Beta-peptides

Ribbon diagram representations of a beta-peptide bundle illustrating packing between helices and within the hydrophobic (green) core.
(Credit: Schepartz/Yale)

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Chemists at Yale have done what Mother Nature chose not to -- make a protein-like molecule out of non-natural building blocks, according to a report featured early online in the Journal of the American Chemical Society.

Nature uses alpha-amino acid building blocks to assemble the proteins that make life as we know it possible. Chemists at Yale now report evidence that nature could have used a different building block -- beta-amino acids -- and show that peptides assembled from beta-amino acids can fold into structures much like natural protein.

The ability to mimic natural proteins makes beta-peptides powerful new tools for basic research and drug discovery. Like a taped recording, their greatest value may be in their difference from a live performance.

Natural proteins are composed of linear chains of alpha-amino acids. Beta-peptides are composed of beta-amino acids, which have an extra carbon in their backbone. Like alpha-amino acids, beta-amino acids are generated under simulated pre-biotic conditions, are isolated from meteorites, and are byproducts of metabolism, but they are not genetically encoded like natural proteins, nor are they built into chains by cells.

Citation: J. American Chemical Society, ASAP Article DOI:10.1021/ja068678n 19/01/07
More From: Science Daily releases 6/02/07
Nature Could Have Used Different Protein Building Blocks, Chemists Show
Man-made Proteins from the Howard Hughes Medical Institute
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Electrons Travel Through Proteins Like Urban Commuters
Electron movements through certain "electron-transfer" proteins that lie at the heart of many processes essential for life. Such processes include harvesting light in photosynthesis in plant cells and generating energy in animal cells.

"I think we have discovered the physical framework for thinking about all such protein electron-transfer chemistry," said David Beratan of Duke University. "Having this rule book in place will let scientists pose some hard but interesting questions about evolutionary pressures on protein structures.

"Another payoff may be new insight for designing biologically based artificial systems that, for instance, can capture solar energy or make fertilizer from air," he added.

For more than 50 years, theoreticians have been pondering the most likely itineraries that electrons follow through electron-transfer proteins. These proteins are believed to shuttle electrons around, one at a time, but not to do any chemistry that involves the forming or breaking of chemical bonds.

Earlier theoretical work from Beratan's group indicated that electrons can take short cuts through the proteins by following the spooky guidelines of quantum mechanics.

That means the electrons may sometimes leak from one chemical bond to a neighboring bond, he said. They also can take forbidden walks on the wild side by tunneling through open space.

Those findings prompted scientists to conjecture that electron-transfer proteins actually evolved their shapes to allow electrons the option of using quantum rules in negotiating molecular folds and crevices. The possibilities of such quirky routing options have vastly increased the challenge for theoreticians such as Beratan.

Using ever larger networks of computers to calculate the most favorable routes of electron travel, Beratan and his colleagues analyze these proteins in much the same way that commuters pore over transportation maps to plot the fastest destination routes.

Read more from Science Daily release 05/02/07
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