Video summary
The lecture introduces the cutting-edge field of computational protein design, moving beyond the traditional approach of stabilizing new sequences within existing natural folds. Instead, researchers aim to create entirely novel protein structures that have never been observed in nature. Since bioinformatics alone cannot predict these unknown forms, scientists must rely on physical laws and computational tools like the Rosetta program to assemble small structural fragments into a new fold. This process involves iteratively placing side chains and running simulations to enhance stability, followed by rigorous laboratory testing to validate successful designs before further modifications are made.
A significant advancement in this field comes from David Baker's group, which has pioneered the creation of custom protein building blocks designed to self-assemble into larger, periodic structures resembling crystals. By combining small helices and sheets with disulfide bridges and chemical treatments, they create rigid components that can spontaneously aggregate into miniature machines on a nanometer scale. This approach represents a form of biological nanotechnology, operating at scales far smaller than traditional mechanical nanotechnology, and holds the potential for future applications in bacteria and other advanced biotechnological fields.
The lecture also highlights the successful design of beta-barrel membrane proteins, which are notoriously difficult to fold due to their delicate stability and complex insertion mechanisms into cell membranes. Designing these proteins requires not just constructing a stable structure but also performing "anti-design" to ensure the protein does not form its final shape prematurely in water. By carefully tuning the hydrophobicity of the pore and reducing the tendency to form beta sheets outside the membrane, researchers achieved a state where the structure only folds correctly upon inserting into the lipid bilayer.
Ultimately, these breakthroughs demonstrate that computational design can overcome the limitations of natural evolution to create functional proteins with unprecedented properties. The ability to engineer completely new folds, from rigid crystalline arrays to specialized membrane channels, opens up limitless possibilities for synthetic biology and medicine. As research progresses, we are likely to see the emergence of miniature biological machines that perform tasks far beyond current capabilities, marking a transformative era in protein science where human design dictates the architecture of life's fundamental machinery.
Read the full video transcript
so that's the last thing we do i want to
show you something that's really state
of the art today
most of the previous proteins design
i've showed you have the fact in common
that they kind of piggybacked on
existing folds and i just try to
stabilize a new sequence in that fold
that is smart and it's in general what
you want to do don't reinvent the wheel
but what if we could create completely
new faults
remember this landscape that i spoke
about in the bioinformatics lecture that
we know most of the existing fold space
but instead of this base what if i could
design a protein out here
it's a completely new fold a fold that
we've never seen in nature before
in this case there is no way we could
rely on plain bioinformatics it's not
going to work
we don't have anything like it this is
something that i need to stabilize
based on the laws of physics basically
there is one group in the world that i
would argue significantly further ahead
than
anybody else here and that's david baker
in washington the groups that are behind
this
rosetta program and what they do in most
of this case
is roughly the same thing as for rosetta
but you can't piggyback as much unknown
structures
you're assembling small fragments in
this case we try to assemble small
fragments
into a new fold that we've either
guessed or have divine inspiration
or try to optimize what it should look
like and then we're iteratively
placing side chains see if we can
improve the stability
moving the side chains around maybe
running a short simulation to see if we
can stabilize things
and then we need to go in the lab test
this take back
the successful cases try to modify the
successful cases a bit
there's an insane amount of work here
but there is also an exceptionally
impressive stream of new papers coming
out from
where they showed that they can't do
this they can't design vaccines they can
design proteins
and they can design completely new folds
for proteins
this is david one
thing that they did just two years ago i
think it was that
they instead of building traditional
proteins they figured out what if we
could design some sort of large building
blocks
almost like the fibrous proteins we
talked about earlier in this class
now we can't have very long genes so
that their idea is that what if we start
by creating some small bricks
and what they did here is that they
usually use small helix and sheet
combinations two three secondary
structure elements
then they would use several disulfide
bridges so
cysteines that would mean that i'm going
to lock them up with disulfides create
very nice small
rigid components and for a few of these
they also used chemical treatment
afterwards to try to get the n
and the c terminal to stick together
again the reason for doing this is
creating small
building blocks where each building
block will be very rigid and stick
together
once you've done that you have your
small bricks and if these bricks now
stick together we can start to change
the amino acids on the surface of the
brick
so if i have two bricks here what if i
create a periodic pattern here so that
the bricks would like to pack
then the bricks might spontaneously
self-aggregate into larger structures
and do they this is a shock and all
paper too that i have for you
in canvas they had a whole range of
structure where they can create almost
crystals
formed out of proteins with repeating
patterns because again
each building block here is small but
the patterns they create
and not quite with macroscopic scales
but almost
the use cases for this is unlimited
you can imagine using this in bacteria
we might create those small miniature
structures and everything
the reason why i don't have any super
specific examples for you yet is that
it's still research of course
but we're literally creating a type of
protein structure
engineering that is like nanotechnology
the only difference is that traditional
mechanics-based nanotechnology
that has structures in the ballpark of
900 nanometers
these proteins they have structures in
the ballpark of 10
nanometers so that it's almost on the
border pico technology
not quite but far smaller structures
that can do
far more advanced things and i bet we're
going to start to see
miniature machines here in the near
future too
when i introduce the membrane protein
class to you i figure that there's only
one class of proteins that is not so
common the beta
barrel proteins and membranes so maybe i
could let go of those
chance has a way of fun playing funny
tricks at you because
because i did that just two weeks later
after that lecture of course david baker
published an amazing paper in nature
where they showed that they could design
beta barrels so now i have to share beta
barrels with you anyway
so beta barrels are not common membrane
proteins but they do exist
and when they fold they kind of they
form some sort of semi-beta
heat like structure on the outside and
then they gradually slide into the
membrane by themselves
we know very little about their folding
we also know that their
delicate stability and everything so
this is probably some of the hardest
proteins imaginable to fold but david
managed to do that
this is also a paper i've shared you
because it's a remarkable example how to
use
protein design in practice and designing
completely new beta-barrel proteins so
what did they do
well first they used all these rules
that we've gone through having
anchors on the top of the membrane
proteins to anchor say tyrosines to the
head group regions here
you need a hydrophobic exterior of the
pore
and then a moderately hydrophilic
interior of the pore so literally have a
poor functionality
to go through it and then carefully
select the number of
beta strands we have to form a large
beta sheet but it turns out that's not
enough
because if you do this and create
something that is a very stable beta
sheet it's not going to work at all
the reason for that is that if something
is too stable as a beta sheet they will
just form a beta sheet
out in the water and if it's stable as a
beta sheath out in the water
it's no particular reason for it to go
into the membrane
so the challenge here is not just design
but for proteins you also need to do
anti-design
so the greatest challenge for them here
was actually not to design a beta sheet
anybody me included could do that
the hard part is that they had to reduce
the property of this
protein to form a beta sheet out in
water
and when they reduced this property
sufficiently enough and made it
relatively hydrophobic
then you got it to a state where it
would not form beta sheets out in water
but it will form beta sheets
while it is inserting into the membrane
and then they managed to show that it
doesn't hurt so these actually do
form stable new folds of beta
barrel membrane proteins