By simulating complex protein and polynucleotide structures on a
supercomputer, a Wesleyan professor has been able to study one the
fundamental events that lead to gene expression in biological systems.
David Beveridge, University Professor of the Natural Sciences and
Mathematics, professor of chemistry, has spent the past 20 years studying
various aspects of the structures, molecular motions and binding properties
of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) using theoretical
methods. DNA and RNA are informational macromolecules that control the
composition of proteins necessary to life structures and processes.
Beveridge recently received a $241,950 Academic Research Enhancement Award
from the National Institute of General Medical Sciences to continue his
project "Theoretical and Molecular Dynamics Simulation Studies of U1A-RNA
Binding and Specificity.” U1A is an important human protein that interacts
“Biological processes involved in gene expression are all controlled by
protein-DNA and protein- RNA interactions,” Beveridge explains. “We study
the nature of these interactions at the molecular level, and how the
molecules involved recognize each other with such high fidelity.”
An understanding of how RNA-protein complexes form and are stabilized is
important for understanding the splicing out of stretches of DNA.
Molecular dynamics simulations in this project were motivated by questions
posed in experiments performed by Anne Baranger, associate professor of
chemistry; and they have been collaborating on protein RNA projects for
several years. Bethany Kormos, who is supported by a National
Institutes of Health postdoctoral fellowship, and Surjit Dixit, senior
research associate, are key coworkers on this project and “really do the
work,” Beveridge says.
“David has been a fantastic colleague to collaborate with because he is
particularly talented at developing projects that aim to investigate and
understand fundamental important problems in his field,” Baranger explains.
“It has been valuable to me as an experimentalist to work with a person who
has developed theoretical methods to answer questions that are difficult to
To progress in his research, Beveridge and his colleagues study the factors
contributing to the stability of RNA-protein complexes with a particular
emphasis on “dynamical structure,” the nature and significance of molecular
motions involved in the complex formation.
Molecular simulations of this type are quite computationally intensive. The
Beveridge group carries out their calculations with high performance
computers at the National Center for Supercomputer Applications (NCSA) at
the University of Illinois. The communication between Wesleyan and NCSA to
run simulations involves over the Internet.
The results of a simulation are returned to laboratories
at Wesleyan over the Internet and are analyzed locally for these properties
using advanced computer graphics work stations.
“Remote access to national supercomputer facilities enables cutting edge
research in this field from even a small university vantage point, makes it
possible simulate model systems quite close to those involved in
experiments,” Beveridge says. “We can computer model systems closer to
laboratory conditions than I ever dreamed of 40 years ago.”
Beveridge grew up in the “Sputnik Era” and found the launching of the Soviet
space satellite as an incentive to study science. He received his bachelor’s
degree in chemistry from the College of Wooster in Wooster, Ohio in 1959 and
his Ph.D in physical chemistry from the University of Cincinnati in 1965.
Under a postdoctoral fellowship from the National Institutes of Health, he
studied molecular quantum mechanics at the Centre de Mécanique Ondulatoire
Appliquée in Paris, and continued his postdoctoral studies in quantum
chemistry at Carnegie-Mellon University with Professor J.A. Pople, a Nobel
In addition to research and teaching, Beveridge serves as Wesleyan’s
co-director with Ishita Mukerji of the NIH-supported graduate training
program and the undergraduate certificate in molecular biophysics.
“David is certainly one of the department’s most successful scientists,”
says Mukerji, chair of the Molecular Biology and Biochemistry Department and
associate professor of molecular biology and biochemistry. "He has brought much recognition to the department and to the Molecular Biophysics program."
Beveridge has served Wesleyan as Dean of
Natural Science and Mathematics for seven years and currently holds the
title of University Professor of the Natural Science and Mathematics.
Beveridge has overseen a number of undergraduate research projects at
Wesleyan, and has mentored both bachelor's, master's and Ph.D students in
their dissertation research. Recent master's graduates include Duk Blakaj
‘99, now a medical doctor/Ph.D student at Einstein Medical School, and Laura
Vickers ’05, who is currently a medical doctor student at Mount Sinai School
of Medicine. Matthew Young ’92, who initially worked with Beveridge as an
undergraduate and continued on to get a Ph.D, has just been appointed to the
faculty of the University of Michigan’s Medical School as an assistant
professor of biological chemistry and bioinformatics. Five former research
students now hold positions as college or university professors – “my
greatest achievement,” Beveridge says.
By Olivia Bartlett,
Wesleyan Connection editor
Professor Looks for Similarities in
Six years ago, David Beveridge
began combining teaching and personal interests in the visual arts with
Along with Mariah Klaneski ’04, he developed two classes,
Science and Modernism and more recently, Science and Art. In Science and
Art, interested students, even those with no particular science background,
learn basic concepts in class and in the associated laboratory make paper
and fresco, synthesize their own pigments using chemical reactions, make
paint of various types, and use all their own materials to make original
works of art.
“An ultimate experience in learning by doing,” Beveridge says.
Beveridge’s teaching at Wesleyan now ranges from topics in physical
chemistry applied to biological systems to general education courses. His
currently active courses at Wesleyan in addition to those mentioned above
are Molecular Biophysics, and Macromolecular Modeling and Simulation.
Beveridge has more than a passing interest in the visual arts and has taken
“a dozen or so” drawing, painting and photography courses offered by
Wesleyan’s Graduate Liberal Studies Program and elsewhere. He is curious
about the parallels between the arts and the sciences.
“Both are very experimental in a sense, but make use of images in very
different ways,” Beveridge explains. "It is interesting to investigate the
extent to which viewer response to art follows natural laws analogous to
those of science, and where the similarities and differences in creative
process occur between scientists and artists."
Wesleyan has given Beveridge the chance to be involved in a wide
range of academic initiatives, both within the sciences and in other areas
of the university.
"I’m pretty much a compulsive learner, and Wesleyan
accommodates my natural instinct to be a ‘perpetual student,'" he says.