OCT 06, 2016 07:55 AM PDT

Science is on the Verge of Modelling Cells on a Computer

WRITTEN BY: Carmen Leitch
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.
 
The image from co-author Arthur Olson's lab at the Scripps Research Institute shows a preliminary model of mycoplasma mycoides. Modeling by Ludovic Autin and David Goodsell, rendering by Adam Gardner./Credit: The Scripps Research Institute

"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: Eurekalert!/AAAS via the University of Kansas, Journal of Molecular Biology
 
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