Structural Biology & Biophysics Program @ Duke University

Faculty research - visual highlights

Dick Brennan: Bacterial multi-drug resistance transcription activator BmrR/DNA/TPP+ complex. The drug changes BmrR conformation, bringing together the ends of the dimers (blue & red) to bind DNA and unwind it, thus positioning the two promoter sites for transcription. PDB 1R8E at 2.4A resolution; J Biol Chem 2004, 279: 20356-62.

Maria Schumacher: Trypanosomal guide-RNA matchmaking protein for large-scale editing of U-bases in the mRNA. T brucei MRP1/MRP2 heterotetramer, with "whirly" TF fold. It binds guide-RNA stem-loop II tightly, but opens out stem-loop I to bind the cognate mRNA sequence. PDBs 2GIA at 1.89A resolution, 2GJE at 3.37A; Cell 2006, 126: 701-11.

Harold Erickson: Model of microtubule organization and assembly/disassembly, showing both protofilaments (vertical) and 3-start helices within the tubule, and inside-out rings curling out from the top end. Subunits in each alpha/beta tubulin dimer are labeled and color-coded. J Cell Biol 1996, 135: 5-8.

Bruce Donald: Computational structure-based redesign of enzyme activity, in the non-ribosomal peptide synthesis system. Uses provably complete search algorithms that generate an ensemble of low-energy structures for the designed sequence changes. PNAS 2009, 106: 3764-9.

Dan Kiehart: Time-course studies of the interacting forces involved in dorsal closure of drosophila embryo, using laser-cut perturbations (blue line), fluorescent labels, mutants, and mathematical analysis of the forces. HFSP J 2008, 4: 220-37.

Seok-Yong Lee: Mapping of co-evolved residues (reddish patches), showing that two separate binding interfaces are required for function of voltage-dependent K+ channels. (A-C are in stereo) PLoS Biol 2009, March 7(3):e1000047.

Jane Richardson: Original hand-drawn ribbon schematic of triose phosphate isomerase. Chosen as Wikipedia picture-of-the-day for Nov. 19 2009. The 1981 Anatomy and Taxonomy of Protein Structures article that introduced ribbon drawings is available on-line at Anatax.

Terry Oas: The calculated folding mechanism through 38 partially folded substates of wild type monomeric lambda repressor. Circles correspond to helices, either folded (white) or unfolded (black) and contacting in either native (red) or non-native pairs. The width of a line between substates corresponds to the relative rate of substate formation. Non-native intermediates occur, and the final step to native is a slow one. PNAS 2009, 106: 13737-41. A related current study assigned NMR spectra of a folding intermediate and measured the flux through alternate pathways of coupled folding and ligand binding for the "intrinsically disordered" RNAse P protein. PNAS 2009, 106: 13737-41.

Terry Oas: apo-RNAse P protein is "intrinsically disordered", however even with small ligands it can become partially ordered, and even fully ordered. The entire protein structure is shown with helicies in gray that are disordered in the intermediate state. The black NMR peaks are from the partially ordered form, the red peaks are those additional that appear for the fully ordered state to compose the entire assigned spectrum.

Dave Richardson: Detailed view and analysis of conformation and interactions at the binding site of the 1U8D G-riboswitch, displayed in KiNG (Protein Sci 2009, 18: 2403-9). Electron density is shown as gray contours, all-atom contact analysis (Acta Cryst 2010, D66: 12-21) is shown with color-coded dot patches, and RNA backbone conformers are labeled with 2-character "suite names" defined in RNA 2008, 14: 465-81.