Dartmouth College Office of Public Affairs • Press
Release Posted 06/23/04 • Contact Sue Knapp (603)
646-3661
Bruce Donald
|
The field of structural genomics - the study of the
three-dimensional geometric structures of proteins - is
complicated by vast amounts of data, expensive experiments and
cumbersome methods of analysis. Computer Science
Professor Bruce
Randall Donald and his students are working to ease this
burden by developing techniques that simultaneously minimize
the number of experiments and accelerate the data analysis
involved in determining the structure of proteins.
Learning about protein structure is especially relevant for
treating illnesses that alter protein function, such as
cancer.
Published in consecutive months of the Journal of
Biomolecular NMR (nuclear magnetic resonance), Donald, a
graduate student and a post-doctoral fellow present new
algorithms that interpret NMR data to reveal a protein's shape
and molecular architecture. NMR surveys a protein's molecular
structure and uses tiny, spectroscopic protractors and rulers
to generate a network of geometric measurements.
"In these papers, we discuss a new framework for thinking
about how to solve these problems, and our algorithms are
highly accurate," says Donald, the Joan P. and Edward J. Foley
Jr. 1933 Professor of Computer Science and an Adjunct
Professor of Chemistry and of Biological
Sciences.
The first paper, published in June 2004, explains the work
of Christopher
Langmead, a doctoral student in Donald's laboratory who is
now an assistant professor of computer science at Carnegie
Mellon University. Langmead's algorithm introduced new
techniques for assigning NMR measurements to specific
molecular bonds. Most NMR experiments measure a protein,
reporting distances between molecules and angles of chemical
bonds, but the data doesn't indicate which atoms or bonds the
measurements correspond to. "It's a little like taking all the
heights and weights of everyone at a cocktail party, but you
don't know which height goes with which person," says Donald.
Langmead's and Donald's technique assigns the measurements to
the correct nuclei, which helps to unveil the architecture of
the protein.
Lincong Wang
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A second paper by Donald and Lincong Wang, a Dartmouth
post-doctoral fellow, will be published in July 2004. This
paper describes a new protein structure determination
algorithm, which solves complex algebraic equations that
relate the experimental data to the protein's geometry. "Our
algorithm requires less data and yet the resulting protein
structures are incredibly accurate," says Donald. Unlike
previous techniques, Wang's equations can be solved exactly in
a manner similar to solving the quadratic equation of high
school algebra fame. Wang and Donald hope that their work
proves helpful to both structural genomics researchers as well
as to those in the broader structural biology field.
Research in Donald's laboratory is supported by the National Institutes of Health
and the National Science
Foundation. |