them so that the user has a choice
about which operations to combine for
best performance,” he explains.
The result, Yoshioka says, is a new
era in understanding the mechanisms of life at a molecular scale. Although Cryo-EM microscopes can
cost $6 million or more, their use lets
researchers visualize biological molecules at an atomic scale, and see them
in their natural state. In contrast, X-ray crystallography requires scientists
to order billions of molecules into
well-ordered crystals, which can complicate the process of understanding
of how they appear or function in a living cell. Using Cryo-EM, “We are better able to understand how proteins
behave, how different substances or
drugs affect them, and how modifications can change the way a drug binds
to the protein,” Frank says.
Genetic research is also leading biologists down the path of other computational methods that extend the
boundaries of programmable biology. For instance, at the University of
Groningen in the Netherlands, bio-technologists have used a modeling
method to redesign the enzyme aspartase and convert it into a catalyst
for asymmetric hydro-amination reactions that produce larger quantities of
the substance. Working with researchers in China, the group was able to
produce high volumes of extremely
pure building blocks of aspartase that
could be used in pharmaceuticals and
other bioactive compounds.
Meanwhile, at the University of
beams scatter from crystallized mole-
cules, but is difficult to apply to all sam-
ples. “It can be exceedingly difficult to
get proteins to crystalize, sometimes
nearly impossible,” Yoshioka explains.
Cryo-electron microscopy fundamentally changes the equation. Researchers place biological specimens
under a transmission electron microscope and study them under cryogenic
temperature conditions: -130oF or less.
The system produces digital images
that are run through specialized algorithms that dramatically reduce noise
and sharpen the image using a method of frame alignment that studies
particle behavior in different images.
“The software processes the images
and identifies the values of the key parameters,” says Henderson, who pioneered imaging techniques that, along
with fellow 2017 Nobel Prize winners
Jacques Dubochet and Joachim Frank,
led to modern Cryo-EM.
Henderson says Cryo-EM addresses a basic problem with conventional
electron microscopy: the interaction
of electrons with organic matter
causes a breakdown in their molecular structure, which generates a high
level of visual noise. “It’s a bit like
looking for a roe deer in a forest with
dappled sunshine. It’s not easy to pick
them out because they’re disguised,”
he explains. To bypass the problem,
Cryo-EM combines more advanced
hardware with image-processing software that averages the position and
behavior of thousands of individual
particles and extrapolates the data to
produce much clearer images of a biological structure. As a result, Cryo-EM
can achieve atomic-level resolution
models of complex, dynamic molecular assemblies.
Nobel laureate Frank, a professor of
biochemistry and molecular biophysics at Columbia University in New York,
says advances in graphics processing
units (GPUs) and better algorithms
have revolutionized the field. “Speed is
no longer a problem, with the emergence of GPU software and clever algorithms,” he explains. Moreover, the
field is continuing to advance and incorporate new computational methods. For example, “There are now software platforms … that combine
different packages under one umbrella
and provide interoperability among
microscopy is “a bit
like looking for a roe
deer in a forest with
It’s not easy to pick
them out because
Massachusetts, Amherst, researchers
led by computational biophysicist Ji-anhan Chen are developing sophisticated computer modeling algorithms
and molecular simulation models
that allow researchers to study a newly recognized class of substances
called intrinsically disordered proteins (IDPs). These proteins contain
highly flexible 3D structural properties that are extraordinarily difficult
to observe. Chen’s technique relies
on sheer computational power, because high-resolution imaging techniques like X-ray crystallography and
nuclear magnetic resonance (NMR)
cannot provide data about the highly
flexible and fast-changing nature of
Nogales believes these different genetic observation and engineering techniques will continue to break barriers
and further advance science. “We are
beginning to understand biology, chemistry, and physics at deeper and broader
levels than ever before. We are now
studying molecules that were almost unknown in the past, and we are putting
the knowledge to work through gene editing tools such as CRISPR. We will see
enormous changes in the biological
world as a result of these techniques.”
Noble, C., Adlam, B., Church, G.M.,
Esvelt, K.M., and Nowak, M.A.
Current CRISPR Gene Drive Systems are
Likely to be Highly Invasive in Wild
Populations, eLife, e 2018;7:e33423. DOI:
Cheng, Y., Glaeser, R.M., and Nogales, E.
How Cryo-EM Became so Hot. Benchmarks.
Volume 171, Issue 6, 30 November 2017,
Pages 1229-1231. https://doi.org/10.1016/j.
Wright, VW., Liu, J., Knott, G.J., Doxzen, K. W.,
Nogales, E., and Doudna, J.A.
Structures of the CRISPR genome
integration complex. Science, 20 Jul 2017:
eaao0679. DOI: 10.1126/science.aao0679.
Russo, C.J. and Henderson, R.
Microscopic Charge Fluctuations Cause
Minimal Contrast Loss in Cryo-EM,
Ultramicroscopy, Volume 187, April 2018,
Pages 56-63. https://doi.org/10.1016/j.
Samuel Greengard is an author and journalist based in
West Linn, OR, USA.
© 2019 ACM 0001-0782/19/2 $15.00