SIGHTINGS
Watching Water Channels
Felice Frankel
When judging this year's Science and Engineering Visualization
Challenge contest sponsored by the National Science Foundation,
I knew I wanted to share this first-place illustration with
American Scientist readers. Emad Tajkhorshid is a computational
biophysicist at the National Institutes of Health Resource for
Macromolecular Modeling and Bioinformatics at the Beckman
Institute, University of Illinois at Urbana-Champaign. Klaus
Schulten directs the Theoretical and Computational Biophysics
Group, whose purpose is to develop software for biomedical and
other investigators. The most popular software developed, called
VMD, was used to generate this image. For more information, go
to http://www.ks.uiuc.edu/Research/vmd.
F. F. Can you explain to readers unfamiliar with
molecular biological representations how to read the image?
E. T. The image can be broken into proteins, lipids
and water. Small molecules can be shown in an all-atom
representation, explicitly showing all atoms and bonds. Biomolecular
macromolecules are much more crowded. Showing all atoms and bonds
makes the visualization useless. So people have come up with simpler
representations. For example, in proteins we can look at the
backbone atoms in the polypeptide chain and ignore the side chains
of individual amino acids. If backbone atoms are arranged in a
helical shape, we show the protein in that region using rods; if we
have multiple strands lying next to each other, we show them as ribbons.
Now, in our simulation system, we have a box packed with 106,000
atoms. Naturally showing all of these components in full atomic
detail does not get us anywhere, since there are way too many atoms.
At the same time, we really wanted to show as much detail as
possible. So we used different representations for different parts.
Water molecules are shown always using a stick representation
(representing the only two chemical bonds in their structure) in
light blue. In the membrane region, sandwiched between the two water
layers, we see two major components: in the middle an array of four
identical proteins (a tetramer) and on the left and right lipid
molecules forming the so-called lipid bilayer structure embedding
our protein.
F. F. You exaggerate the size of the water
molecules as they pass through the channel. Did you think that might
be misleading?
E. T. It was indeed one concern we had. The first
reaction of some viewers was to ask why we have
"different" water molecules inside the channel. It seemed
to them that something happens to water as it enters the channel
that makes it special. This is both right and wrong, depending on
how you look at it. The chemical nature of water molecules does not
change. But the configuration of water has indeed been influenced by
the channel. In the bulk we have always several water molecules
surrounding every single water molecule. Inside the channel,
however, water molecules are forced to form a single file. This is
not something a water molecule likes, as it loses some of its
favorable interactions with other water molecules. This fact turned
out to be very important for the selective function of this channel.
So we used an exaggerated representation.
F. F. Can you give us some sort of hierarchy of the
information you hoped a reader would glean from looking at the
image for the first time? It's obvious how "packed" all
the molecules are. What else was important to convey?
E. T. The density and complexity of the molecular
system was certainly one of our main objectives. The second most
important message is the water configuration. The membrane fatty
core (shown in red sticks) is very efficiently isolating the water
on the two sides. But there is a conduit inside the protein that
allows water to get to the other side. The viewer, we hope, sees how
closely water interacts with the channel. Also when one pays a
little attention, the flip of water molecules at the center of the
channel becomes obvious. Water comes in head first, turns 180
degrees and goes out head-last. The oxygen atom at the center of
each water molecule is always facing the center of the channel. It's
like a ballet in which the dancers who come onto a stage have been
asked to face a singer standing in the center of the scene.