Scientific Publications 2004
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2004. "Hyperdigraph-Theoretic Analysis of the EGFR Signaling Network: Initial Steps Leading to GTP:Ras Complex Formation." Journal of Computational Biology 11(5):812-842. Abstract We construct an algebraic-combinatorial model of the SOS compartment of the EGFR biochemical network. A Petri net is used to construct an initial representation of the biochemical decision-making network, which in turn defines a hyperdigraph. We observe that the linear algebraic structure of each hyperdigraph admits a canonical set of algebraic-combinatorial invariants that correspond to the information flow conservation laws governing a molecular kinetic reaction network. The linear algebraic structure of the hyperdigraph and its sets of invariants can be generalized to define a discrete algebraic-geometric structure, which is referred to as an oriented matroid. Oriented matroids define a polyhedral optimization geometry that is used to determine optimal subpaths that span the nullspace of a set of kinetic chemical reaction equations. Sets of constrained submodular path optimizations on the hyperdigraph are objectively obtained as a spanning tree of minimum cycle paths. This complete set of subcircuits is used to identify the network pinch points and invariant flow subpaths. We demonstrate that this family of minimal circuits also characteristically identifies additional significant biochemical reaction pattern features. We use the SOS Compartment A of the EGFR biochemical pathway to develop and demonstrate the application of our algebraic-combinatorial mathematical modeling methodology.
2004. "Solid-State Ru-99 NMR Spectroscopy: A Useful Tool for Characterizing Prototypal Diamagnetic Ruthenium Compounds." Journal of the American Chemical Society 126(35):10972-10980. Abstract The feasibility of 99Ru NMR spectroscopy as a tool to characterize solid compounds is demonstrated. Results of the first solid-state 99Ru NMR investigation of diamagnetic compounds are presented for Ru(NH3)6Cl2, K4Ru(CN)6 ‚ xH2O (x) 0, 3), LaKRu(CN)6, and Ru3(CO)12. The sensitivity of the ruthenium magnetic shielding tensor to subtle changes in the local structure about the ruthenium nucleus is highlighted by comparing the 99Ru isotropic chemical shift of Ru(NH3)6Cl2 in aqueous solutions and in the solid state. The narrow isotropic 99Ru NMR peak observed for solid Ru(NH3)6Cl2 indicates that this compound is an ideal secondary reference sample for solid-state 99Ru NMR studies.
2004. "NMR Assignments for a Helical 40 kDa Membrane Protein ." Journal of the American Chemical Society 126 (16):5048-5049. Abstract Abstract: Backbone nuclear magnetic resonance (NMR) assignments were achieved for diacylglycerol kinase (DAGK) in detergent micelles. DAGK is a homotrimeric integral membrane protein comprised of 121 residue subunits, each having three transmembrane segments. Assignments were made using TROSY-based pulse sequences. DAGK was found to be an almost exclusively helical protein. This work points to the feasibility of both solving the structure of DAGK using solution NMR methods and using NMR as a primary tool in structural studies of other helical integral membrane proteins of similar size and complexity.
