Recent work
in the Journal of Molecular Biology has described how advances in technology
and biology could produce a three-dimensional computer model of cells,
something that has so far been elusive. Such a development could revolutionize
biomedical research and have tremendous impact on human and animal health and
well being.
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"Cells are the foundation of life,"
explained one co-author of the paper, Ilya Vakser, a Professor of Computational
Biology and Molecular Biosciences and Director of the Center for Computational
Biology at the University of Kansas. "Recently, there has been tremendous
progress in biomolecular modeling and advances at understanding life at the
molecular level. Now, the focus is shifting to larger systems -- up to the
level of the entire cell. We're trying to capture this emerging milestone
development in computational structural biology, which is the tectonic shift
from modeling individual biomolecular processes to modeling the entire
cell."
The study reviews a variety of techniques that
aim at simulating a 3D cell; the investigations of complex biological networks,
automated 3D cell model creation using experimental data, the modeling of
protein interactions and protein complex formation, modeling of cell membranes
and the kinetic and thermodynamic impacts of crowding on those membranes, and
the architecture of chromosomes are all included.
"A lot of techniques that are required for
this are already available -- it's just a matter of putting them all together
in a coherent strategy to address this problem," explained Vakser.
"It's hard because we're just beginning to understand the principal
mechanisms of life at the molecular level -- it looks extremely complicated but
doable, so we're moving very fast -- not only in our ability to understand how
it works at the molecular level but to model it."
These disparate techniques can be woven
together, say the authors. Taken together, the methods can enable a better
"understanding of life at the molecular level and lead to important
applications to biology and medicine."
"There are two major benefits," Vakser
continued. "One is our fundamental understanding of how a cell works. You
can't claim you understand a phenomenon if you can't model it. So this gives us
insight into basic fundamentals of life at the scale of an entire cell. On the
practical side, it will give us an improved grasp of the underlying mechanisms
of diseases and also the ability to understand mechanisms of drug action, which
will be a tremendous boost to our efforts at drug design. It will help us
create better drug candidates, which will potentially shorten the path to new
drugs." Such a 3D cell model could
be applicable to many fields. The work that has been done leading to this point
has varied levels of precision; in some cases there may be more work to be done
in order to understand how various parts of the cell relate to one another.
"We've made advances in our ability to
model protein interactions," he said. "The challenge is to put it in
context of the cell, which is a densely populated milieu of different proteins
and other biomolecular structures. To make the transition from a dilute
solution to realistic environment encountered in the cell is probably the
greatest challenge we're facing right now." For now, Vakser suggests work focus on the modeling
of straightforward, single-celled organisms. More complex cell types could be
developed in the future.
"We go for the simplest cell possible.
There are small prokaryotic cells, which involve minimalistic set of elements
that are much simpler than the bigger and more complicated cells in mammals,
including humans," he said. "We're trying to cut our teeth on the
smallest possible cellular organisms first, then will extrapolate into more
complicated cells."
Sources : University of Kansas, Journal of Molecular
Biology
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