A paper recently published in the Journal of Molecular Biology shows how advances in molecular biology and computer science around the world soon may lead to a three-dimensional computer model of a cell, the fundamental unit of life.
According to the authors, the development could herald a new era for biological research, medical science, and human and animal health.
"Cells are the foundation of life," said Ilya Vakser, professor of computational biology and molecular biosciences and director of the Center for Computational Biology at the University of Kansas, one of the paper's co-authors.
"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, titled "Challenges in structural approaches to cell modeling," surveys a range of methodologies joining the march toward a simulated whole 3-D cell, including the studies of biological networks, automated construction of 3-D cell models with experimental data, modeling of protein complexes, prediction of protein interactions, thermodynamic and kinetic effects of crowding cellular membrane modeling, and modeling of chromosomes.
"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," Vakser said. "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."
While most of these techniques are being developed separately, the authors say that considered together they represent a push forward that could provide a better basic "understanding of life at the molecular level and lead to important applications to biology and medicine."
"There are two major benefits," Vakser said. "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."
As an example, the KU researcher said a working 3-D molecular cell model could help to replace or augment phases of time-consuming and expensive drug development protocols required today to bring drug therapies from the scientist's bench to the marketplace.
Vakser said that facets of the research that could lead to a computer-simulated cell are at different levels of refinement.
"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."
While modeling more complex human cells might be on the agenda soon, Vakser said that for the time being, research efforts will focus on modeling simple single-celled organisms.
"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."
Along with Vakser, the paper's authors are Wonpil Im of Lehigh University, Jie Liang of the University of Illinois at Chicago, Arthur Olson of The Scripps Research Institute and Huan-Xiang Zhou of Florida State University.
Brendan M Lynch | EurekAlert!
New insight into a central biological dogma on ion transport
26.06.2017 | Aarhus University
UK chemistry researchers develop catalyst that mimics the z-scheme of photosynthesis
26.06.2017 | University of Kentucky
An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.
Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...
Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.
Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...
Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.
As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...
Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.
With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...
Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine
Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...
19.06.2017 | Event News
13.06.2017 | Event News
13.06.2017 | Event News
26.06.2017 | Agricultural and Forestry Science
26.06.2017 | Life Sciences
26.06.2017 | Health and Medicine