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The Coronavirus Structural Task Force

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    Herald: So, willkommen zusammen. Heute
    Abend gibt es den Talk von Andrea über den
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    "Corona Virus Structural Task Force". Ich
    bin melzai_a Herald für die Session. Wir
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    haben einen Signal Angel, Dia, sie wird
    die Fragen sammeln, die in den Chat
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    gestellt werden und am Ende gehen wir im
    Vortrag über diese Fragen. So viel zum
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    Ablauf. Der Vortrag wird aufgezeichnet.
    Und ist danach nachträglich verfügbar auf
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    Media.ccc.de irgendwann in den nächsten
    Tagen oder Wochen. Und damit würde ich mich
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    freuen, Andrea, du als
    Nachwuchsruppenleiterin an der Uni
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    Hamburg, du hast die letzten zwei Jahre
    mit den Codona Virus beschäftigt, und
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    daraus wunderbare Visualisierung gemacht.
    Wie lief es denn ab und wie sieht Corona
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    eigentlich aus?
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    Andrea: Ja, vielen dank! Erstmal danke für
    die Einladung. Und ja, genau darum geht es
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    in dem Talk jetzt, was wir die "corona
    virus structure task force" nennen. I'm
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    going to give the presentation in English;
    so that international listeners can also
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    listen in. But you can ask your questions
    in, well, any language anyone here speaks.
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    I understand German, English and Japanese.
    And I want to start with a quote by Marie
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    Curie. I know the room Mary is not named
    after Marie Curie, but she said something
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    that is very true in this pandemic, which
    is: "nothing in life, is to be feared,
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    only to be understood. Now is the time to
    understand more so that we may fear less."
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    And indeed, this holds true for the corona
    virus more than anything, because as you
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    all know, you cannot see the virus. You
    can only see it indirectly visualized by
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    science or you can see the measures against
    it or you can see ill people. But the
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    virus itself is invisible. And I'm going
    to start this talk with questions. There
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    will be many questions. And the first one
    is, what does the corona virus look like?
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    Now you may think, you know, but the
    reality of it is that even German news has
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    no idea. And I know that ZDF is now using
    a different picture, which looks more
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    similar to what I'm going to show, but
    it's very wrong as well. This picture? Is
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    what most people think the virus looks
    like. And I also brought you like two top
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    model and models of the virus. One can
    even make sounds. Any spiky ball of
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    this days really passes as a corona virus
    because no one seems to know what the
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    thing really looks like. Only it's like
    crowned. And it has spikes. That's the
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    only thing that all the models have in
    common. But some things look like you can
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    just, you know, like they are little Shrek
    ears type things or have tentacles. No
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    one really knows. So how do we know as
    scientists and can viruses, be seen? If we
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    imagine so, this is an electron
    microscopic picture of a human hair. It's
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    0.1 millimeters. It's the length of this
    line, so the hair is a little bit less.
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    The little red dot, which you may or may
    not be able to see inside that circle is
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    the size of the corona virus. Now if we
    zoom into the picture of the hair, you can
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    see, I hope, a little red dot here. And
    that's the corona virus to measure. So it
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    is 150 nanometers, or 0.0001.5 mm large. That is tiny
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    even by scientists sentence. However. Even
    smaller than the virus with 150
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    nanometers. It's a single atom,
    which is represented here again by a
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    dot, which is barely visible and is 0.1
    nanometers in diameter or one. Angstrom.
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    Atoms are tiny, even compared to the
    virus. A virus is composed being matter of
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    very, very many atoms. How can we
    visualize something this small? Can we see
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    it with a light microscope? And what color
    would the virus be? This is to scale.
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    Yellow light. It is 600 nanometer
    wavelength meaning from this point to
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    this, it is 600 nanometers. So the
    wavelength of visible light, which ranges
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    from 400 to 780 nano meters, is actually
    longer than the virus is white. So there
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    is no chance whatsoever to ever observe a
    single virus with light just physically
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    not possible. We need something that has a
    smaller wavelength, and there are two
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    things we use X-rays, which have 0.1 nanometer wavelength. So they
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    are very, very small. They're like light. They're also photons. We call it
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    also X-ray light (Röntgenstralung,
    Röntgenlicht). But they have so high energy
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    that their wavelengths are tiny. The other
    thing are electrons, which have even
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    smaller wavelengths. If you choose to
    regard them not as particles, but as
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    waves. So we can use electrons and X-rays
    to observe the virus, and we do. And for
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    this, we have several possibilities. One
    of them is large particle accelerators
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    like the one I'm working on in Hamburg,
    which produces very intense X-rays.
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    Another one is an electron microscope. So
    here is a model of an electron microscope.
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    In order to use it, you need a scientist
    and then you shoot an electron beam from
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    an electron cannon. That's the official
    scientific term. It's an electron cannon
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    onto both an electron gun electron cannon
    electron gun. You shoot your electrons
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    through lenses, which are magnetic.
    Electrons are negatively charged so the
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    magnetic field can be used as a lens
    system onto a sample. For example, the
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    virus and then you have a detector. What
    do we see on this detector? We should
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    viruses with electrons and record how many
    electrons pass through the sample? What we
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    see looks like this. So of course, it's
    black and white because electrons come.
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    There's no colors involved. And what you
    can see is a dark shadow. And then around
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    it, a little bit of bright spots, almost
    like a corona during a sun eclipse. So
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    this is why the corona virus is called
    corona virus, because it spikes under the
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    electron microscope look like a corona.
    And these pictures have no colors, but
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    scientists like to colored them in
    particular in order to tell people that
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    this is a dangerous virus and that is the
    background. So if we colored, it may look
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    like this. And this is an official picture
    released very early in the pandemic by the
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    National Institutes as one of the first
    pictures of the new corona virus. We can
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    also do scanning electron microscopy,
    which is a similar measure where you coat
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    the entire surface and then you get a
    pretty three dimensional picture. What you
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    can see here are lung cells, the lung
    carpet like the like hairy structure here.
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    That's lung cells that are single type two
    alveolar epithelial cells. So there are
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    like a little like their job is to
    get rid of stuff the lungs don't want
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    there, like a carpet, they can move and
    they get rid of stuff for you. However,
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    these cells, you have a problem. They're
    infected with corona virus. You can see
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    some slime or mucus here, and you can see
    the viruses here. Because of the coating,
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    they look a little bit like cauliflower.
    So that's nice. But it doesn't give us the
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    full picture, but so much for people who
    say we cannot isolate the virus. We can
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    actually even like, make it visible. So we
    can make this invisible enemy visible. It
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    is just a question of having the right
    equipment and a good sample of the virus
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    and many hours of work. The virus
    therefore exists and can be made visible
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    using electron microscopes or, for
    example, as a particle accelerator. But
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    I'm not going to go into detail here. We
    have not enough time tonight. I'm only
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    going to talk about electron microscopes
    here. So what is the virus made of. Those
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    This is the virus. We're going to talk about
    this picture later in the talk when we
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    talk about model a little bit more. But
    here is one Spike, I think you've all
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    heard in news from spike proteins, which
    cover the surface of the virus or the
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    virion. If we draw this schematically, as
    Thomas Splettstösser presented for us, he's an
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    illustrator, burst in Berlin, it looks
    like this. And then we take only the head
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    of the spike, which is the region of the
    spike we know most about, and then comes
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    an animation that I did. So it's not quite
    as pretty. If we zoom in, we see the
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    surface and below that surface we see
    things represented as a ribbon. However,
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    we can show this differently. We can show
    the individual atoms connected to each
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    other. The problem with this display is
    that it's really hard to find anything
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    here. It is super difficult to get an
    overview with this picture, so we prefer
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    to show these complicated and fake
    molecules made up of atoms as surfaces and
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    ribbons. And this ribbon diagram, by the
    way, has also been found by a great female
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    scientist, Jane Richardson, several
    decades ago, which was quite revolutionary
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    for my field. So the virus is made up of
    atoms and molecules, and they are
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    structures can be found out by NMR, X-ray
    crystallography and electron microscopy.
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    For now, this is all I'm going to tell
    you. We're now going to dive very deeply
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    into the biology of the virus and what the
    structures tell us. And then in the end,
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    I'm going to tell you a little bit more
    exactly how we actually get from the
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    measurement to the model, which holds some
    pitfalls and problems for us. And it's an
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    area in which I do usually my research.
    But first, I'm going to talk about the
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    model, you all know this picture from the
    CDC, right? And by the way, this thing for
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    a scientist, this thing is not a virus,
    it's a variant. It's only the transport
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    form of the virus, the virus. That's a few
    more things that are not contained in this
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    little show. That's just a transport form
    for its RNA to get into a whole cell. We
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    call this a variant. But most people, even
    scientists, can also refer to it as the
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    virus. So this is the CDC model, right?
    That's the picture that went all through
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    the press around the world. That's like
    THE picture of this pandemic, and it was
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    made by the CDC very early on by two
    scientific illustrators there. However,
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    already then it had some problems. They
    made it in quite a rash and it has some
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    errors. So we decided to make a new
    picture, which looks like this. And. If
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    you compare it, two pictures, here are the
    differences. The head of the spike in this
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    illustration sits directly into the
    surface, while in reality it is singing
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    sitting on a long, very bendy like rope
    like structure that tethers it. So the
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    virus, the head of the spike, which binds
    to the host cell, is quite flexible. The
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    surface is not quite as coarse as shown
    here. It's smaller. The virus actually
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    relatively large for a virus, and it's got
    other proteins swimming in its surface. If
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    you look exactly, you'll see the virus is
    also not exactly round. Now we thought
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    this is not enough. It's nice to have a
    picture, but wouldn't it be nice if we
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    could actually touch it? So we made a 3D
    printable model for those interested. You
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    can find also all that information on our
    homepage. I'm going to show you the 3D
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    model. Let's see. So. This is the virus
    model. As you can see, the virus is not
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    exactly round because it's outside, it's
    very soft. It's like a soap bubble. It can
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    change its shape quite drastically. It's
    wobbly and the spikes are actually
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    stochastic highly distributed. They're not
    like regularly arranged and they are
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    swimming in the skin. And there are other
    proteins in the surface as well, which you
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    can perhaps see whether they really formed
    as little flower shapes, we don't know.
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    And the virus is huge. So this on the same
    scale, one to one million as a rhinovirus
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    for the common cold. The corona virus is
    huge. 20000 base pairs RNA makes it one of
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    the largest virus genomes we know. And a
    virus, therefore as soft on the outside,
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    while rhinovirus has a very hard and rigid
    shell that is always composed the same.
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    And we need this model in the hopes that,
    like other scientists and perhaps schools
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    would like to print it at home and
    actually like, get something tangible and
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    it turned out they did. So we got quite a
    few requests from people, from child care
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    facilities and from schools and from other
    scientists. And even my administration
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    like to have them printed. One even
    proposed we may have them as Christmas
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    ornaments, but I found that a little bit
    like tasteless. We didn't do it. And like,
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    just before I left Hamburg, we got a new
    model. This model is now already a year
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    old, and in 2021, signs made quite a lot
    of progress. So we now know there are
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    fewer spikes and a virus. All in all, it's
    a little bit smaller, so it's not quite
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    like this, but perhaps less so. It's not
    15 centimeters in diameter. The model is
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    12, and it is still like potato shaped.
    It's not round because now what's
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    important for me to show, and I would have
    like to show you this model like in front
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    of the camera tonight, but. It went into
    the museum, it was the first one we had,
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    and we brought it to the opening of this
    exhibition in Hamburg "Pandemierück in ide
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    Gegenwart" the gigawatt, so you can now
    see it in the museum and we'll be back in
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    my office when they have assembled theres.
    And this also holds true. I'm going to
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    talk about the task force in the second
    half of this talk. But one thing that is
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    really true and what's true for this
    project as well is the task force is
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    typically more interested in new
    communication projects than in all the
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    pile of stuff we need to finish. You may
    notice from home. Right. So this is how
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    our model. Now, let's dive deeper into the
    thing, because so far we have only talked
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    about the virion and only about it's
    outside. So the virion has to spike
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    proteins on the outside. Two other
    proteins M and E protein, it has a double
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    membrane hull, which is very thin and
    nucleocapsid, which is wrapping the RNA.
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    The RNA of actually containing the genes
    for everything that the virus needs in
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    order to like, take possession of the host
    cell. So the RNA is the important bit the
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    virion is transporting and nucleocapsid
    and everything else kind of packs it and
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    makes sure it gets into the host cell. And
    I'm going to show you quickly a video
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    because I think this is so nice to
    understand, and it's the answer to the
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    question why does soap help against corona
    virus? Because very many, like other
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    viruses, are relatively hard to wash off,
    but not corona virus, because it's so
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    large, it has only a double membrane
    shell. And this is a very nice video from
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    the protein data bank from our colleagues
    there. So this is the virus double
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    membrane. It has lipid molecules. You can
    see there are hydrophobic on the inside
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    and hydrophilic on the outside, so they
    lock water on the outside, but not the
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    inside. Green molecules are soap. Soap
    also has a hydrophobic tail and a
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    hydrophilic head. So unlike the water
    which stays outside the soap just gets
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    into the membrane and kind of like goes in
    between the lipids. And then they make
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    whole sort of water molecules can get
    inside the virus. They can even assemble.
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    In around bits of the membrane and get it
    out of the virus hull or around a spike
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    and remove to spike, which is hydrophobic
    to stock out of the virus. This leads to a
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    total decomposition of the membrane and
    therefore it can be completely dissolved
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    by soap. As soon as the nucleocapsid and
    an RNA are exposed, the virus is no longer
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    infectious. It needs a spike in order to
    infect so, you don't need to disinfect
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    your hands. You can just wash them with
    soap, which I find is so lucky in this
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    pandemic because, you know, it would be
    really ugly if we would need to disinfect
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    everything all the time, but we can
    actually just use soapy water. Although,
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    let's be honest, I like to use
    disinfectant every here, and then it gives
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    me just a feeling of more safety. It's
    kind of like a ritual to protect me. I
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    suspect several of you are the same. So,
    so much for the virion, that's like the
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    outer shell, that's like the transport
    form. But there is more much more. This is
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    the corona virus life cycle, or I should
    be more correct. It should be called
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    infection cycle because technically
    speaking, viruses are not life. They need
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    a host cell to reproduce. So we're going
    to come back to this picture. We're going
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    to take this apart bit by bit. First of
    all, there is entry entry into oh yeah.
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    Let's quickly go back. The thing at the
    bottom here, the big thing here. That's
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    the host cell. And a little one is
    the virus, right? We're clear on that
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    Holbrook's here, right? And is the
    outside. So this is like your lung
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    outside. That's your lung cell inside or
    hopefully not your lung cell, right?
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    There's the virus. And this is the spike,
    the spike as a vaccine target, as you
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    know, it's what's encoded in RNA vaccines
    and it's also contained in all the like
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    vector vaccines we see. And I brought you
    another model for that, which saw the
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    picture here. So this is one to 10 million
    scale model of the spike. And this is an
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    antibody. Now if you are vaccinated either
    by RNA or by a vector vaccine, your body
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    overproduce as far as injected with
    spikes, which are usually on something to
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    carry it a host cell or a cell of your
    body if it's an RNA vaccine or a vector.
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    Your body needs a few days to recognize
    this thing, so once it has, it will build
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    antibodies that perfectly fit onto that
    they can recognize the spike very, very
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    exactly. They have a specific binding
    site, which is much more rigid than
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    anything else the antibody can bind to.
    Then this gets decomposed because the
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    vaccine is not viable. What remains in
    your body is information for these
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    antibodies. So now if you get infected
    with corona? The immune system antibody
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    recognizes the spike it has previously
    seen in the vaccine, and that is how the
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    vaccine actually works. So having this
    protects you, one of the biggest problems
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    with COVID 19 infections is that the
    immune system responds too late. And then
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    too much. So having these makes much more
    certain that you will not get severe
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    COVID, which is, I think, very nice. And
    what we also did, together with the
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    animation lab in Utah is not only make
    those life life cycle or infection cycle,
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    we also made an animation the
    scientifically most accurate animation
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    available on how the virus actually binds
    onto the whole cell. There's a lot we
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    don't know, but everything we do know we
    have shown here. So here is the virus. You
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    know the spike protein already. Yes,
    nucleocapsid inside there is RNA, which
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    encodes for the rest, we're going to go
    into the rest after this. And then at the
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    bottom here is the host cell. So lung
    cells actually have ACE2 receptors shown
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    in purple, and a spike protein recognizes
    those specifically meaning that items like
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    a puzzle piece fit exactly onto the purple
    receptors on the lung cells. The spikes
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    bind there and then something else
    happens. Another enzyme also being in the
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    membrane of the host cell cuts the spike,
    so it's not like the name spike suggests
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    it would like shoot something into. But
    that's not the case. It gets cut and then
  • 23:12 - 23:16
    comes to bed where we are a little bit
    unclear how this happens. So what we know
  • 23:16 - 23:20
    is after it's cut, it somehow ends up
    being tethered into the host cell and we
  • 23:20 - 23:25
    don't know the mechanism of this. So we
    decided to illustrated here with like a
  • 23:25 - 23:31
    refolding process and then it's
    energetically unstable. So in order to
  • 23:31 - 23:36
    become more stable, the whole thing clamps
    and folds together, thereby dragging the
  • 23:36 - 23:42
    virus and the host cell membrane together,
    the two membranes to buy a lipid membranes
  • 23:42 - 23:50
    Fuze. The virus material is inserted into
    the cell. The RNA is now inside the host
  • 23:50 - 23:57
    cell, and this is how infection happens.
    So we felt it was particularly important
  • 23:57 - 24:02
    to show this to people. We have made this
    animation Creative Commons, but
  • 24:02 - 24:06
    unfortunately only American television
    caught up on it, so we're really hoping
  • 24:06 - 24:10
    that one of the German like documentaries
    will show this, because we think it's
  • 24:10 - 24:20
    really nice to see this process like as
    accurately as we can depicted. So here is
  • 24:20 - 24:25
    the spike. That's the role of the spike.
    Now the nucleocapsid, an RNA a half
  • 24:25 - 24:33
    entered into the host cell. What happens
    now is that the nucleocapsid dissolves.
  • 24:33 - 24:38
    How that exactly happens, we don't know,
    but it dissolves and RNA gets immediately
  • 24:38 - 24:45
    translated into protein. So the genome
    gets RET inside the cell because the cell
  • 24:45 - 24:50
    believes it's own either comes from the
    host cell and it starts building. The
  • 24:50 - 24:54
    proteins encoded in proteins are again
    molecules. And actually, it makes one
  • 24:54 - 25:01
    very, very long protein chain really long,
    which is called the poly protein, which
  • 25:01 - 25:07
    then gets cleaved. So D'Souza's in this
    case, the thing that cleaves all the long
  • 25:07 - 25:12
    protein chain into individual molecules
    that don't actually can work is called the
  • 25:12 - 25:17
    main protease because it's cutting protein
    that's called the protease. And these are
  • 25:17 - 25:22
    the little triangle shaped things here.
    Only when that happens to these bits
  • 25:22 - 25:27
    become functional. So if it doesn't
    happen, if we can like hindered this like
  • 25:27 - 25:33
    cutting off the long polypeptide chain, we
    have an efficient drug against corona,
  • 25:33 - 25:38
    which is why main protease is a major drug
    target. And what you can see here in red
  • 25:38 - 25:45
    is the drug actually bound two main
    protease. So that's what it looks like. We
  • 25:45 - 25:48
    are looking specifically for inhibitors,
    which will stop this molecule from
  • 25:48 - 25:52
    function. So you can imagine this like a
    screwdriver that we put out of right point
  • 25:52 - 25:58
    in a machine where it fits and it stops
    the entire machinery. That's what we want.
  • 25:58 - 26:02
    And that's like called structure based
    drug design. When you actually know the
  • 26:02 - 26:06
    structure of the molecule and then you
    find a molecule, a small molecule, a drug
  • 26:06 - 26:13
    molecule that specifically stops whatever
    that protein molecule is doing. It's also
  • 26:13 - 26:21
    how many antibiotics work or, for example,
    if you've been up long yesterday aspirin.
  • 26:21 - 26:29
    Then. From here, where we have the poly
    protein thing. Something happens inside
  • 26:29 - 26:34
    the cell, the cell is making some kind of
    foam, which is connected to the
  • 26:34 - 26:40
    endoplasmic reticulum. That's just warm
    and inside it. These like enzymes that
  • 26:40 - 26:44
    have now been cut in our functional start,
    like a copy machine to make more and more
  • 26:44 - 26:50
    copies of the RNA genome of the virus. The
    whole cell kind of like foams up and makes
  • 26:50 - 26:57
    more RNA. And it does so by a copy
    machine, which is called RNA polymerase,
  • 26:57 - 27:05
    because RNA is a polymer and a polymerase
    is an enzyme that's making polymers and an
  • 27:05 - 27:14
    RNA polymerase is an enzyme that makes
    more RNA. So one way to block that process
  • 27:14 - 27:19
    of making more RNAs, which was similarly,
    you know, stop the infection cycle because
  • 27:19 - 27:24
    if it can't produce more RNA, it's got
    nothing to put into new viruses is to use
  • 27:24 - 27:29
    remdesivir or so we thought for a long
    time. So does this remdesivir. Remdesivir
  • 27:29 - 27:36
    looks to the host cell and to RNA
    polymerase in particular, like a
  • 27:36 - 27:42
    nucleotide, like a building block for RNA.
    So basically, things are it's new paper it
  • 27:42 - 27:47
    can copy on when in reality it's kind of
    explosive like blocks the entire
  • 27:47 - 27:53
    polymerase. So you can imagine this like a
    Trojan horse, remdesivir is the Trojan
  • 27:53 - 27:59
    horse and RNA dependent RNA polymerase is
    sure looks like RNA to me and just built
  • 27:59 - 28:06
    that into the strand. So we'll have a look
    at this molecule. This is, by the way, I
  • 28:06 - 28:10
    should probably go back and explain this
    for a moment. This is what we get out of
  • 28:10 - 28:15
    our measurements and electron microscopy.
    So this is the so-called reconstruction
  • 28:15 - 28:19
    density, and that's what we built a
    molecule in. So that's like what the
  • 28:19 - 28:23
    measurement gave us, everything else we
    have to do by hand. So here is the
  • 28:23 - 28:31
    density, and this is what the researcher
    built into it. The template strand, the
  • 28:31 - 28:37
    old one, which is to be copied, is green,
    the new one is orange. Remdesivir is
  • 28:37 - 28:43
    purple and connected to the end, although
    the program doesn't display it as such.
  • 28:43 - 28:47
    What you can also see is free magnesium
    ions. That's their own thing and a de
  • 28:47 - 28:54
    phosphate. So what are more molecules that
    researchers modeled in there? Where are
  • 28:54 - 28:58
    around it as the protein? So I've just
    quickly depicted it without so you can see
  • 28:58 - 29:02
    what's happening because it's all very
    crowded and difficult to see around it as
  • 29:02 - 29:07
    the protein and a jump of two proteins to
    copy the RNA and to attach one after the
  • 29:07 - 29:12
    other, another building block to the
    bottom of the orange chain. It's gotten a
  • 29:12 - 29:17
    remdesivir and it tried to put it there
    and it successfully did. And this
  • 29:17 - 29:22
    structure was taken as to prove that
    remdesivir will stop corona. But if you
  • 29:22 - 29:26
    look at the density, you can see that the
    free magnesium ions and DIPHOSPHATE has no
  • 29:26 - 29:32
    density and are not covered by this great
    cloud, right? So we think they were never
  • 29:32 - 29:39
    really there. And the remdesivir itself is
    also not having so much density. So it
  • 29:39 - 29:43
    turns out that a structure is not quite
    seeing what the researchers did because
  • 29:43 - 29:48
    the density doesn't match up with the
    structure they built. And as we later
  • 29:48 - 29:53
    found out in clinical trials, is that
    remdesivir, in fact, doesn't really do
  • 29:53 - 29:58
    what people hoped, which, among other
    things, has to do with the fact that RNA
  • 29:58 - 30:03
    polymerase from corona virus is able to
    proofread go like, Oh, there's a
  • 30:03 - 30:09
    remdesivir, then go back free nucleotides
    take rip out the remdesivir, throw it away
  • 30:09 - 30:15
    and get the proper nucleotide to build in.
    So. We're hoping that one over pea-rel will
  • 30:15 - 30:19
    be better, which, by the way, uses a
    similar mechanism. It's called a
  • 30:19 - 30:32
    nucleotide. Yeah, it's similar to a
    nucleotide. Here's another arrow we found
  • 30:32 - 30:35
    in the bottom of the structure, only going
    to show you because I think the software
  • 30:35 - 30:40
    by Tristan Kroll is so cool, it does a
    real time molecular dynamics simulation
  • 30:40 - 30:45
    while you're dragging around your
    structure. We found that there is an error
  • 30:45 - 30:48
    in the way the whole molecule was
    arranged. If there's any specialist, there
  • 30:48 - 30:52
    was a nine amino acid out of reach
    associate. OK, I'm going to stop like
  • 30:52 - 30:56
    geeking out. There was just an error. Let
    me show you how he correct that. So first
  • 30:56 - 31:01
    you marks up the wrong region and then he
    releases it and quickly flying-away noise it goes where it's up to
  • 31:01 - 31:05
    go. I wish my life would always be like
    this, you said were free days glasses in
  • 31:05 - 31:08
    front of your computer. You need hours to
    do this by hand, but his software just
  • 31:08 - 31:15
    does it. Sorry. It's just if you've spent
    months doing this, you're totally excited
  • 31:15 - 31:22
    by this wobbly molecule. I just wanted to
    show you because I think it's so cool. All
  • 31:22 - 31:30
    right. Back to a more general content. We
    have an hour RNA and a let's imagine we
  • 31:30 - 31:35
    didn't get any like good drugs so far, so
    the infection cycle is still ongoing. The
  • 31:35 - 31:40
    RNA now is exported from the endoplasmic
    reticulum. By the time we make this, we
  • 31:40 - 31:44
    didn't know how. But Hamburg researchers
    and Dutch researchers have now found out
  • 31:44 - 31:49
    how this actually works as a pore here and
    the pore gets the RNA out. The RNA then
  • 31:49 - 31:54
    gets packed into new nucleocapsid
    were also coded by the genome
  • 31:54 - 32:00
    of the virus, then gets wrapped into a new
    double membrane, which is host membrane.
  • 32:00 - 32:06
    Just it has no spikes, which also were
    produced from the genome. And then, of
  • 32:06 - 32:12
    course, due the Golgi apparatus is somehow
    involved, it gets exported. Of course, for
  • 32:12 - 32:18
    everyone that infected a cell, there will
    be thousands that are produced and that's
  • 32:18 - 32:26
    the entirety of the SarsCoV 2 viral
    life cycle. I know, this was a little bit
  • 32:26 - 32:32
    much, but I think this is cool and
    exciting and just about what, you know. I
  • 32:32 - 32:37
    hope the public can understand about this.
    It hopefully also tells you why molecular
  • 32:37 - 32:43
    structures are important, so they let us
    understand how the virus works, how host
  • 32:43 - 32:48
    cells are infected. They can help us to
    find drug targets and to do structure
  • 32:48 - 32:53
    based drug design, where we find drugs
    that specifically block these big
  • 32:53 - 33:00
    molecular machines from doing their work.
    They also help us to understand the
  • 33:00 - 33:07
    structures of vaccines and antibodies, and
    they also let us understand changes due to
  • 33:07 - 33:11
    two mutations, I haven't got an example
    because of the time. But when we get a
  • 33:11 - 33:16
    mutation with the structure, I can kind of
    tell you, that it is going to change or
  • 33:16 - 33:21
    that it is going to change only by knowing
    the new genome. I can already make a
  • 33:21 - 33:25
    prediction about what the mutation is
    going to change in a functionality. That's
  • 33:25 - 33:32
    really important. So in my group, we have
    some theories what a Micron actually does.
  • 33:32 - 33:36
    We haven't published and we haven't even
    tweeted about them yet because we're still
  • 33:36 - 33:43
    waiting for research results. But it's
    important to understand these molecular
  • 33:43 - 33:52
    structures, however, is not very easy to
    get them. So what are the problems? When we
  • 33:52 - 33:59
    do our measurement, we get density in this
    case, the density is blue. It's from the
  • 33:59 - 34:02
    spike head that I've shown in the
    beginning, right? So the top that you may
  • 34:02 - 34:06
    recognize, this looks a little bit like
    the blue density here. This is the result
  • 34:06 - 34:11
    from our research. And in this case, I
    have built almost all of the molecule
  • 34:11 - 34:15
    already, so I'm going to show it. This is
    like the software. We're actually using a
  • 34:15 - 34:20
    tenfold to speed I'm usually using, and I
    would usually be sitting there with 3D
  • 34:20 - 34:24
    glasses. So here's the density. I said
    that with my 3D glasses and this bit
  • 34:24 - 34:31
    hasn't been built, so you can now see me
    like by hand. And one bit of molecule
  • 34:31 - 34:35
    after the other trying to get the murder
    ought to be, and you can quite well see
  • 34:35 - 34:40
    that the computer is not able to do it all
    automatically. So I have to help it a
  • 34:40 - 34:44
    little bit. And as I said, it's about 10
    times the speed. It's even got like the
  • 34:44 - 34:49
    warning from the bin program not reacting
    all of the software, it's also not
  • 34:49 - 34:54
    commercial. This has been developed by
    other scientists, so the usability is like
  • 34:54 - 35:00
    so-so cool, just an amazing program. But
    if you want some new functionality, you
  • 35:00 - 35:04
    better program it yourself, because perhaps
    no one else is going to do it. And we have
  • 35:04 - 35:11
    actually contributed with a plug in or two
    to cut. Yeah, you can see it's not always
  • 35:11 - 35:14
    easy, so I try and go, like, now it's
    good. Settings should nicely in the
  • 35:14 - 35:22
    density and here it's fairly easy. My
    students love doing this is like for them.
  • 35:22 - 35:25
    It's like computer gaming. They do it for
    three months straight. If you don't like,
  • 35:25 - 35:30
    get them off the chair, go right up your
    physics. They'll do it forever. And
  • 35:30 - 35:35
    secretly, I'm jealous. Because I also like
    doing this. I don't know if you can
  • 35:35 - 35:45
    follow, but this is like playing a game.
    Away, if you're interested in playing this
  • 35:45 - 35:54
    game, we are also having. Like practical
    places and stuff. Right! So building,
  • 35:54 - 35:59
    building, building, going like, oh,
    there's another alanine, I need a pralines
  • 35:59 - 36:04
    or mutated it. I go like, Yeah, OK, now
    it's all nicely sitting. So that was easy.
  • 36:04 - 36:09
    But what do I do here? So I've built for
    something here. But is it correct? The
  • 36:09 - 36:13
    density does not really tell me what's
    going on here, and I'm going to show it
  • 36:13 - 36:19
    this to you in slower again. So you
    understand the problem, right? In this
  • 36:19 - 36:23
    then part of the density, I can really not
    tell only from the density what's going
  • 36:23 - 36:29
    on. I know approximately what a molecule
    must look like due to the sequence. So
  • 36:29 - 36:32
    I've got some information. I know which
    Atom is connected to which, but how it all
  • 36:32 - 36:37
    three dimensionally fits in here, even if
    I know which lines have to go in, there is
  • 36:37 - 36:42
    super hard. So it would be very easy for
    me to make an error here, because the
  • 36:42 - 36:46
    measurement data don't tell me enough
    about what the model actually should look
  • 36:46 - 36:56
    like and several interpretation., everal
    models would all be possible. So this is
  • 36:56 - 36:59
    kind of difficult. I'm just seeing a
    questionnaire that I may want to answer
  • 36:59 - 37:04
    right away. Within could is it possible to
    verify if you have chosen created the
  • 37:04 - 37:09
    right building blocks, you know, the
    building blocks because of the genome? So
  • 37:09 - 37:15
    Gene tells you the order of amino acids
    you want to put after each other. So if
  • 37:15 - 37:22
    you started at the right point, the rest
    will also be like the correct atoms and
  • 37:22 - 37:26
    the correct connection. But how it like
    three dimensionally faults, you don't
  • 37:26 - 37:37
    know. You have to make that on the
    density. So it is possible to do it. You
  • 37:37 - 37:42
    have to write building blocks at hand.
    Usually if there are if there is like, you
  • 37:42 - 37:46
    know, if a magnesium ion, for example, is
    sitting there, the magnesium ion was not
  • 37:46 - 37:51
    in your genomic information. You just need
    to know what you're doing to recognize
  • 37:51 - 37:58
    this is a magnesium ion ore does this a
    diophosphate or something like this?
  • 37:58 - 38:06
    Right. Going to answer the rest of the
    questions later. Molecular models need to
  • 38:06 - 38:11
    be built by hand. This can lead to errors.
    There a few automatic algorithms do work
  • 38:11 - 38:17
    under favorable circumstances, but most of
    the stuff still has to happen by hand. As
  • 38:17 - 38:22
    of today, and I got my postdoc from like
    holidays for 15 minutes today, and he gave
  • 38:22 - 38:26
    new numbers. So we've got 1909
    molecular structures
  • 38:26 - 38:32
    today. New structures come out every
    Wednesday. There are 1334 from X-ray
  • 38:32 - 38:36
    crystallography. That's the thing. With
    the particle accelerator in Hamburg, I
  • 38:36 - 38:41
    thought, they have been measured at
    synchrotrons all over the world. Not only
  • 38:41 - 38:46
    Hamburg, where BioNTech structures have
    been measured, but also had SARS. There
  • 38:46 - 38:52
    have been large screens a diamond in Japan
    and China at Sesamia, at Solemy, in
  • 38:52 - 38:57
    America. Synchrotrons all over the world
    contributed to this. 35 from nuclear
  • 38:57 - 39:02
    magnetic resonance, which is a little bit
    of a niche method for this type of study.
  • 39:02 - 39:09
    And 566 from electron microscopy.
    So 1909 molecular structures
  • 39:09 - 39:16
    of different states of 17
    macromolecules, 17 proteins from a total
  • 39:16 - 39:27
    of 28. So corona virus in total has 28
    different genes, 4 proteins. There are 28
  • 39:27 - 39:33
    proteins. And we only structurally know 17
    of them. And then we have like different
  • 39:33 - 39:37
    versions of them, different ph, different
    temperatures, spike, head bit of spike
  • 39:37 - 39:47
    head, spike head with antibody, things like
    that. So a 1900 data sets that's in total.
  • 39:47 - 39:52
    Errors and structures, as we've
    just seen, can happen because fit between
  • 39:52 - 39:59
    the data and model is bad, because complete
    automation is not possible. Models are
  • 39:59 - 40:05
    built manually expertize in many different
    areas needed. You need to be good
  • 40:05 - 40:08
    software. You need to have done all the
    lab work. The measurement needs to be done
  • 40:08 - 40:12
    right. Processing needs to be made. You
    need to know your statistical validation.
  • 40:12 - 40:17
    You need to know your chemistry. You need
    to know your biology. So it's really not
  • 40:17 - 40:22
    easy and you need to know your 3D goggles
    unless you get sick from them, in which
  • 40:22 - 40:28
    case you can't use them. One of the major
    aspects of software, the methods you're
  • 40:28 - 40:36
    using and this is where we come in. Small
    structural errors can lead to big
  • 40:36 - 40:41
    structural problems downstream. Imagine
    the bid was to remdesivir, the diphosphate
  • 40:41 - 40:46
    there, the fact that there was something
    bound into that structure that was not
  • 40:46 - 40:52
    really there. But the model had dose like
    additional free magnesium ions down the
  • 40:52 - 41:00
    line, as I know from insiders, led to like
    waste of hundreds thousands of dollars
  • 41:00 - 41:05
    and many hours of work time in drug
    discovery because they kind of like fed
  • 41:05 - 41:10
    this model in order to find a drug that
    ultimately never bound because of
  • 41:10 - 41:18
    magnesium ion wasn't actually there. So
    if we make small structures, that builds
  • 41:18 - 41:22
    up hugely for the downstream applications
    where they need these molecular
  • 41:22 - 41:31
    structures. Errors are common. And now we
    add to this an ongoing pandemic. Right.
  • 41:31 - 41:36
    And her scientists are there to rescue
    today. Lockdown happened, you're sitting
  • 41:36 - 41:41
    at home, there are no colleagues to help
    you. Your child is home schooling. The dog
  • 41:41 - 41:45
    wants to be fed, your grandma calls,
    because she's worried and you've got to
  • 41:45 - 41:51
    solve the spike structure on which lives
    will depend as fast as possible. Normally,
  • 41:51 - 41:54
    we take a year to five to solve a
    structure, and in the pandemic you only
  • 41:54 - 42:04
    got three months. Of course, errors are
    going to happen. So that's well, just a
  • 42:04 - 42:09
    matter of fact. We've got to arrange
    ourselves with it. It's not the fault of
  • 42:09 - 42:14
    individuals, it's how the whole thing
    works. It's such a complex process. Errors
  • 42:14 - 42:20
    are going to happen! Now in normal life my
    team and I methods developers and
  • 42:20 - 42:25
    structural biology. We are the people, who
    give us the experimental techniques and
  • 42:25 - 42:31
    software to solve their structures as best
    as we and they can. We're not usually in
  • 42:31 - 42:37
    the in the stage like we're usually, you
    know. For every Nobel Prize, there have
  • 42:37 - 42:41
    been like dozens of Nobel Prizes in
    structural biology has been methods
  • 42:41 - 42:45
    developed in the background to develop the
    methods that made it possible to see, you
  • 42:45 - 42:49
    know, the structure of the DNA double
    helix or structure of the ribosome, or the
  • 42:49 - 42:56
    structure of the influenza virus. It's
    just that normally we're just enablers.
  • 42:56 - 43:05
    However, here was the pandemic and very
    many structures that had errors. So we did
  • 43:05 - 43:11
    what we needed to do. We came together as
    a relatively large team under my
  • 43:11 - 43:17
    leadership, we are today 23 people, we
    peaked at 27 last year from nine countries
  • 43:17 - 43:21
    to check an improve the molecular
    structures of SARS-CoV-1 and SARS-CoV-2.
  • 43:21 - 43:31
    So. We are methods developers, most of are
    methods developers, we are specialists in
  • 43:31 - 43:36
    solving structures. We evaluate all the
    published Structures and Protein Data
  • 43:36 - 43:44
    Databank or PDB from SARS and SARS-
    CoV-2. We reprocess all of them and we
  • 43:44 - 43:50
    remodel them, although not all are looked
    at manually, because that would be just
  • 43:50 - 43:53
    too much. We also do a scientific
    dissemination, putting these structures
  • 43:53 - 43:58
    into context for people who want to start
    doing molecular research on corona virus.
  • 43:58 - 44:05
    And we do public outreach. I'll give you a
    quick insight into our pipeline because I
  • 44:05 - 44:10
    thought the software might be interesting
    for you. So every Wednesday come new
  • 44:10 - 44:15
    entries of molecules in the protein
    databank, which is, by the way, the World
  • 44:15 - 44:19
    Wide Protein Databank is an open, open
    resource. Everyone in the world can
  • 44:19 - 44:23
    download the new structures, and all the
    journals require people who make new
  • 44:23 - 44:28
    structures to put them there, which is
    nice. I'm really privileged to be in a
  • 44:28 - 44:33
    field where the data are public. We
    compared the new structures with the NCBI
  • 44:33 - 44:38
    proteomics, so the genes from corona virus
    to find the structures that belong to
  • 44:38 - 44:44
    corona virus, put everything into an sql
    metha database. Then we calculate how
  • 44:44 - 44:49
    different the structures are from the ones
    we already know. We look whether all
  • 44:49 - 44:52
    measurement data available, so we have a
    big problem of not all measurement data
  • 44:52 - 44:59
    being published. I hope we are going to be
    like astronomy one day, where everything
  • 44:59 - 45:06
    gets published. I am sitting in the some
    German cometies to that end STIKO AM which
  • 45:06 - 45:11
    is a very new hub. And then we run a
    number of specialized programs which all
  • 45:11 - 45:16
    do validation and put the results on
    GitHub immediately. On Thursday, at the
  • 45:16 - 45:22
    latest, researchers can find our elevation,
    remodeling and the quality indication for
  • 45:22 - 45:29
    the structure everything, that can be done
    automatically online. We then, for some
  • 45:29 - 45:34
    structures, manually rebuilt them, so we
    actively look weathered our problems, that
  • 45:34 - 45:38
    was, for example, the case with the
    remdesivir structure. We tried to do this
  • 45:38 - 45:42
    for those structures that we think drug
    designers will use the most or that are
  • 45:42 - 45:48
    really important. And when we find errors,
    we contact our original office first and
  • 45:48 - 45:55
    tell them we found an error here is the
    corrected structure. Use our data, you
  • 45:55 - 46:01
    don't need to cite us, just correct your
    structure in the database, please. This
  • 46:01 - 46:05
    means we won't get credit, but I meant
    that at the beginning of the pandemic,
  • 46:05 - 46:11
    people were adjusting their structures
    already when the preprint was out, so
  • 46:11 - 46:15
    there would not be problems downstream.
    And I have often been asked I would like
  • 46:15 - 46:21
    to like this again. That was really like
    why people accepted our corrections,
  • 46:21 - 46:26
    because they didn't need to give anyone
    credit. They could just like change them.
  • 46:26 - 46:30
    And the database is also online, so
    everyone from the Philippines to the U.S.
  • 46:30 - 46:35
    can just use them, whether it's like a
    commercial person or a taxpayer, or a
  • 46:35 - 46:41
    private person research institution, a
    foundation, everyone can use our data.
  • 46:41 - 46:44
    They're just online there for everyone,
    and we only ask them to give us credit in
  • 46:44 - 46:51
    the form of a reference citation. We
    disseminate the data via GitHub via
  • 46:51 - 46:57
    Twitter. 3D bio notes, which is a three
    dimensional database linking directly into
  • 46:57 - 47:07
    our database, we contact the offers. We
    also have entries in Proteopedia. Molprobity,
  • 47:07 - 47:11
    which is a virtual bioinformatics
    institute, links directly into our
  • 47:11 - 47:15
    database. So they're always like up to
    date showing what we are doing. We have a
  • 47:15 - 47:20
    homepage and we do reviews. There's a lot
    of downstream users. The biggest ones are
  • 47:20 - 47:29
    the EU Jedi Grand Challenge folding at
    home, which peaked out in July last year.
  • 47:29 - 47:37
    I think a 2.4 xTFLOPs computing power for
    molecular simulations and used in the
  • 47:37 - 47:44
    majority our models to start from. And
    also very big is IBM open pandemics. But
  • 47:44 - 47:48
    there are a number of others, plus many
    individual apps. So we found a great new
  • 47:48 - 47:55
    many friends. Here is our homepage, that's
    where you can find it. There's also an
  • 47:55 - 48:01
    English version, you can find blog posts
    for the public and for scientists. And in
  • 48:01 - 48:07
    the end, I would like to talk for like
    five minutes about daily life in ritual
  • 48:07 - 48:15
    mobility. So my team is over 20 people
    from nine to ... we cover nine time zones,
  • 48:15 - 48:22
    right? Where nine hours time shift apart.
    And we had several lockdowns. So.
  • 48:22 - 48:27
    Actually, the majority of people in the
    task force, about half of them don't work
  • 48:27 - 48:32
    for me. They are volunteering their
    researchers elsewhere that volunteer to be
  • 48:32 - 48:36
    a part of this effort. And there are many
    people in the task force who have never
  • 48:36 - 48:44
    like personally met. So how do you make
    group coherence if you are working for 20
  • 48:44 - 48:49
    months or 22 months by now in an
    environment like this, right? We founded
  • 48:49 - 48:56
    ourselves in March 2020 as a chat group
    called the Coronavirus Structural Task
  • 48:56 - 49:03
    Force, which was a job back then. It
    didn't remain a joke. But that's how life
  • 49:03 - 49:08
    plays. We have everyday Zoom meetings at
    10 o'clock, one time per week in the
  • 49:08 - 49:15
    afternoon. So do people from Oregon can
    join us. We do a lot of like media
  • 49:15 - 49:20
    outreach in international and German
    media. We've been like on nano and Terra X
  • 49:20 - 49:25
    and Planet E, we've been in breakfast
    television. That was a particularly
  • 49:25 - 49:30
    interesting experience. My email got link
    to Querdenker and I got a few very
  • 49:30 - 49:35
    interesting email exchanges. I also must
    say I never got insulted or frightened by
  • 49:35 - 49:42
    anyone, so I just discussed with them and
    it worked out. And I'm happy because like
  • 49:42 - 49:49
    I understood, like how, what the theories
    are, and that was very interesting. Keep
  • 49:49 - 49:54
    the media also like to write about my
    hair, my eyes, blah blah blah on these
  • 49:54 - 49:58
    things. I just want to note that Streeck
    is about my age, and Drosten is only nine
  • 49:58 - 50:06
    years older than me. So really? OK,
    whatever. Most importantly, they're
  • 50:06 - 50:11
    talking about our research. We also did a
    lot of social media. I got a Twitter
  • 50:11 - 50:16
    account. Everyone else did as well. You
    can watch us work on Twitch if you're
  • 50:16 - 50:19
    interested. We found that people find it
    soothing to see us modeling these
  • 50:19 - 50:24
    structures. I was requested to make
    stickers for the team as soon as we got a
  • 50:24 - 50:29
    grant and we got funded by the Federal
    Ministry for Research and Education in
  • 50:29 - 50:34
    2020. We have a YouTube channel where you
    can, for example, see the entry animation
  • 50:34 - 50:41
    and the students brought a cactus, which
    is called Corina the Corona Cactus. I
  • 50:41 - 50:47
    know. It looked like we had fun, and we
    did. I can tell you being caught, you
  • 50:47 - 50:55
    know, being at home, having to care for
    your children. Having people dying. Having
  • 50:55 - 51:00
    an ongoing pandemic, knowing that I 'd be
    more open pandemics is going to spend
  • 51:00 - 51:05
    another million based on your research.
    And also that ZDF wants to talk to you and
  • 51:05 - 51:10
    the Berliner Abendblatt. This is so
    stressful! Think about all the
  • 51:10 - 51:15
    responsibility we had, and it was really
    terrible for us, so we needed to cheer up
  • 51:15 - 51:20
    every here and then, the whole group kind
    of like grew together and we all became
  • 51:20 - 51:26
    friends. This was unheard. For us, it was
    very uncommon as researchers. Typically,
  • 51:26 - 51:29
    our behavior with each other is much more
    formal than their behavior and this group
  • 51:29 - 51:36
    was. But these were like exceptional
    times, and we wanted to fight the pandemic
  • 51:36 - 51:41
    and inform the public. That's what we were
    there for and was not so much about
  • 51:41 - 51:49
    personal gain. And that was nice. We have
    a group chat. You know, I mean, I'm
  • 51:49 - 51:53
    talking to right audience, right? We have
    a group chat. Do you know what that looks
  • 51:53 - 51:58
    like? Let me tell you. Typically,
    professors don't communicate with this.
  • 51:58 - 52:06
    We have a virtual, Oh, we have a
    virtual space. We hope to change to work
  • 52:06 - 52:13
    adventure soon. We all want to play games
    in the evening occasionally with the
  • 52:13 - 52:18
    group, so we do some team building
    efforts. When people can meet in person,
  • 52:18 - 52:23
    they usually do and sometimes they go and
    travel and like, meet each other. But this
  • 52:23 - 52:31
    has been very limited. And we did grow
    together as a network, that will be there
  • 52:31 - 52:37
    after the pandemic, so we are 25 people
    all over the planet that did this
  • 52:37 - 52:44
    together. And even if we wouldn't have
    made any difference against the virus, I
  • 52:44 - 52:50
    would still be happy to have done it for
    the friendships I made. However, we did
  • 52:50 - 52:55
    make a dent. We don't quite know how big
    it is because our science was open science
  • 52:55 - 53:01
    and the results could be gotten by
    everyone without reference. But we know a
  • 53:01 - 53:08
    few things wouldn't have happened without
    us. And I'm. Deeply grateful for having
  • 53:08 - 53:18
    had a purpose during this pandemic. In the
    end, I have a little bit of a more serious
  • 53:18 - 53:27
    topic. My contract is going to run out in
    May. I think it's going to be prolonged.
  • 53:27 - 53:36
    When it will, I'll be signing my 14 work
    contract since 2008. 14, like I had 13
  • 53:36 - 53:44
    year contracts already out of all my task
    force members, there is only one holding a
  • 53:44 - 53:51
    permanent position and two which are
    retired. Everyone else, including six
  • 53:51 - 53:57
    people whose contract is going to run out
    next year, are on temporary contracts and
  • 53:57 - 54:02
    not students. Students are extra. That the
    students are on time limited contracts is
  • 54:02 - 54:08
    OK, but Germany's got a problem. 84
    percent of academics in German
  • 54:08 - 54:18
    universities are on time limited
    contracts. So are we. Only one task force
  • 54:18 - 54:23
    member has was a permanent position
    signed, and that's not me. And this is not
  • 54:23 - 54:27
    so much on my behalf, because I'm going to
    find my way through life. Look at all the
  • 54:27 - 54:32
    exposure I had, but there are people out
    there who are single moms and dads, who
  • 54:32 - 54:37
    come from less privileged backgrounds or
    had a harder life and who can just not
  • 54:37 - 54:45
    afford to be on one year contracts all the
    time while holding a Ph.D.. We're losing
  • 54:45 - 54:49
    all these bright people and I'm seeing
    them right. They leave my institute and
  • 54:49 - 54:53
    they go to industry. And then the
    universities complain that they're not
  • 54:53 - 55:01
    competitive. We need to change the system.
    We need to have more permanent positions
  • 55:01 - 55:07
    in science. I promise we won't perform
    worse, if you give us permanent contracts.
  • 55:07 - 55:17
    We love what we are doing. So back to the
    corona topic. In order to understand the
  • 55:17 - 55:22
    virus and its life cycle, we need to
    understand its molecular biology. This
  • 55:22 - 55:28
    will help with the design of therapeutics.
    We evaluated these molecular structures
  • 55:28 - 55:33
    with a bespoke pipeline, an expert
    knowledge provided context and reached out
  • 55:33 - 55:38
    to the taxpayer and the general public to
    inform them. We also wrote a paper
  • 55:38 - 55:43
    together with long off a list making the
    invisible enemy visible, which is our
  • 55:43 - 55:49
    motto. And as we started this all with
    questions, I'm going to end with
  • 55:49 - 55:55
    questions. Structural biology remains
    difficult. What can we learn from our
  • 55:55 - 56:01
    findings? Should we, as a scientists
    community, change our attitudes towards
  • 56:01 - 56:11
    errors? Should this serve as a model for
    other projects, cannot serve as a model
  • 56:11 - 56:14
    for other projects? I hadn't thought about
    this, but a nature editor asked me when I
  • 56:14 - 56:19
    was writing a comment whether we believe
    that science should always be like this?
  • 56:19 - 56:23
    My God, that would be awesome. I would
    totally be up for it if science would
  • 56:23 - 56:27
    always be like this! Come together with a
    bunch of friends, but without funding!
  • 56:27 - 56:32
    Start doing something to, you know, fight
    a global pandemic, then get some funding.
  • 56:32 - 56:39
    Still, having like no senior people on a
    project. Can open science compete? I don't
  • 56:39 - 56:49
    know. We get pretty little credit. It
    would, definitely. OK, science compete. I
  • 56:49 - 56:53
    don't know, it doesn't quite look like it
    still getting measured only by the
  • 56:53 - 56:59
    citations my paper gets. And well, at
    least a paper is not behind a paywall, but
  • 56:59 - 57:03
    if we would have published all our stuff
    in like papers would possibly get more
  • 57:03 - 57:09
    credit. I really don't know, but we need
    to work on this. If we want science, we
  • 57:09 - 57:17
    need to change how people are rewarded.
    How senior they really need to be. I'm 39.
  • 57:17 - 57:22
    It seems I'm called a junior group leader.
    All of us are young. The youngest is 24.
  • 57:22 - 57:27
    He's writing our first Alpha article about
    a corona virus protein. I feel that the
  • 57:27 - 57:31
    German academic system and all over the
    world, actually you need to be older and
  • 57:31 - 57:37
    older to become a professor and be
    permanent and be like a grant holder. I
  • 57:37 - 57:41
    don't think it's necessary, I think that
    professors could be 30 and the world
  • 57:41 - 57:49
    wouldn't, you know, like, go down. Well,
    what will change in science after a
  • 57:49 - 57:54
    pandemic? We had like large exposure. It
    certainly will also have to do with like
  • 57:54 - 57:59
    questions like did the virus now come from
    an app or didn't it? That, you know, would
  • 57:59 - 58:04
    change how people view science, I'm sure.
    How will scientists be viewed by the
  • 58:04 - 58:09
    public? Right. Right now, of course, you
    know, mom and dad are very proud, but.
  • 58:09 - 58:14
    What's going to change? Are we going to
    still be the bad guys because we often
  • 58:14 - 58:19
    are. But I'm like general, exclusively
    taxpayer funded. I never took any money
  • 58:19 - 58:24
    from the pharmaceutical industry. I have
    like, you know, no stakes in this game.
  • 58:24 - 58:32
    I'm just like earning tax money, so I
    feel that, there is a whole complex of
  • 58:32 - 58:35
    difficult things there, how people regard
    science, but definitely the pandemic is
  • 58:35 - 58:40
    going to change, how science is going to
    be viewed. What's that going to be?
  • 58:40 - 58:48
    Exspiration In the end. I'd like to
    thank all the task force members and all
  • 58:48 - 58:54
    our collaboration partners and our
    scientific fairy godmother, Alvin Pearson,
  • 58:54 - 58:59
    who had little role in this research but
    much role in our mentorship and bringing
  • 58:59 - 59:04
    us forward. My home, the University of
    Hamburg, the Coronavirus Structural
  • 59:04 - 59:08
    Taskforce, our we are funded by the
    Deutsches Officials Command Trust and the
  • 59:08 - 59:14
    Federal Ministry for Research and
    Education. I would like to point out that
  • 59:14 - 59:19
    we are looking for student assistance, not
    only for scientific work, but also for
  • 59:19 - 59:25
    social media video and programing work and
    3D printing. So if you know anyone who's
  • 59:25 - 59:31
    interested, please point him in my
    direction. My email is there. We are also
  • 59:31 - 59:36
    offering Bachelor, Master and Ph.D. thesis
    in areas that cover both Lab work and
  • 59:36 - 59:44
    computer work, which is a rare thing these
    days. You can find us on YouTube and the
  • 59:44 - 59:51
    internet and on Twitter and. I'm looking
    forward to the discussion. And thanks for
  • 59:51 - 59:54
    listening.
    melzai_a: You write it, so.laughing
  • 59:54 - 59:58
    Andrea: I just brought it up, must have
    bmbF because I'm now sitting on the screen
  • 59:58 - 60:02
    on dislike committees more and more, I'm
    reaching an age where I'm sitting on
  • 60:02 - 60:05
    committees and I told them legacy software
    is a problem.
  • 60:05 - 60:08
    melzai_a: It's a real.big problem.
    Andrea: You know, it's very troubling that
  • 60:08 - 60:13
    the software is written in Fortran. Not
    every second Linus go to, so it's written
  • 60:13 - 60:18
    like assembler. No one knows what's in
    there anymore. And if a person dies, we're
  • 60:18 - 60:22
    not going to be able to do anything about
    the algorithms. They're just going to be
  • 60:22 - 60:25
    lost.
    melzai_a: Exactly. And they are. So you
  • 60:25 - 60:28
    have to first influence to grant writing
    institutes that there are grants out so
  • 60:28 - 60:33
    that this software can read is reversed.
    And this software is not easy. So that's
  • 60:33 - 60:37
    not your typical web page, so you need to
    work together in such groups. And so it's
  • 60:37 - 60:42
    a very interesting piece of the problem, I
    have to say. So sadly, as a PhD student went,
  • 60:42 - 60:46
    we weren't we were looking into this for
    the second. Ah.. This is too big of a cake
  • 60:46 - 60:50
    to eat. laughing It was very
    interesting. So I can also this and you
  • 60:50 - 60:54
    let you do it. The nudel tool suite, and
    that's also only maintained by, I think,
  • 60:54 - 61:01
    three people also. So even that one, it's
    with many more. It's still not good. So
  • 61:01 - 61:06
    just my sense of that one.
    Andrea: So I brought my Ph.D. thesis. I
  • 61:06 - 61:08
    worked on chalex?? and that faces similar
    problems.
  • 61:08 - 61:15
    melzai_a: Yeah, it's it's just used in the
    entire world to solve every small molecule
  • 61:15 - 61:20
    structure. There is more or less it was
    like, Yeah, so questions were the
  • 61:20 - 61:25
    questions. Frankly, we ain't got a first
    question, I think around 20 or 30 minutes
  • 61:25 - 61:30
    ago, if we yeah, that's that's why that
    was so great as a signal angel, she's
  • 61:30 - 61:35
    picking up all of these points. And so the
    first question was how do the virus
  • 61:35 - 61:37
    variants affect the shape or form of the
    virus?
  • 61:37 - 61:44
    Andrea: I think they so no matter like,
    OK, this is the old model as we know, then
  • 61:44 - 61:49
    there should be fewer spikes and should be
    a bit smaller. But nothing would change on
  • 61:49 - 61:55
    this view, like the scale is way too
    large. The mutations each change about 10
  • 61:55 - 62:01
    atoms, so every like amino acid at this
    different, it's about 10 atoms. And those
  • 62:01 - 62:06
    changes would be so small you could not
    see them on the virus model. You'd
  • 62:06 - 62:10
    actually need to look at the head of the
    spike in order to see the mutation and
  • 62:10 - 62:16
    what it actually does. So the changes are
    too small to show them in the model. That
  • 62:16 - 62:20
    doesn't mean they're not meaningful. So as
    you've seen, like the head of the spike
  • 62:20 - 62:28
    binds to the host, to the host cell, to
    ACE2 receptor, and that binding is highly
  • 62:28 - 62:36
    influenced by this by the mutations. Now
    we found that we may end up lucky because
  • 62:36 - 62:42
    the same paths were to antibody as binding
    is also the piece that binds to the host
  • 62:42 - 62:47
    cell. So everything that would mate
    despite change in a way that the antibody
  • 62:47 - 62:55
    couldn't bind any more to it. For its head
    would have also changed how it bound to
  • 62:55 - 63:03
    the host cell. However, it seems that
    Omicron is still able to bind human cells
  • 63:03 - 63:09
    very efficiently, while antibodies cannot
    recognize it so easily. That may have to
  • 63:09 - 63:13
    do with like this finger's actually like
    packed and you could imagine like putting
  • 63:13 - 63:18
    cotton wool around it. That's called
    glycosylation. It's got long sugar changes
  • 63:18 - 63:23
    that are rule, and they're there to
    obscure the immune system, like the
  • 63:23 - 63:28
    antibody goes like orders, wool. I can't
    really find where I'm on to bind. Is it
  • 63:28 - 63:34
    here? I don't know. And that's changed in
    Omicron, but it's not fully understand
  • 63:34 - 63:41
    yet. I saw there was a new structure this
    week, but I haven't looked at it yet.
  • 63:41 - 63:45
    However, the changes are too small to show
    it in the virus model. They're like really
  • 63:45 - 63:51
    tiny changes. And another change that
    happens in Omicron as well is the
  • 63:51 - 63:57
    proofreading mechanism. When the RNA is
    copied is like damaged and we think it's
  • 63:57 - 64:02
    damaged. So their so-called eNd RNA, which
    is a proofreading protein, its sharp is
  • 64:02 - 64:07
    like to go like a star and correct? Yes,
    correct, correct. Correct. That seems to
  • 64:07 - 64:11
    be a little bit broken. So it could be
    that Omicron is accumulating so many
  • 64:11 - 64:17
    mutations because it's RNA copy machine.
    It's like not working as it should is
  • 64:17 - 64:22
    basically not proofreading. That would
    mean that more viruses are produced that
  • 64:22 - 64:27
    are not viable and cannot survive. But it
    would also mean that it mutates much
  • 64:27 - 64:32
    faster, and we think that may have an
    influence. But that's just theory. So far
  • 64:32 - 64:37
    this hypothesis, we haven't proven it yet.
    So this is why I haven't tweeted about it
  • 64:37 - 64:42
    yet, because it's just a theory, but it
    would make sense, right?
  • 64:42 - 64:46
    melzai_a: Connected to that, I would have
    a question the ice receptor of small children
  • 64:46 - 64:51
    is a little bit different than that one
    of the adults to you do know about that
  • 64:51 - 64:56
    because all the concern to what's more,
    the smaller children are the defense.
  • 64:56 - 65:01
    Andrea: I can't. I have read that, but I
    haven't looked into it properly. So I'm
  • 65:01 - 65:06
    I'm afraid I'm not going to answer this
    question because I feel I would rather not
  • 65:06 - 65:08
    say anything about it than say something
    that's wrong especially.
  • 65:08 - 65:12
    melzai_a: Well. We're looking forward to
    the secretary's right in the public PDB so
  • 65:12 - 65:19
    that everybody can look at them and.
    Andrea: Know we live in an age of
  • 65:19 - 65:23
    preprint, and very often the PDB papers
    are there when a preprint comes out, which
  • 65:23 - 65:28
    is how we called so many errors, right?
    They published a preprint, they put out a
  • 65:28 - 65:32
    structure. We went like, there's errors in
    the structures. And then when they
  • 65:32 - 65:35
    published actual paper, everything was
    corrected.
  • 65:35 - 65:39
    melzai_a: And she's agreed that believe
    the changes, I think are checked on the
  • 65:39 - 65:43
    PDB.
    melzai_a: This is, in fact, because yes,
  • 65:43 - 65:46
    that's that's what IT people like
    because then that, you know, there's a
  • 65:46 - 65:52
    history is very important. And there's a
    second question and it goes towards the
  • 65:52 - 65:54
    tools that I use to simulate those
    molecules.
  • 65:54 - 65:59
    Andrea: Wait, wait, wait, wait. I have a
    follow up to this: thing that I would
  • 65:59 - 66:04
    really like to see, but it hasn't happened
    yet. The PDB is a very static repository
  • 66:04 - 66:09
    where only original offers are allowed to
    change their structures. Now, imagine if
  • 66:09 - 66:15
    the protein data bank would be like GitHub
    with pull requests. We could go like, go
  • 66:15 - 66:19
    like, changed the molecule around. Go
    like, no, it's a better fit to your data.
  • 66:19 - 66:23
    Please pull.
    Herald: That would be a very subversive
  • 66:23 - 66:26
    proposition. I would say.
    Andrea: Yeah, wouldn't that be nice? I'm
  • 66:26 - 66:31
    like, Why aren't we doing this? It's like
    the system is already there. It happens
  • 66:31 - 66:36
    that we have like repositories for a while
    in software development. We could do the
  • 66:36 - 66:44
    same thing with models fitted to our
    experimental data. But I think I need to
  • 66:44 - 66:48
    go into more committees.
    melzai_a: Yeah, it sounds like this. I
  • 66:48 - 66:54
    would agree for that proposal. There was a
    person that was asking about the toolsset
  • 66:54 - 66:59
    that you would use to simulate those
    molecules and structures and so on. And if
  • 66:59 - 67:04
    you then create these more usable pictures
    for the public, how do you balance
  • 67:04 - 67:08
    artist's impression simplified models and while keeping the scientific truth as
  • 67:08 - 67:14
    much as well as possible.
    Andrea: The question you don't need the
  • 67:14 - 67:18
    public even to have this problem. You have
    it already when you make pictures
  • 67:18 - 67:22
    scientifically. Because sometimes you want
    to show our certain aspects of a molecule
  • 67:22 - 67:27
    very clearly, which means you have to cut
    away, for example, a part of the molecule.
  • 67:27 - 67:31
    So one answer to this is the program that
    does. The modeling is not a program that
  • 67:31 - 67:35
    you use to make the pictures. That's the
    first thing you do. So you make your model
  • 67:35 - 67:39
    with one program and then you take all the
    coordinates of the atoms and you throw
  • 67:39 - 67:45
    them into a professional rendering program
    that like, we'll do it all pretty. But you
  • 67:45 - 67:49
    still have to make an executive decision
    on what to show in your graphics, in your
  • 67:49 - 67:57
    paper. And I think that in particular,
    structural biologists, who deal with three
  • 67:57 - 68:01
    dimensional and two-dimensional pictures,
    we would do very well to think a lot more
  • 68:01 - 68:08
    about scientific illustration. So all my
    team likes thinking about these things,
  • 68:08 - 68:12
    which is, I think, how we got where we are
    now, right? They actually like stuff like
  • 68:12 - 68:18
    this. They go like, Oh, we can print it 3D
    and we can put a magnet on it and it's
  • 68:18 - 68:22
    going to stick. But it turns out that
    scientists also need these tools to
  • 68:22 - 68:27
    understand what's going on. It's like
    actually having a 3D model helps you so
  • 68:27 - 68:32
    much with thinking about things. Crick and
    Watson. They build a model of their DNA in
  • 68:32 - 68:37
    metal for a reason. Because we're looking
    at three dimensional things, making them
  • 68:37 - 68:44
    like understandable with our hands. So
    yes, as a good researcher, you're not only
  • 68:44 - 68:49
    able to explain your research to the
    cleaning woman, you should also be able to
  • 68:49 - 68:53
    visualize it properly. And it's part of
    the art. If you are a structural biologist
  • 68:53 - 68:58
    and you're not able to make good pictures
    of your molecules, you're not a good
  • 68:58 - 69:02
    structural biologist. End of story. You're
    in the wrong discipline, you should have
  • 69:02 - 69:05
    possibly chosen something where you need
    less graphics.
  • 69:05 - 69:12
    melzai_a: And I think one of your industry
    does is actually a of biologist by
  • 69:12 - 69:18
    training. Right? I think you've got...
    Andrea: Tomasello is a proper biologist.
  • 69:18 - 69:26
    Thomas Splettstössersplit shrews as a prop about like a
    Ph.D. in bioinformatics and Janet Erosa,
  • 69:26 - 69:33
    and LiU are both scientists who are having
    a group that only deals with illustration.
  • 69:33 - 69:36
    So it's actually in science. We have
    several groups in the world and structural
  • 69:36 - 69:42
    biology who only do illustration as
    science. So David Goodsell with his
  • 69:42 - 69:48
    watercolors, is very well known, but Janet
    Erosa is another one. So actually making
  • 69:48 - 69:55
    these animations and pictures is so
    complicated that television can't do it.
  • 69:55 - 70:00
    And the ZDF made a series of animations,
    so they made very nice ones for Planet E
  • 70:00 - 70:06
    Rizzo and Nano with us. But then they
    asked my expertize to make another
  • 70:06 - 70:11
    animation. And they only had like a call
    with us, and they never came back and then
  • 70:11 - 70:19
    published a completely wrong animation of
    the entire viral mechanism under my name.
  • 70:19 - 70:25
    And I'm still sad every time I see it
    three times a day. Heute Journal shows a
  • 70:25 - 70:29
    wrong structure of the virus for which
    they claim that I helped them make it, and
  • 70:29 - 70:35
    I wrote to them and told them, Your
    depiction of the virus is wrong. I can
  • 70:35 - 70:43
    help you make a new one. But it seems that
    it's 2. deutsche Fernsehen der heute Journal at least didn't
  • 70:43 - 70:50
    care on. I guess they think it's not
    important enough, but I think with a
  • 70:50 - 70:55
    threat like this where we really cannot
    see the virus, it is important to bring to
  • 70:55 - 71:01
    the public the best possible depiction we
    can deliver. Sometimes, however, as I
  • 71:01 - 71:05
    said, you omit certain aspects, for
    example, to show the effects of a mutation
  • 71:05 - 71:13
    yet only showed a side of the mutation.
    You don't show all the atoms. But. That's
  • 71:13 - 71:16
    really an important part of what we are
    doing. Like pointing out the important
  • 71:16 - 71:18
    bits of ...
    melzai_a: Scientific information is so
  • 71:18 - 71:24
    important, I think we have one final
    question, which I would say comes out
  • 71:24 - 71:30
    comes towards the direction of the immune
    system. And the question would be can you
  • 71:30 - 71:36
    can you define vaccine on purpose so that
    the immune system can forget how to
  • 71:36 - 71:40
    produce the antibodies after a defined
    period of time? And I think the concern
  • 71:40 - 71:49
    here is about increasing your
    financial gain in the crisis, for example.
  • 71:49 - 71:56
    So programed obsolescence, as both of
    those mentioned. So you're a bit late. So
  • 71:56 - 72:01
    if you could keep it short, that would be
    great. OK? Andrea: The quick answer is no,
  • 72:01 - 72:08
    that's not possible. You can make. You can
    enhance how long vaccines and how much
  • 72:08 - 72:14
    immune response you get from a vaccine or
    certain additives. But you can not, like
  • 72:14 - 72:19
    make them a definite time because
    everybody is different. So even when you
  • 72:19 - 72:22
    get your booster shot, they say six
    months, but you may need it after three
  • 72:22 - 72:28
    months or you may need it after 12
    authorityto. It's very hard to tell. And
  • 72:28 - 72:33
    pharma industry does not have tools that
    would allow them that, to my knowledge. So
  • 72:33 - 72:39
    I think that's not a risk.
    melzai_a: I mean, it's it's a human
  • 72:39 - 72:44
    system, and so complex is the rocket to
    the Moon. So.
  • 72:44 - 72:47
    Andrea: I think it's a it's a valid
    concern. It's just technologically not
  • 72:47 - 72:53
    possible. Luckily, I guess.
    melzai_a: The final and really last question, I think,
  • 72:53 - 72:57
    is where can somebody find the 3D models
    out there?
  • 72:57 - 73:02
    Andrea: Oh, you can go to inside
    Corona..de and find a blog post about a 3D
  • 73:02 - 73:13
    thing or you go to Thingy Reuss and you
    look for inside corona. I can. Yeah. Yeah.
  • 73:13 - 73:21
    I just go to. I just put it in. Why not
    that? That's our home page and then on
  • 73:21 - 73:29
    thingy worse. It's also called inside
    corona. And you can also write me a
  • 73:29 - 73:37
    message on Twitter if you don't find it at
    a turn up. And remember, we're going to
  • 73:37 - 73:43
    put out a new model soon in January, but
    I'm still waiting for the final files and
  • 73:43 - 73:50
    holiday. So it will be a few more weeks.
    melzai_a: So but that trend in January,
  • 73:50 - 73:53
    not in December 2008. Yeah, exactly. Or
    printed?
  • 73:53 - 74:00
    Andrea: Yes. So thank you very much for
    having me.
  • 74:00 - 74:03
    melzai_a: Yeah, it was good. Thank you.
    And I think if they are no more questions.
  • 74:03 - 74:08
    Everybody. All right. Oh, you know how it
    looks like? I think that's really
  • 74:08 - 74:12
    important. I think one and a half years
    ago, I came across the first pictures was
  • 74:12 - 74:18
    like, This is how it looks like. Now I can
    tell it to the people who who don't read
  • 74:18 - 74:26
    the scientific original papers because
    they are so difficult to read. So. Yeah.
  • 74:26 - 74:34
    Good. You know. And thanks for being here
    and looking forward to hearing and seeing
  • 74:34 - 74:38
    more and hopefully once this will be over.
    I think
  • 74:38 - 74:44
    Andrea: I hope so too. Going back out of
    the spotlight to being just a Methods
  • 74:44 - 74:46
    developer, that would be nice.
    Herald: That would be nice, yes.
  • 74:46 - 75:05
    Subtitles created by c3subtitles.de
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Title:
The Coronavirus Structural Task Force
Description:

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Video Language:
English
Duration:
01:15:05

English subtitles

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