A team of researchers from Johns Hopkins has received
a five-year $17 million grant under the National Institutes
of Health's Roadmap for Medical Research to develop new
technologies to comprehensively examine proteins'
interactions in systems ranging from yeast to human
cells.
The grant is one of the first two awarded as part of
the NIH's plan to support in-depth study of cells' complex
biological interactions from the perspective of proteins
rather than genes. Many people are by now familiar with
genes, which carry the blueprint for proteins. But as
scientists develop tools to figure out on very large scales
how proteins interact, these workhorses of cells will be
making headlines more often.
"These tools will give us a completely new way of
looking at complex biological processes, allowing us to
actually watch them in action," says NIH Director Elias A.
Zerhouni. "As the centers refine the technologies, these
valuable resources will be made available to hundreds of
investigators across the country who are working in every
disease area."
Leader of the Hopkins project is Jef Boeke, professor
of molecular biology and
genetics and director of the HighThroughput Biology
Center, a brand-new component of the Institute for Basic
Biomedical Sciences at Johns Hopkins. "We're going to
develop several key technologies to look at proteins and
their interactions, to measure proteins' modifications and
see how those change over time," Boeke explains. "In the
request for applications, the NIH said they wanted to
support really new ways of looking at proteins, and we're
certainly doing that."
Boeke himself uses genes to study protein function and
the components of various biological pathways, mostly using
single-celled yeast as an instructive model organism.
Through techniques developed in his laboratory, scientists
can quickly identify pairs of genes that, when missing at
the same time, cause the organism to die. The knowledge
gained from these "synthetic lethal" screens isn't just
genetic, he says.
"The key is that the yeast die because the two genes'
proteins weren't available to interact with one another,"
Boeke says. "From the results of these studies — for which
we use a special type of "barcode" microarrays that
provides a list of yeast mutants present, much like a
supermarket scanner detects your purchases — we can put
together maps of proteins that interact with one another
and then use those maps as a starting point to probe the
interactions."
A simple example might be some critical complex that
is ideally formed by three proteins but that can work well
enough if at least two of the three are present — knock out
two in a synthetic lethal screen, and the organism dies.
But much harder to figure out is the web of proteins that
represent different steps along a number of interacting
biological pathways.
To try to tackle these difficult "big picture"
problems in biology, the team of researchers will develop
technologies in genomics, proteomics, mass spectrometry and
microarray techniques and sort, analyze and process the
information using cutting-edge computational biology. With
colleagues at the Wistar Institute and the University of
Wisconsin, Madison, they'll use the new tools to build maps
of protein networks and clarify how different modifications
of proteins, particularly of histones, affect the proteins'
activities.
In one sense, histone proteins act as scaffolding on
which cells' chromosomes are arranged for compact storage.
But they also play a more active role, helping open
chromosomes at particular times and places so that specific
genes can be "read" and their instructions used to make
proteins. Attaching and removing modifying groups is
thought to be a major controller of histones'
gene-revealing activities, but much about the processes
involved is unknown.
So, in addition to figuring out which proteins
interact with which other proteins, the team will develop
ways to detect the modifications present on proteins such
as histones and to track how they change with time, with
cell function or in response to different triggers — say a
drug or a chemical.
Those efforts will largely rely on advances in mass
spectrometry, which, in general, uses subtle differences in
the proteins' masses to separate and identify them, and
computational biology, which would organize and analyze the
information gained from all these experiments.
"The computational side is very important, and we have
experts on the project who can build pictures of protein
networks and track very complex changes in these networks,
such as changes in the amount of the protein present or
which pathways are active," Boeke says. "But what's been
missing are good tools to see how the proteins themselves
change over time — not just how much is there, but how the
proteins are 'decorated.' We hope to create those
tools."
These "decorations" are small groups of particular
atoms, and their modification of proteins, particularly of
a building block called lysine, is very common. The
research team will be examining lysine because it is
modified by a variety of groups: methyl groups, acetyl
groups, ubiquitin and a molecule called SUMO.
The NIH awarded another grant in the National
Technology Centers for Networks and Pathways program to the
Burnham Institute in California. The research team there
will be developing and applying technologies to determine
the network of genes, proteins and biological signals
responsible for breaking down proteins, a process called
proteolysis.
Technologies developed through the two funded projects
will be useful in future disease research. Improper histone
modification is likely to contribute to diseases like
cancers whose incidence increases as people age. Faulty
proteolysis, the process studied by the California team,
probably contributes to a number of neurologic diseases,
such as Alzheimer's, which are characterized in part by a
buildup of abnormal proteins that then cause cell death.
The NIH Roadmap is a series of far-reaching
initiatives designed to transform the nation's medical
research capabilities and speed the movement of research
discoveries from the bench to the bedside. The TCNP program
is administered by the NIH's National Center for Research
Resources.
Leaders in the Hopkins TCNP project, Networks and
Pathways of Lysine Modification, are Boeke, Heng Zhu, Joel
Bader, Akhilesh Pandey, Bob Cotter, Phil Cole, Patrick
Onyango, Andrew Feinberg, Cecile Pickart, Andre Levchenko
and Jonathan Pevsner, all affiliated with Johns Hopkins;
Shelley Berger, of the Wistar Institute; and Jorge
Escalante-Semerena, of the University of Wisconsin,
Madison.
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