Craig John Benham
Position: Professor
Year joining UC Davis: 2000
Degree: Ph.D., 1972, Princeton University
Refereed publications: Via
Math Reviews
Recent publications: Via
math arXiv
Professor Craig Benham studies the relationship between
structure and function in macromolecules such as DNA and proteins.
He has an unusually strong interdisciplinary perspective,
and has joint appointments at the Departments of Mathematics,
Bioengineering, and the Center for Bioinformatics.
For example, he has developed statistical mechanical methods for the
analysis of superhelical DNA duplex destabilization. The predictions of
this analysis are in precise agreement with experimental results
regarding the location and extent of strand separation in DNA
sequences. This quantitative accuracy allows these methods to be
applied to other sequences, on which experiments have not yet been
performed.
He has also investigated the topological properties of protein
structures and their functional and evolutionary correlates. The
topological properties of greatest interest are the patterns of loops
created by disulphide bonds or beta sheet associations, and the
knot types of the protein backbone. Benham has enumerated
the number of possible topologies that can arise, studied which of these
posiblities are realized in known protein structures, and examined
the functional and evolutionary relationships between proteins with
identical or similar topologies.
Professor Benham has an AB degree in mathematics from Swarthmore College
and a Ph.D. in mathematics from Princeton University, where he worked
in complex manifold theory. As an assistant professor at the University
of Notre Dame he encountered Dr. John Kozak, a theoretical chemist
working on protein structure problems. He became interested in the
field because many of the important problems had significant
mathematical components. "To get additional training in the area of
molecular structure," he recalls, "I spent a year as a postdoc with Dr.
Max Delbruck in the Biology Division at the California Institute of
Technology. There I switched my interests to DNA, primarily because the
mathematical problems relating to DNA structure involved an intricate
interplay among topology, geometry, and mechanics. I have been working
in this field ever since."
Selected publications
[1] Benham, C.J. Sites of predicted stress-induced DNA duplex
destabilization occur preferentially at regulatory loci. Proc. Natal.
Acad. Sci. USA. 90:2999-3003, 1993.
[2] Bauer, W.R., and Benham, C.J. The free energy, enthalpy and entropy of
native and of partially denatured closed circular DNA. J. Mol. Biol.
234:1184-1196, 1993.
[3] Benham, C.J., and Jafri, M.S. Disulfide bonding patterns and protein
topologies. Protein Science 2:41-54, 1993.
[4] Bauer, W.R., Ohtsubo, H., Ohtsubo, E. and Benham, C.J. Energetics of
coupled twist and writhe changes in closed circular pSM1 DNA. J. Mol.
Biol. 253: 438-452, 1995.
[5] Sun, H.-Z., Mezei, M., Fye, R. and Benham, C.J. Monte Carlo analysis of
conformational transitions in superhelical DNA. J. Chem. Phys.
103:8653-8665, 1995.
[6] Benham, C.J. Duplex destabilization in superhelical DNA is predicted to
occur at specific transcriptional regulatory regions. J. Mol. Biol.
255: 425-434, 1996.
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