Physical Sciences and Mathematics Commons^™

Evidence For A Bind-Then-Bend Mechanism For Architectural Dna Binding Protein Ynhp6a, Manas Kumar Sarangi, Viktoriya Zvoda, Molly Nelson Holte, Nicole A. Becker, Justin Peters, L. James Maher Iii, Anjum Ansari

Faculty Publications

The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60◦. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18- base-pair DNA oligomer …

Calculating Heat Of Formation Values Of Energetic Compounds: A Comparative Study, Michael S. Elioff, Jordon Hoy, John A. Bumpus

Faculty Publications

Heat of formation is one of several important parameters used to assess the performance of energetic compounds. We evaluated the ability of six different methods to accurately calculate gas-phase heat of formation (Δ _𝑓𝐻^𝑜 _298,g) values for a test set of 45 nitrogencontaining energetic compounds. Density functional theory coupled with the use of isodesmic or other balanced equations yielded calculated results in which 82% (37 of 45) of the Δ _𝑓𝐻^𝑜 _298,g values were within ±2.0 kcal/mol of the most recently recommended experimental/reference values available. This was compared to a procedure using density functional theory …

A Meta Analysis Of Pancreatic Microarray Datasets Yields New Targets As Cancer Genes And Biomarkers, Nalin C. W. Goonesekere, Xiaosheng Wang, Lindsey Ludwig, Chittibabu Guda

Faculty Publications

The lack of specific symptoms at early tumor stages, together with a high biological aggressiveness of the tumor contribute to the high mortality rate for pancreatic cancer (PC), which has a five year survival rate of less than 5%. Improved screening for earlier diagnosis, through the detection of diagnostic and prognostic biomarkers provides the best hope of increasing the rate of curatively resectable carcinomas. Though many serum markers have been reported to be elevated in patients with PC, so far, most of these markers have not been implemented into clinical routine due to low sensitivity or specificity. In this study, …

Mining Functional Subgraphs From Cancer Protein-Protein Interaction Networks, Ru Shen, Nalin Goonesekere, Chittibabu Guda

Faculty Publications

Background: Protein-protein interaction (PPI) networks carry vital information about proteins’ functions. Analysis of PPI networks associated with specific disease systems including cancer helps us in the understanding of the complex biology of diseases. Specifically, identification of similar and frequently occurring patterns (network motifs) across PPI networks will provide useful clues to better understand the biology of the diseases.

Results: In this study, we developed a novel pattern-mining algorithm that detects cancer associated functional subgraphs occurring in multiple cancer PPI networks. We constructed nine cancer PPI networks using differentially expressed genes from the Oncomine dataset. From these networks we …