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Biomolecular Modeling: Scientists = Discover=20 'Breakwater' to Help Control Electron Transfer
ScienceDaily (June 16, 2010) = =E2=80=94 Researchers=20 at the University of Calgary found that amino acid residues form a type = of=20 barrier to help in the process of electron transfer between = proteins.
"This raises the bar for biomolecular modeling," says Dennis Salahub, = U of C=20 co-author of a paper published in the journal Proceedings of the = National=20 Academy of Sciences (PNAS). "At a fundamental level, it is by far = the most=20 detailed insight that has been obtained for the dynamic role of water in = this=20 kind of electron transfer, or for that matter any biochemical = reaction."
Electron transfer between proteins is the cornerstone of biological = energy=20 transfer. Every life-form uses this process to convert food or sunlight = into=20 chemical energy.
The interdisciplinary team of researchers found that the electron = travels=20 over a bridge made of a water molecule, while residues on one of the = proteins=20 form a sort of 'molecular breakwater' to keep other water molecules away = while=20 the electron travels across the bridge.
"You don't want too many (water molecules around the bridge) because = it gets=20 too crowded and they're all bumping into each other and you can't get = one to fit=20 at just the right position and the right angle (for the bridge) for any = length=20 of time," says PhD student and co-author Nathan Babcock. "It's like = being on a=20 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=20 examined a 40 nanosecond period of electronic coupling of the proteins=20 methylamine dehydrogenase and amicyanin from the bacterium = Paracoccus=20 denitrificans.
"This is fundamental research but you can imagine how studies like = this can=20 be applied to various genetically modified organisms, and if you can = gain=20 control over some, you can use it to either speed up or slow down a = particular=20 reaction," says Salahub.
He says the work was made possible with the collaboration of two of = the U of=20 C's interdisciplinary research institutes; the Institute for = Biocomplexity and=20 Informatics (IBI) and the Institute for Quantum Information Science = (IQIS).
Babcock, whose background is in quantum information theory, was = pleased to do=20 research at the union of these two disciplines.
"When you think of quantum mechanics, usually you're thinking solid = state=20 semi conductors, atoms trapped with lasers, etc. It's usually cold = laboratory=20 stuff, not warm globby biological stuff," says the PhD student. "I think = the=20 union of biology and quantum mechanics is very, very exciting."
The study was published on June 14 in the journal Proceedings of = the=20 National Academy of Sciences by Nathan Babcock and Aurelien de la = Lande,=20 now at the CNRS in France, Jan Rezac, now at the Czech Academy of = Science, Barry=20 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.
Story Source:
The above story is reprinted (with editorial adaptations by=20 ScienceDaily staff) from materials provided by University=20 of Calgary, via EurekAlert!, a service of AAAS.
Journal Reference:
Note: If no author is given, the source is cited=20 instead.
![3D""=20](3D"http://www.sciencedaily.com/images/2010/06/100614160203.jpg")
The=20
paper published in PNAS explores the role of water molecules (red and =
white) in=20
forming a bridge (yellow) between proteins (green and blue) and that =
certain=20
protein residues (beige) form a breakwater help the process. (Credit: =
Aurelien=20
de la Lande)
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