Engineering Commons^™

Structures Of Human Thymidylate Synthase R163k With Dump, Fdump And Glutathione Show Asymmetric Ligand Binding, Lydia M. Gibson, Lesa R. Celeste, Leslie L. Lovelace, Lukasz Lebioda

Faculty Publications

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that …

Genome3d: A Viewer-Model Framework For Integrating And Visualizing Multi-Scale Epigenomic Information Within A Three-Dimensional Genome, Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng

Faculty Publications

Background
New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

Results
We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …