Large macromolecular assemblies involving multiple proteins and genomic DNA are important themes in biological mechanism and regulation in all organisms. An integral aspect of many systems involved in genetic recombination, gene expression, DNA replication, and DNA repair is that proteins bound at different locations along a single DNA molecule interact through looping and wrapping of the bound DNA. Understanding the detailed structure and interactions of these large assemblies poses a major challenge to structural biologists because the intact protein-DNA complexes are too large for high-resolution techniques such as x-ray crystallography or NMR. Other techniques such as single-molecule experiments require at least a low-resolution model of the complex for their interpretation. Tangle analysis, a branch of mathematical knot theory, in conjunction with difference-topology experiments has become a powerful emerging approach for the analysis of looped nucleoprotein assemblies both in vitro and in vivo. At present, tangle analysis provides only two-dimensional information in the form of solutions to topological equations; moreover, the solutions to many problems of interest are often not unique. Knowledge of the relative energies of tangle solutions is essential in order to evaluate the physical and biological plausibility of a particular structural model. Tangle analysis will be fused with semi-analytical and numerical calculations of DNA-loop free energies to develop a theoretical description of the structure of complex nucleoprotein assemblies. These new methods will be implemented in the computer program KnotPlot, a powerful and extensible multi-platform tool for visualizing and manipulating physical knots.

Insights into the structures of looped protein-DNA assemblies are crucial for developing new molecular strategies for treating cancer, understanding the immune system, and ameliorating the biological effects of aging. These insights can be gained from knowledge of the geometry and energetics of DNA bound by multiple protein molecules and are critical for understanding underlying principles of biological mechanism and regulation. The importance of DNA looping in living cells is underscored by an abundance of accessory proteins that facilitate looping by effectively altering the mechanical properties of DNA. The team will apply a mathematical and computational approach along with novel biophysical techniques to elucidate the relationship between biological structure and mechanism in Mu transposition, a model system for retroviral integrases such as that of human immunodeficiency virus (HIV). Because these methods can be applied both in living cells as well as in solution, it is possible to investigate the role of the intracellular or intranuclear environment and intrinsic levels of DNA-bending accessory proteins, in regulating loop-mediated protein-DNA interactions. These insights will advance our understanding of biological regulatory networks and pathways, which will have direct benefit to multiple areas of molecular medicine.

Agency
National Science Foundation (NSF)
Institute
Division of Mathematical Sciences (DMS)
Application #
0800929
Program Officer
Junping Wang
Project Start
Project End
Budget Start
2008-08-15
Budget End
2014-07-31
Support Year
Fiscal Year
2008
Total Cost
$1,363,633
Indirect Cost
Name
University of Texas at Dallas
Department
Type
DUNS #
City
Richardson
State
TX
Country
United States
Zip Code
75080