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Industry updates: Jun 14
2010

Raising the bar for biomolecular modeling

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Source:EurekAlert

Contact: Leanne
Yohemas
[email-masked]
403-220-5144
University of Calgary

University of Calgary scientists discover 'breakwater' to
help control electron transfer

IMAGE: The paper published in PNAS explores the role of water
molecules (red and white) in forming a bridge (yellow) between proteins
(green and blue) and that certain protein residues (beige)...

Click here for more information.

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."

###

"Surface residues dynamically organize water bridges to enhance electron
transfer between proteins" was published on June 14 in the journal
Proceedings of the National Academy of Sciences (PNAS) by Nathan Babcock
and Aurelien de la Lande, now at the CNRS in France, Jan Rezac, now at the Czech
Academy of Science, Barry Sanders, iCORE Chair of Quantum Information Science
<http://icore.ca/research_quantum.htm>
at U of C and Dennis Salahub, Director of the Institute for Biocomplexity and
Informatics and Professor in the Department of Chemistry.

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