding opportunities: information services, specialized organizational and managerial counselling, planning and technical assistance (Project Management) for participation to calls.
GROUP LEADER
Mr. Riccardo Carelli
SECONDEES
RICCARDO CARELLI
Riccardo Carelli is currently the financial and administrative manager of projects financed by Horizon 2020 for Sapienza Innovazione.
He was external consultant of MIUR, holding the role of National Coordinator of National Contact Points (NCP) and NCP for the “Financial and legal aspects in the context of FP7; in the context of FP6 he was NCP for the “Financial and legal aspects”, for the “Specific actions for SMEs” and for the “Support for the coordination and cooperation of research and innovation activities”.
He was also a National Representative in the Expert Groups belonging to the Member and Associated States for the drafting of the “FP7 Model Grant Agreement” and Alternate Member of CREST.
He worked at the European Commission, as Project Officer responsible for projects funded under the 4th and 5th FP and at the National Research Council with the task of enhancing, disseminating and transferring the results, through licensing, to companies Italian and foreign; in the same period he participated in projects financed under the 3rd and 4th FP.
The experience makes him an expert connoisseur of European institutions and the world of Italian university research.
PARTNER ORGANIZATION
COMPPÅ
Center on Membrane Protein Production and Analysis
NYSBC
New York Structural Biology Center
Website: comppaa.org
89 Convent Avenue
New York, NY 10027, USA
READ EXPERTISE
COMPPÅ (Center on Membrane Protein Production and Analysis) represents a pivotal asset for training and development of Prometeus research projects. It provides and develops state-of-the-art methodologies for the scientific community. Integral membrane proteins present formidable challenges for structural and functional analyses: in recombinant systems membrane proteins perform poorly. Further, once extracted from the lipid bilayer, they demand the use of detergents, not all suitable for all membrane proteins universally. This requires many optimization steps in a trial-and-error fashion. For a scientist the number of variables that must be addressed is daunting. Strategies that can employ high-throughput approaches, or to rapidly screen multiple constructs and conditions simultaneously, particularly with the use of robotics, are extremely valuable.
High-throughput cloning and expression of both prokaryotic and eukaryotic targets.
COMPPÅ counts on approximately 150 prokaryotic genomes from which to clone homologs of any target of interest. Eukaryotic targets will instead be obtained as sequence verified cDNAs, or by gene synthesis. The availability of robotics at COMPPÅ allows large numbers of targets to be produced and cloned into a wide variety of vectors for expression in prokaryotic and eukaryotic hosts.
The application of robotically-assisted, high-throughput expression and purification methods for recombinant membrane proteins from both E. coli and eukaryotic hosts permits to overcome the next critical hurdle by identifying and producing promising candidates for structural and functional studies. Recombinant proteins is not limited to analysis of structure, but they will be used also for activity and inhibition assays.
COMPPÅ has implemented automated systems that can sequentially screen multiple proteins, in multiple different detergent types, by size exclusion chromatography. This has proven valuable towards rapidly identifying candidates for in-depth structural analyses. This approach allows to single out the appropriate conditions to obtain a stable and monodisperse preparation of a given membrane protein.
GROUP LEADERS
Professor Wayne Hendrickscon
E-Mail: wayne@xtl.cumc.columbia.edu
Wikipedia: Wayne Hendrickson
Professor Filippo Mancia
E-Mail: fm123@cumc.columbia.edu
Website: Mancia Lab
CUNY
The City University of New York
Department: Advance Science Research Center (ASRC) Dept of Chem and Biochem
Website: asrc.cuny.edu
85 St. Nicholas Terrace
New York, NY 10031, USA
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The Advanced Science Research Center at the City University of New York (CUNY) houses FEI Titan Halo 300 kV cryo-Electron microscope with Gatan K2 direct detector camera and Volta phase plate.
In-house availability of the most advanced Cryo-EM instrument is extremely valuable, at a time when highly performing Cryo-EM instruments in the world are heavily oversubscribed and training in structural determination by single particle Cryo-EM is in high demand.
The resolution limits of single-particle Cryo-EM have been overcome by the advent of direct-electron detectors. Cryo-EM has reached the resolutions formerly only available through crystallography, without requiring the growth of crystals.
We will therefore pursue in parallel structure determination by Cryo-EM, of the protein targets, keeping in mind the complementarity of crystallography and Cryo-EM, as the former can still provide higher resolution, but the latter can provide information on conformational flexibility, both relevant for drug design.
GROUP LEADER
Professor Amédée des Georges
E-Mail: amedee.desgeorges@asrc.cuny.edu
COMPPÅ
Center on Membrane Protein Production and Analysis
NYSBC
New York Structural Biology Center
Website: comppaa.org
89 Convent Avenue
New York, NY 10027, USA
READ EXPERTISE
COMPPÅ (Center on Membrane Protein Production and Analysis) represents a pivotal asset for training and development of Prometeus research projects. It provides and develops state-of-the-art methodologies for the scientific community. Integral membrane proteins present formidable challenges for structural and functional analyses: in recombinant systems membrane proteins perform poorly. Further, once extracted from the lipid bilayer, they demand the use of detergents, not all suitable for all membrane proteins universally. This requires many optimization steps in a trial-and-error fashion. For a scientist the number of variables that must be addressed is daunting. Strategies that can employ high-throughput approaches, or to rapidly screen multiple constructs and conditions simultaneously, particularly with the use of robotics, are extremely valuable.
High-throughput cloning and expression of both prokaryotic and eukaryotic targets.
COMPPÅ counts on approximately 150 prokaryotic genomes from which to clone homologs of any target of interest. Eukaryotic targets will instead be obtained as sequence verified cDNAs, or by gene synthesis. The availability of robotics at COMPPÅ allows large numbers of targets to be produced and cloned into a wide variety of vectors for expression in prokaryotic and eukaryotic hosts.
The application of robotically-assisted, high-throughput expression and purification methods for recombinant membrane proteins from both E. coli and eukaryotic hosts permits to overcome the next critical hurdle by identifying and producing promising candidates for structural and functional studies. Recombinant proteins is not limited to analysis of structure, but they will be used also for activity and inhibition assays.
COMPPÅ has implemented automated systems that can sequentially screen multiple proteins, in multiple different detergent types, by size exclusion chromatography. This has proven valuable towards rapidly identifying candidates for in-depth structural analyses. This approach allows to single out the appropriate conditions to obtain a stable and monodisperse preparation of a given membrane protein.
GROUP LEADERS
Professor Wayne Hendrickscon
E-Mail: wayne@xtl.cumc.columbia.edu
Wikipedia: Wayne Hendrickson
Professor Filippo Mancia
E-Mail: fm123@cumc.columbia.edu
Website: Mancia Lab
CUNY
The City University of New York
Department: Advance Science Research Center (ASRC) Dept of Chem and Biochem
Website: asrc.cuny.edu
85 St. Nicholas Terrace
New York, NY 10031, USA
READ EXPERTISE
The Advanced Science Research Center at the City University of New York (CUNY) houses FEI Titan Halo 300 kV cryo-Electron microscope with Gatan K2 direct detector camera and Volta phase plate.
In-house availability of the most advanced Cryo-EM instrument is extremely valuable, at a time when highly performing Cryo-EM instruments in the world are heavily oversubscribed and training in structural determination by single particle Cryo-EM is in high demand.
The resolution limits of single-particle Cryo-EM have been overcome by the advent of direct-electron detectors. Cryo-EM has reached the resolutions formerly only available through crystallography, without requiring the growth of crystals.
We will therefore pursue in parallel structure determination by Cryo-EM, of the protein targets, keeping in mind the complementarity of crystallography and Cryo-EM, as the former can still provide higher resolution, but the latter can provide information on conformational flexibility, both relevant for drug design.
GROUP LEADER
Professor Amédée des Georges
E-Mail: amedee.desgeorges@asrc.cuny.edu
