All living things require proteins, members of a vast family
of molecules that nature "makes to order" according to the blueprints
in DNA. Through the natural process of evolution, DNA mutations generate new or
more effective proteins.
Humans have found so many alternative uses for these
molecules - as foods, industrial enzymes, anti-cancer drugs - that scientists
are eager to better understand how to engineer protein variants designed for
specific uses.
Now Stanford engineers have invented a technique to
dramatically accelerate protein evolution for this purpose. This technology,
described in Nature Chemical Biology, allows researchers to test millions of
variants of a given protein, choose the best for some task and determine the
DNA sequence that creates this variant.
"Evolution, the survival of the fittest, takes place
over a span of thousands of years, but we can now direct proteins to evolve in
hours or days," said Jennifer Cochran, a professor of bioengineering who
co-authored the paper with Thomas Baer, director of the Stanford Photonics
Research Center.
"This is a
practical, versatile system with broad applications that researchers will find
easy to use," Baer said.
By combining Cochran's protein engineering
knowhow with Baer's expertise in laser-based instrumentation, the team created
a tool that can test millions of protein variants in a matter of hours.
"The demonstrations are impressive and I look forward
to seeing this technology more widely adopted," said Frances Arnold, a
professor of chemical engineering at Caltech who was not affiliated with the
study. Making a million mutants The researchers call their tool µSCALE, or
Single Cell Analysis and Laser Extraction.
The "µ" stands for the microcapillary glass slide
that holds the protein samples. The slide is roughly the size and thickness of
a penny, yet in that space a million capillary tubes are arrayed like straws,
open on the top and bottom.
1 / 3 The microcapillary glass slide that holds the protein
samples is roughly the size and thickness of a penny, yet in that space a
million capillary tubes are arrayed like straws. Credit: Cochran Lab, Stanford
The power of µSCALE is how it enables researchers to build upon current
biochemical techniques to run a million protein experiments simultaneously,
then extract and further analyze the most promising results.
The researchers first employ a process termed
"mutagenesis" to create random variations in a specific gene. These
mutations are inserted into batches of yeast or bacterial cells, which express
the altered gene and produce millions of random protein variants. A µSCALE user
mixes millions of tiny opaque glass beads into a sample containing millions of
yeast or bacteria and spreads the mixture on a microcapillary slide.
Tiny amounts of fluid trickle into each tube, carrying
individual cells. Surface tension traps the liquid and the cell in each
capillary. The slide bearing these million yeast or bacteria, and the protein
variants they produce, is inserted into the µSCALE device. A
software-controlled microscope peers into each capillary and takes images of
the biochemical reaction occurring therein. Once a µSCALE user identifies a
capillary of interest, the researcher can direct the laser to extract the
contents of that tube without disrupting its neighbors, using an ingenious
method devised by Baer. "The beads are what enable extraction," Baer
said.
"The laser supplies energy to move the beads, which
breaks the surface tension and releases the sample from the capillary."
Thus µSCALE empties the contents of a single capillary onto a collector plate,
where the DNA of the isolated cell can be sequenced and the gene variant
responsible for the protein of interest can be identified.
More information: http://phys.org/news/2015-12-protein-evolution.html
