The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin bound RCC1 (regulator of chromosome condensation) protein which recruits Ran to nucleosomes and activates Ran’s nucleotide exchange activity. While RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. We have determined the crystal structure of the RCC1-nucleosome core particle complex at 2.9 Å resolution, providing the first atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in our nucleosomes forms a 145 bp and not the expected canonical 147 bp nucleosome core particle.

The synthesis and reactivity of geometrically constrained tricoordinate phosphorus (σ(3)-P) compounds supported by tridentate triamide chelates (N[o-NR-C6H4]2(3-); R = Me or (i)Pr) are reported. Studies indicate that 2 (P{N[o-NMe-C6H4]2}) adopts a Cs-symmetric structure in the solid state. Variable-temperature NMR studies demonstrate a low-energy inversion at phosphorus in solution (ΔG(‡)(exptl)(298) = 10.7(5) kcal/mol), for which DFT calculations implicate an edge-inversion mechanism via a metastable C2-symmetric intermediate. In terms of reactivity, compound 2 exhibits poor nucleophilicity, but undergoes oxidative addition at ambient temperature of diverse O-H- and N-H-containing compounds (including alcohols, phenols, carboxylic acids, amines, and anilines). The resulting pentacoordinate adducts 2·[H][OR] and 2·[H][NHR] are characterized by multinuclear NMR spectroscopy and X-ray crystallography, and their structures (which span the pseudorotation coordinate between trigonal bipyramidal and square planar) are evaluated in terms of negative hyperconjugation. At elevated temperatures, the oxidative addition is shown to be reversible for volatile alcohols and amines.

Ammonia, alkyl amines, and aryl amines are found to undergo rapid intermolecular N-H oxidative addition to a planar mononuclear σ(3)-phosphorus compound (1). The pentacoordinate phosphorane products (1·[H][NHR]) are structurally robust, permitting full characterization by multinuclear NMR spectroscopy and single-crystal X-ray diffraction. Isothermal titration calorimetry was employed to quantify the enthalpy of the N-H oxidative addition of n-propylamine to 1 ((n)PrNH2 + 1 → 1·[H][NH(n)Pr], ΔHrxn(298) = -10.6 kcal/mol). The kinetics of n-propylamine N-H oxidative addition were monitored by in situ UV absorption spectroscopy and determination of the rate law showed an unusually large molecularity (ν = k[1][(n)PrNH2](3)). Kinetic experiments conducted over the temperature range of 10-70 °C revealed that the reaction rate decreased with increasing temperature. Activation parameters extracted from an Eyring analysis (ΔH(⧧) = -0.8 ± 0.4 kcal/mol, ΔS(⧧) = -72 ± 2 cal/(mol·K)) indicate that the cleavage of strong N-H bonds by 1 is entropy controlled due to a highly ordered, high molecularity transition state. Density functional calculations indicate that a concerted oxidative addition via a classical three-center transition structure is energetically inaccessible. Rather, a stepwise heterolytic pathway is preferred, proceeding by initial amine-assisted N-H heterolysis upon complexation to the electrophilic phosphorus center followed by rate-controlling N → P proton transfer.

We present a fluorogenic method to visualize misfolding and aggregation of a specific protein-of-interest in live cells using structurally modulated fluorescent protein chromophores. Combining photo-physical analysis, X-ray crystallography, and theoretical calculation, we show that fluorescence is triggered by inhibition of twisted-intramolecular charge transfer of these fluorophores in the rigid microenvironment of viscous solvent or protein aggregates. Bioorthogonal conjugation of the fluorophore to Halo-tag fused protein-of-interests allows for fluorogenic detection of both misfolded and aggregated species in live cells. Unlike other methods, our method is capable of detecting previously invisible misfolded soluble proteins. This work provides the first application of fluorescent protein chromophores to detect protein conformational collapse in live cells.

A Crystallogral structure is described for the Mg2+-BeF3--bound receiver domain of Sinorhizobium meliloti DctD bearing amino acid substitution E121K. Differences between the apo- and ligand-bound active sites are similar to those reported for other receiver domains. However, the off and on states of the DctD receiver domain are characterized by dramatically different dimeric structures, which supports the following hypothesis of signal transduction. In the off state, the receiver domain and coiled-coil linker form a dimer that inhibits oligomerization of the AAA+ ATPase domain. In this conformation, the receiver domain cannot be phosphorylated or bind Mg2+ and BeF3-. Instead, these modifications stabilize an alternative dimeric conformation that repositions the subunits by approximately 20 A, thus replacing the a4-b5-a5 interface with an a4-b5 interface. Reoriented receiver domains permit the ATPase domain to oligomerize and stimulate open complex formation by the s54 form of RNA polymerase. NtrC, which shares 38% sequence identity with DctD, works differently. Its activated receiver domain must facilitate oligomerization of its ATPase domain. Significant differences exist in the signaling surfaces of the DctD and NtrC receiver domains that may help explain how triggering the common two-component switch can variously regulate assembly of a AAA+ ATPase domain.