Elettra 2.0: New Structural Biology Opportunities

Monday Jul 3, 2023, 8:40 AM → 8:00 PM Europe/Rome

AREA Science Park

After nearly 30 years of service to the international research community, the Elettra 3rd generation synchrotron source will be replaced by the new Elettra 2.0 diffraction limited storage ring. The 4th generation light source will boost the spatial, energy and temporal resolution of all imaging, scattering and spectroscopic techniques, opening new opportunities in many fields of science.

A new dedicated MX beamline, μXRD, will replace the present XRD2 beamline at Elettra 2.0 and will be complemented by a new cryogenic electron microscopy facility (cryo-EM) that the Italian National Research Council and Elettra Sincrotrone Trieste are establishing. An interconnected network of support laboratories for MX and cryo-EM sample preparation and characterization with ancillary analytical techniques will further widen the offer.

The goal of the hybrid-mode workshop “Elettra 2.0: New Structural Biology Opportunities” on July 3rd is to present and discuss our upgrade plans. During this event, speakers from facilities across Europe will share their experience and discuss the main challenges encountered by structural biology users.

We look forward to your participation either in person or virtual mode, to share our vision and gather feedback from our scientific community in order to leverage our future state-of-the-art facilities.

We would like to encourage you to participate and actively contribute to the workshop by providing us with information about your present and perspective needs. In this respect, we would appreciate if you could take a few minutes to respond to our survey at: https://forms.gle/ctmWKK8anY123zoU6 by June 26th 2023.

 

HowToReachUs_AreaSciencePark.pdf

9:00 AM → 9:20 AM Welcome

9:00 AM Welcome by Alfonso Franciosi and Salvatore La Rosa

Speakers: Alfonso Franciosi (Elettra Sincrotrone Trieste), Salvatore La Rosa (AREA Science Park)

9:20 AM → 2:00 PM Session 1 Macromolecular Crystallography Chair: Michele Cianci (Università Politecnica delle Marche)

9:20 AM Elettra 2.0 project and IVU beamlines

After 27 years of successfully serving the user community, Elettra is undertaking a major upgrade towards a diffraction limited light source, called Elettra 2.0, enabling new science and the development of new technologies to the general benefit.

Due to a substantial reduction of the emittance of the stored electron beam, the new machine will be able to host in particular also in-vacuum undulators (IVU), allowing for new microfocus beamlines in the range of hard X-rays. Among these, in particular a new beamline dedicated to macromolecular crystallography (μXRD) has been designed to support the requests of structural biology community, offering high photon fluxes on a micron-sized spot, opening to a fast characterization of smaller samples and to data collection strategies of increasing complexity.

The talk will highlight some characteristics of the new machine and report design and expected features of the new beamline.

Speaker: Maurizio Polentarutti (Elettra Sincrotrone Trieste)

9:40 AM The new MX beamline at Elettra 2.0: μXRD

The new high brilliance microfocus μXRD beamline will be presented. μXRD aims to fullfill the needs of current XRD2 community and will open new opportunities to Elettra MX users.

Speaker: Nicola Demitri (Elettra Sincrotrone Trieste)

10:00 AM Combining visual and X-ray sample characterization information in design of macromolecular crystallography experiments

The best thing one can do to determine the structure of a biological macromolecule at atomic resolution is to grow a large homogeneous crystal of it, then probe it with flat X-ray beam of the matching size, while rotating it using a perfect goniometer while measuring the complete reciprocal image of its electronic density with a perfect detector.

Though this ideal is not feasible in practice, it should stay the northern star of our struggle for quality. In this contribution we will address three points that have a promise of bringing us closer to the ideal.

First we will unravel the problem of achieving perfect sample alignement at arbitrary goniometer datum with mechanically imperfect goniometers.

Second we will address the problem of merging optical and x-ray sample characterization information into a coherent whole.

Third we will attempt to establish a way of optimal sampling of available diffracting volume for a more perfect measurement with beams of arbitrary size and intensity.

The talk will conclude with a discussion of the most desirable properties of a new MX beamline, with a view to the problems we will have attempted to unravel.

Speaker: Martin Savko (SOLEIL)

10:30 AM Coffee

Coffee

11:00 AM New opportunities for time resolved serial crystallography experiments at 4th generation synchrotrons

Speaker: Daniele de Sanctis (ESRF)

11:30 AM Infrastructure requirements for running high-throughput crystallographic fragment screening

i04-1 at Diamond Light Source is a fixed wavelength, high throughput beamline, dedicated to running unattended data collection queues. We utilise the beamtime to run XChem fragment screening experiments for both industry and academic users, allowing us on average to collect 2000 samples per week. In addition to what we require from the beamline, this talk will focus on the infrastructure requirements to support high-throughput fragment screening, covering laboratory requirements, computing, staff and logistics.

Speaker: Ailsa Powell (Diamond Light Source)

12:00 PM IT integration with Elettra facility upgrades

Speaker: Roberto Pugliese (Elettra)

12:30 PM Lunch at the canteen (Area di Ricerca)

2:00 PM → 4:20 PM Session 2 Cryo-Electron Microscopy Chair: Rita De Zorzi (Università degli Studi di Trieste)

A new facility for cryoEM will soon be available in Trieste. Introduction to its future capabilities and perspective from other facilities in Europe will be presented.

2:00 PM The Structural Biology program at Elettra: present and future

Speaker: Silvia Onesti (Elettra Sincrotrone Trieste)

2:20 PM CryoEm Facility in Trieste: Instrumentation and complementarity with IOM-CNRLabs

Speaker: Simone dal Zilio (CNR-IOM (Istituto Officina dei Materiali))

2:40 PM Development and implementation of cryo-electron microscopy at the National Institute of Chemistry, Slovenia

Integrated structural biology aims to provide high-resolution structural information about biological molecules and their complexes in isolated form or in biological context based on data obtained by various experimental and theoretical methods. This helps to understand biological processes and enables drug and vaccine discovery and other applications in biotechnology. For atomic resolution approaches, X-ray crystallography has long been the gold standard, but the immense power of cryo-electron microscopy (cryo-EM) has recently contributed increasingly to the field, providing detailed structural information on many complex (biological) macromolecular systems. Recent dramatic scientific achievements have been based on the use and continuous development of high-end structural biology infrastructure, which is large both in terms of its physical size and cost. The latter could be a major disadvantage for smaller but ambitious scientific communities. In my talk, I will describe our path to establishing a cryo-EM facility at the National Institute of Chemistry, the first in Slovenia and in the region. I will describe how we combine it with other methodological approaches and show some concrete examples from our research projects. Our cryo-EM facility has been continuously active since its opening in November 2019 to answer Slovenian and foreign academic or industrial research questions and, importantly, also to train new generations of cryo-EM scientists.

Speaker: Marjetka Podobnik (NIC, Ljubljana)

3:10 PM Application of cutting-edge cryo-EM methodologies to study DNA replication and repair

Cryo Electron Microscopy (cryo-EM) has revolutionized structure biology, allowing direct visualization of entire molecular machines at atomic resolution. In this talk, I will outline some of the applications of single-particle cryo-EM analysis we use in the lab to investigate the structure and function of enzymes operating in human DNA replication and repair.

Speaker: Alfredo de Biasio (KAUST, Kingdom of Saudi Arabia )

3:40 PM Machine Learning in Structural Biology

We review the current progress and challenges in the field of Machine Learning for Structural Biology. We will discuss existing machine learning algorithms such as AlphaFold for structural prediction, the use of large language models for protein design, and generative models applied to protein-protein docking. The aim of the seminar will be to encourage experts from relevant communities to imagine new applications and explore potential future collaborations in the field.

Speaker: Alessio Ansuini (AREA Science Park)

4:00 PM Coffee

4:20 PM → 7:10 PM Session 3 Facilities for Structural Biology Chair: Alberto Cassetta (CNR-IC)

4:20 PM Protein production facility at Elettra: past, present and future.

Speaker: Paola Storici (Elettra Sincrotrone Trieste)

4:50 PM The EMBL Protein Expression and Purification Core Facility: bringing structural biology tools to the non-structural biology community

The goal of the EMBL Protein Expression and Purification Core Facility is to provide high-level services and advice regarding all aspects of protein expression, purification and characterisation. We aim to support our users with all individual steps of the workflow, going from the choice of the expression host organism and construct design to small scale screening, expression scale-up and protein purification using a combination of chromatographic methods to protein quality control and biophysical characterisation. We are based at EMBL Heidelberg and are embedded in the local Structural and Computational Biology unit, which allows us to stay up-to-date of the latest developments in structural biology. We also work closely with our colleagues at EMBL Hamburg and EMBL Grenoble, whose laboratories are located on the German Synchrotron Research Centre (DESY) campus and the European Synchrotron Radiation Facility (ESRF) campus, respectively. Even though we cooperate frequently with the different EMBL structural biology groups and facilities across the EMBL sites, one of our core tasks is to make structural biology tools accessible to the non-structural biology community as well. We collaborate with research groups from a large variety of scientific disciplines that are typically not immediately associated with structural biology, ranging from developmental biology, neurobiology and medicine to marine biology, planetary biology and human ecosystems. We produce samples for structural characterisation by NMR, crystallisation and cryo-electron microscopy, but also for other applications such as nanobody/antibody generation and biochemical or biophysical experiments. By doing so, we hope to assist these research groups in introducing more interdisciplinary approaches into their projects as well.

Speaker: Kim Remans (EMBL Heidelberg)

5:20 PM Leading a Protein Production facility for HT structural biology

Speaker: Opher Gileadi (SGC Karolinska)