MLZ Conference 2021: Neutrons for Life SciencesOnline only

Europe/Berlin
Description

Life Sciences is a rapidly expanding field in the use of neutrons. The number of users at the Heinz Maier-Leibnitz-Zentrum (MLZ) performing experiments related to life sciences is constantly growing. Be it contrast variation for matching out protein, DNA or lipids or the hunt for catalytical important hydrogen atoms, neutrons play an important role in determining structures of biologically relevant molecules or membranes. Neutron tomography on living plants or tissue uses the huge difference in incoherent scattering of hydrogen as compared to deuterium. Using incoherent and coherent inelastic neutron scattering, investigation of equilibrium dynamics of biological systems is possible on the picosecond and nanosecond time scale. With future neutron sources, time resolved investigations will become more and more important. Dedicated sample environment and additional in situ measurement techniques all optimized for small sample volumes will be needed in the future.

This is why the MLZ Conference 2021 intends to bring together experts in the field of Life Sciences regardless whether they have used neutron scattering techniques or not. The conference will try to cover all relevant fields of life sciences and will discuss  on how to improve neutron instrumentation, access to neutron beam time, sample environments and support labs for future life sciences users.

We warmly welcome contributions on the following topics:

  • Protein structure, function and dynamics
  • Biological membranes, surface and interfaces
  • Drug design and delivery
  • Biological processes
  • Neutron and complementary methods in biology
  • Life Sciences with neutrons in Russia
  • Neutrons in the fight against virus diseases

Initially this Conference was intended to be held in June 2020; due to the Covid-19 pandemic it has been postponed to 2021. In the light of the current  development of the Covid-19 disease the organizers have decided to opt for a purely virtual format in 2021. 

We hope that this decision will allow all scientists interested in this special topic to participate.

We are very much looking forward to welcome you at the virtual MLZ Conference

Neutrons for Life Sciences!

    

Prof. Dr. Martin Müller                        Prof. Dr. P. Müller-Buschbaum          

Registration
Regular registration
MLZ Conference 2021 "Neutrons for Life Sciences" Support
    • 10:15 10:30
      Welcome of the MLZ directors

      Welcome of the MLZ directors

    • 10:30 12:00
      Biological membranes, surfaces and interfaces
    • 12:00 13:00
      Lunch Break 1h
    • 13:00 14:30
      Neutron and complementary methods in biology
    • 14:30 15:30
      Break & "Wonder" tutorial 1h
    • 15:30 16:10
      Life Sciences at Russian Neutron Sources
    • 16:10 16:40
      Coffee Break 30m
    • 16:40 17:50
      Protein structure, function and dynamics
      • 17:10
        High-resolution structure studies of NADH-cytochrome b5 reductase 20m

        NADH-cytochrome b5 reductase (b5R) on endoplasmic reticulum membrane in mammalian liver cell plays a variety of roles concerning lipid unsaturation and xenobiotic metabolism. b5R transfers electrons from two-electron carrier of NADH to one-electron donor of cytochrome b5. In the redox cycle of b5R, a hydride transfer from NADH to oxidized FAD and deprotonation from the reduced FADH take place in b5R. Therefore, high-resolution structure analyses including the information about hydrogen atoms and valence electron densities are required for understanding molecular mechanisms of the b5R redox reaction. High-resolution X-ray crystal structures were previously determined using the oxidized form of b5R (M. Yamada et al., J. Mol. Biol., 2013; K. Takaba et al., Sci. Rep., 2017). In this work, the neutron crystal structures of the oxidized form of b5R were determined including hydrogen atoms of solvent molecules, and the X-ray crystal structures of the reduced form of b5R were determined including hydrogen atoms of the NADH cofactor. Recently, neutron diffraction data sets of the reduced form have been collected at BIODIFF of FRM II. The neutron structure analysis of the oxidized form clearly shows the hydrogen-bonding network from the FAD cofactor to the protein surface. The X-ray structure analysis of the reduced form reveals the NAD+ and NADH bound states using wildtype and T66V mutant. These structural features indicate a proton transfer pathway from FAD to the protein exterior.

        Speaker: Dr Yu Hirano (National Institutes for Quantum and Radiological Science and Technology)
      • 17:30
        Neutron structures of Leishmania mexicana triosephosphate isomerase complexes with reaction intermediate mimics shed light on the proton shuttling steps 20m

        Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP). This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from the ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the following enediol intermediate by phosphoglycolohydroxamate (PGH). We have determined the neutron structure of Leishmania mexicana TIM with both inhibitors and performed joint neutron-X-ray refinement followed by quantum refinement. The structures show that in the PGA complex, the postulated general base Glu-167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu-167 in the PGA–TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of active site protonation states allows us to investigate the reaction mechanism with density functional theory calculations.

        Speaker: Esko Oksanen (European Spallation Source ESS ERIC)
    • 09:00 10:30
      Drug design and delivery
    • 10:30 10:50
      Coffee Break 20m
    • 10:50 11:50
      Protein structure, function and dynamics
    • 11:50 13:00
      Lunch Break 1h 10m
    • 13:00 15:00
      Poster Session
    • 15:00 15:30
      Coffee Break 30m
    • 15:30 16:50
      Protein structure, function and dynamics
    • 16:50 17:10
      Coffee Break 20m
    • 17:10 17:50
      Biological membranes, surfaces and interfaces
    • 09:00 10:30
      Biological processes
    • 10:30 10:50
      Coffee Break 20m
    • 10:50 11:50
      Protein structure, function and dynamics
    • 11:50 13:00
      Lunch Break 1h 10m
    • 13:00 14:00
      History of FRM II & MLZ
    • 14:00 15:00
      Biological membranes, surfaces and interfaces
    • 15:00 15:30
      Coffee Break 30m
    • 15:30 17:00
      Neutrons in the fight against virus diseases
      • 15:30
        Neutron crystallography in the fight against COVID-19: Drug Design Targeting SARS-CoV-2 Main Protease 30m

        COVID-19, caused by SARS-CoV-2, is a global health and economic catastrophe. The viral main protease (Mpro) is indispensable for SARS-CoV-2 replication and thus is an important target for small-molecule antivirals. Neutrons are an ideal probe to observe protonation states of ionizable amino acids at near-physiological temperature, directly determining their electric charges – crucial information for computer-assisted and structure-guided drug design. Our structures of Mpro collected at near-physiological temperatures revealed the reactivity of the catalytic cysteine, malleability of the active site, and binding modes of clinical protease inhibitors. Neutron crystal structures of ligand-free and covalent inhibitor-bound Mpro allowed direct observation of protonation states of all residues in a coronavirus protein. The catalytic Cys-His dyad exists in the reactive zwitterionic state, with both Cys145 and His41 charged, instead of the anticipated neutral state. Covalent inhibitor binding results in modulation of the protonation states, retaining the overall electric charge of the Mpro active site cavity. High-throughput virtual screening in conjunction with in vitro assays identified a non-covalent compound with micromolar affinity, used as a lead to design novel Mpro inhibitors. Our research is providing real-time data for atomistic design and discovery of Mpro inhibitors to combat the COVID-19 pandemic and prepare for future threats from pathogenic coronaviruses.

        Speaker: Andrey Kovalevsky (Oak Ridge National Laboratory)
      • 16:00
        Structure of SARS-CoV-2 papain-like protease PLpro reveals a framework for antiviral inhibitor design 20m

        The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) is essential for the virus replication. PLpro has the additional function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. PLpro is thus an excellent drug target for a two-fold strategy to develop antiviral compounds that both inhibit viral replication and strengthen the immune response of the host. To provide a structural framework for efficient screening of inhibitor compounds, we expressed, purified and crystallized PLpro. The crystals are stable, reproducible, have a high solvent content of 66% suitable for soaking experiments and diffract to a high resolution of 1.5 Å. Bioinformatics analysis of the active site region based on the PLpro crystal structure coordinates showed interestingly high similarities to the proteasome active site and we screened 37 proteosome inhibitors by soaking and co-crystallization experiments. The PLpro crystals complexed with these compounds diffracted in the resolution range of 1.5 Å-2.5 Å and structural efforts to identify new antiviral compounds to combat the coronavirus spread will be presented.

        Speaker: Dr Vasundara Srinivasan (Universität Hamburg, Department of Chemistry)
      • 16:20
        Small-angle Neutron Scattering Studies of the Replicase Cofactor Nsp7/8 Complex from SARS-CoV-2 20m

        Severe acute respiratory syndrome (SARS) is a viral infectious disease caused by the new coronavirus strain (CoV2). The SARS-CoV2 replication and transcription complex (RTC) is formed with at least 9 NSPs that are arranged into one functional assembly. The non-structural proteins (NSPs) Nsp7 and 8 are important components of this complex. Our overall aim was to investigate the structural basis of mechanism of binding and recognition of nucleic acids by Nsp7/8. First, we studied Nsp8 conformation alone and complexed with Nsp7 using small-angle neutron scattering (SANS). We produced a partially deuterated Nsp7/8 complex (dNsp7/Nsp8) and at the contrast match point of dNsp7 we singled out the scattering from bound Nsp8. The P(r) of dNsp7/8 has a bimodal shape indicating that the bound NSP8s are spatially separated in the complex. This shows that Nsp7 dramatically modifies Nsp8 conformation in the complex. Next, using the contrast match point of nucleic acids we single out the scattering of Nsp7/8 in complex with double stranded (ds) DNA and dsRNA substrates. The SANS profiles of Nsp7/8/DNA and Nsp7/8/RNA are best fit with a mixture of Nsp8/DNA (or RNA) and free Nsp7 dimers, supporting the dissociation of Nsp7/8 complex into smaller subunits. In contrast, Nsp8 alone did not bind the nucleic acids tested suggesting that Nsp7 is needed for Nsp8 to form a complex. Our results provide insight into SARS-CoV2 RTC that may be used to design novel therapeutic strategies for COVID-19.

        Speaker: Wellington Leite (Oak Ridge National Laboratory)
      • 16:40
        Combining small-angle scattering with computational modelling to reveal structural details of Hepatitis B virus 20m

        The genetic material of viruses is typically protected in an icosahedral capsid, which is primarily assembled from over a hundred subunits of the same protein in a spontaneous self-assembly process. Similar highly efficient assembly processes are ubiquitous in biological systems, and viral capsids in particular present a unique platform to exploit for therapeutic advances in the targeted cellular delivery of cargo packaged within the capsid. Our research aims to provide a more detailed understanding of how this precise viral capsid protein assembly process occurs from a pool of single building blocks, and specifically how the RNA is incorporated into the capsid. Here, we present results from small-angle neutron scattering (SANS) experiments using contrast variation to reveal the final assembled structural organization of both the protein and nucleic acid components from recombinant Hepatitis B virus (HBV) capsid protein and a synthetically prepared RNA containing the capsid protein binding domain. Time-resolved small-angle x-ray scattering (SAXS) experiments were also used to determine the HBV assembly pathway in the presence and absence of RNA. We employed Bayesian statistics-based computational methods to extract kinetic parameters of assembly and the overall size and shape of the dominant structural intermediates from the SAXS data. The developed framework can be extended to other hierarchical assemblies in biology.

        Speaker: Wojciech Potrzebowski
    • 17:00 17:20
      Coffee Break 20m
    • 17:20 18:00
      Drug design and delivery
    • 09:00 10:30
      Neutron and complementary methods in biology
    • 10:30 10:50
      Coffee Break 20m
    • 10:50 12:00
      Round Table Discussion & Farewell