|Figure 1: (a) Chemical substructure model representing the possible number of 13C incorporation from 13C6-Glc tracer into UDP-GlcNAc, accounting for the observed FT-ICR-MS isotopologue peaks. (b) Structure of UDP-GlcNAc annotated by its chemical substructures and their biosynthetic pathways from 13C6-Glc, as in Fig. 2. U = uracil, R = ribose, A = acetyl, G=glucose. NAc-Glucose utilizes Gln as the nitrogen donor. (c) Fit of optimized chemical substructure model parameters to FT-ICR-MS isotopologue data of UDP-GlcNAc extracted from a LN3 prostate cancer cell culture after 48 hours of growth in 13C6-Glc.
|Figure 2. A) PCA plot of equine RNAseq datasets. B) Organized groups of enriched GO-terms for PC1. C) STRING interactions between high PC1 loading gene(-product)s annotated with group G1 GO terms (cartilage development).
|Structural bioinformatics of metalloproteins has historically been hampered by significant numbers of aberrant coordination geometries that prevented systematic classification. My lab has developed combined functional and structural analyses of metalloproteins that have identified aberrant clusters of coordination geometries (CG) of metal ion ligation in the top 5 most abundant metalloproteins. Most of these aberrant CGs are due to multidentate ligands that create compressed ligand-metal-ligand angles below 60°. These angles cause serious deviations from canonical CG models and greatly hamper the ability to characterize metalloproteins both structurally and functionally. Our methods detect coordinating ligands without expectations based on canonical CGs and in a statistically robust manner, producing estimated false positive and false negative rates of ~0.11% and ~1.2%, respectively. Also, our improved analyses of bond-length distributions have revealed bond-length modes specific to chemical functional groups involved in multidentation. By recognizing aberrant CGs in our clustering analyses, high correlations above 0.9 are achieved between structural and functional descriptions of metal ion coordination. This work has been impactful to the field by highlighting the unexpected presence of significant numbers of non-canonical CGs and in characterizing their structural, functional, and chemical characteristics. Our publications made the cover of the May 2017 issue of Proteins.