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QUANTUM BIOLOGY

Powerful Computer Models Reveal Key Biological Mechanism

Powerful Computer Models Reveal Key Biological Mechanism

Intein crystal prior to protein splicing
Using powerful computers to model the intricate dance of atoms and molecules, Rensselaer researchers have revealed the mechanism behind an important biological reaction. 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.

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.

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 Philip Shemella, a doctoral student in physics at Rensselaer and corresponding author of the current paper.

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.

The research was funded by a grant from the National Science Foundation to Georges Belfort — principal investigator for the project and the Russell Sage Professor of Chemical and Biological Engineering at Rensselaer — and a grant from the National Institutes of Health to Marlene Belfort at the Wadsworth Center.

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