In collaboration with scientists from the Wadsworth Center of the New York State Department of Health, the team is working to harness the reaction to develop a "nanoswitch" for a variety of applications, from targeted drug delivery to genomics and proteomics to sensors.
The research is part of a burgeoning discipline called "quantum biology," which taps the skyrocketing power of today's high-performance computers to precisely model complex biological processes. The secret is quantum mechanics -- the much-touted theory from physics that explains the inherent "weirdness" of the atomic realm.
Reporting in the February 2007 issue of Biophysical Journal, the researchers describe a mechanism to explain how an intein -- a type of protein found in single-celled organisms and bacteria -- cuts itself out of the host protein and reconnects the two remaining strands. The intein breaks a protein sequence at two points: first the N-terminal, and then the C-terminal. This aspect of the project, which is led by Saroj Nayak, associate professor of physics, applied physics, and astronomy at Rensselaer, focuses on the C-terminal reaction.
Another Rensselaer team previously found that the reaction at the C-terminal speeds up in acidic environments. But to control the reaction and use it as a nanoswitch, a better understanding of the mechanism behind this reaction is needed, according to Philip Shemella, a doctoral student in physics at Rensselaer and corresponding author of the current paper.
"You can use this protein that cuts itself and joins the pieces together in a predictable way," he said. "It already has a function that would be nice to harness for nanotechnology purposes." And because the reaction may be sensitive to light and other environmental stimuli, the process could become more than just a two-way switch between "on" and "off."
The researchers revealed the details of the reaction mechanism by applying the principles of quantum mechanics -- a mathematical framework that describes the seemingly strange behavior of the smallest known particles. For example, quantum mechanics predicts that an electron can be in two different places at the same time; or that an imaginary cat can be simultaneously dead and alive, as suggested by one famous thought experiment.
Until recently, scientists could not apply quantum mechanics to biological systems because of the large numbers of atoms involved. But the latest generation of supercomputers, along with the development of efficient mathematical tools to solve quantum mechanical equations, is making these calculations possible, according to Shemella.
"Typically, quantum mechanics has been applied to solid-state problems because the symmetry makes the calculation smaller and easier, but there's really nothing different physically between a carbon atom in a protein and a carbon atom in a nanotube," he said. "Even though a protein is such an asymmetric, complex system, when you really zoom into the quantum mechanical level, they are just atoms. It doesn't matter if strange things are happening; it's still just carbon, nitrogen, hydrogen, and oxygen."
Quantum mechanics allows researchers to do things that can't be done with classical physics, such as modeling the way chemical bonds break and form, or including the effect of proton "tunneling" -- allowing protons to move through energy barriers that normal logic would deem impossible.
For this project, the researchers used computing facilities at Rensselaer's Scientific Computation Research Center (SCOREC) and the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign. In the future, they hope to take advantage of Rensselaer's new Computational Center for Nanotechnology Innovations -- a $100 million partnership between Rensselaer, IBM, and New York state to create one of the world's most powerful university-based supercomputing centers.
The additional computing power will allow them to model complex biological systems with even greater accuracy: "The more atoms you include, the more accurate your system," Shemella said.
Jason Gorss | EurekAlert!
Tangled magnetic fields power cosmic particle accelerators
14.12.2018 | DOE/SLAC National Accelerator Laboratory
In search of missing worlds, Hubble finds a fast evaporating exoplanet
14.12.2018 | NASA/Goddard Space Flight Center
The more objects we make "smart," from watches to entire buildings, the greater the need for these devices to store and retrieve massive amounts of data quickly without consuming too much power.
Millions of new memory cells could be part of a computer chip and provide that speed and energy savings, thanks to the discovery of a previously unobserved...
What if, instead of turning up the thermostat, you could warm up with high-tech, flexible patches sewn into your clothes - while significantly reducing your...
A widely used diabetes medication combined with an antihypertensive drug specifically inhibits tumor growth – this was discovered by researchers from the University of Basel’s Biozentrum two years ago. In a follow-up study, recently published in “Cell Reports”, the scientists report that this drug cocktail induces cancer cell death by switching off their energy supply.
The widely used anti-diabetes drug metformin not only reduces blood sugar but also has an anti-cancer effect. However, the metformin dose commonly used in the...
A research team from the University of Zurich has developed a new drone that can retract its propeller arms in flight and make itself small to fit through narrow gaps and holes. This is particularly useful when searching for victims of natural disasters.
Inspecting a damaged building after an earthquake or during a fire is exactly the kind of job that human rescuers would like drones to do for them. A flying...
Over the last decade, there has been much excitement about the discovery, recognised by the Nobel Prize in Physics only two years ago, that there are two types...
12.12.2018 | Event News
10.12.2018 | Event News
06.12.2018 | Event News
14.12.2018 | Power and Electrical Engineering
14.12.2018 | Physics and Astronomy
14.12.2018 | Physics and Astronomy