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Raising the bar for biomolecular
modeling

15.06.2010 05:34

category: EDUCATION >
Science

Raising the bar
for biomolecular modeling

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 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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