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Raising the bar for
biomolecular modeling

Published: Monday, June 14, 2010 - 14:34 in Physics &
Chemistry

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Aurelien de la Lande

Researchers at the University of Calgary found that amino acid residues form
a type of barrier to help in the process of electron transfer between proteins.
"This raises the bar for biomolecular modeling," says Dennis Salahub, U of C
co-author of a paper published today in the prestigious journal Proceedings
of the National Academy of Sciences (PNAS). "At a fundamental level, it is
by far the most detailed insight that has been obtained for the dynamic role of
water in this kind of electron transfer, or for that matter any biochemical
reaction."

Electron transfer between proteins is the cornerstone of biological energy
transfer. Every life-form uses this process to convert food or sunlight into
chemical energy.

The interdisciplinary team of researchers found that the electron travels
over a bridge made of a water molecule, while residues on one of the proteins
form a sort of 'molecular breakwater' to keep other water molecules away while
the electron travels across the bridge.

"You don't want too many (water molecules around the bridge) because it gets
too crowded and they're all bumping into each other and you can't get one to fit
at just the right position and the right angle (for the bridge) for any length
of time," says PhD student and co-author Nathan Babcock. "It's like being on a
crowded subway where you can't get comfortable."

In artificial mutations with a faulty breakwater, the water bridge is
disrupted and the rate of electron transfer is markedly reduced, he says.

Using the CHARMM molecular simulation computer program, the research team
examined a 40 nanosecond period of electronic coupling of the proteins
methylamine dehydrogenase and amicyanin from the bacterium Paracoccus
denitrificans.

"This is fundamental research but you can imagine how studies like this can
be applied to various genetically modified organisms, and if you can gain
control over some, you can use it to either speed up or slow down a particular
reaction," says Salahub.

He says the work was made possible with the collaboration of two of the U of
C's interdisciplinary research institutes; the Institute for Biocomplexity and
Informatics (IBI) and the Institute for Quantum Information Science (IQIS).

Babcock, whose background is in quantum information theory, was pleased to do
research at the union of these two disciplines.

"When you think of quantum mechanics, usually you're thinking solid state
semi conductors, atoms trapped with lasers, etc. It's usually cold laboratory
stuff, not warm globby biological stuff," says the PhD student. "I think the
union of biology and quantum mechanics is very, very exciting."

Source: University of Calgary

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Other sources

Biomolecular
modeling: Scientists discover 'breakwater' to help control electron
transfer

from Science Daily

Wed, 16 Jun 2010, 1:40:50 EDT

Raising
the bar for biomolecular modelling

from Science Centric

Tue, 15 Jun 2010, 0:40:16 EDT

Raising
the bar for biomolecular modeling

from Physorg

Mon, 14 Jun 2010, 15:32:35
EDT

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