Kenneth C. Littrell

Pressure-Jump Small-Angle X-Ray Scattering Detected Kinetics of Staphylococcal Nuclease Folding

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique.

Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed.

The thermodynamic origin of the stability of a thermophilic ribozyme

Understanding the mechanism of thermodynamic stability of an RNA structure has significant implications for the function and design of RNA. We investigated the equilibrium folding of a thermophilic ribozyme and its mesophilic homologue by using hydroxyl radical protection, small-angle x-ray scattering, and circular dichroism. Both RNAs require Mg2+ to fold to their native structures that are very similar. The stability is measured as a function of Mg2+ and urea concentrations at different temperatures. The enhanced stability of the thermophilic ribozyme primarily is derived from a tremendous increase in the amount of structure formed in the ultimate folding transition. This increase in structure formation and cooperativity arises because the penultimate and the ultimate folding transitions in the mesophilic ribozyme become linked into a single transition in the folding of the thermophilic ribozyme. Therefore, the starting point, or reference state, for the transition to the native, functional thermophilic ribozyme is significantly less structured. The shift in the reference state, and the resulting increase in folding cooperativity, is likely due to the stabilization of selected native interactions that only form in the ultimate transition. This mechanism of using a less structured intermediate and increased cooperativity to achieve higher functional stability for tertiary RNAs is fundamentally different from that commonly proposed to explain the increased stability of thermophilic proteins.

Structural Studies of Bleached Melanin by Synchrotron Small-angle X-ray Scattering¶

Abstract Small-angle X-ray scattering was used to measure the effects of chemical bleaching on the size and morphology of tyrosine-derived synthetic melanin dispersed in aqueous media. The average size as measured by the radius of gyration of the melanin particles in solution, at neutral to mildly basic pH, decreases from 16.5 to 12.5 Å with increased bleaching. The melanin particles exhibit scattering characteristic of sheet-like structures with a thickness of approximately 11 Å at all but the highest levels of bleaching. The scattering data are well described by the form factor for scattering from a pancake-like circular cylinder. These data are consistent with the hypothesis that unbleached melanin, at neutral to mildly basic pH, is a planar aggregate of 6- to 10-nm-sized melanin protomolecules, hydrogen bonded through their quinone and phenolic perimeters. The observed decrease in melanin particle size with increased bleaching is interpreted as evidence for deaggregation, most probably the result of oxidative disruption of hydrogen bonds and an increase in the number of charged, carboxylic acid groups, whereby the melanin aggregates disassociate into units composed of decreasing numbers of protomolecules.

The Bio-SANS instrument at the High Flux Isotope Reactor of Oak Ridge National Laboratory

Small-angle neutron scattering (SANS) is a powerful tool for characterizing complex disordered materials, including biological materials. The Bio-SANS instrument of the High Flux Isotope Reactor of Oak Ridge National Laboratory (ORNL) is a high-flux low-background SANS instrument that is, uniquely among SANS instruments, dedicated to serving the needs of the structural biology and biomaterials communities as an open-access user facility. Here, the technical specifications and performance of the Bio-SANS are presented. Sample environments developed to address the needs of the user program of the instrument are also presented. Further, the isotopic labeling and sample preparation capabilities available in the Bio-Deuteration Laboratory for users of the Bio-SANS and other neutron scattering instruments at ORNL are described. Finally, a brief survey of research performed using the Bio-SANS is presented, which demonstrates the breadth of the research that the instruments user community engages in.

Solvent quality-induced nucleation and growth of parallelepiped nanorods in dilute poly(3-hexylthiophene) (P3HT) solution and the impact on the crystalline morphology of solution-cast thin film

Understanding the chain conformation of conjugated polymers in casting solutions and its impact on the crystalline morphology of solution-cast thin films is crucial for many electronic applications. Using small-angle neutron scattering, we show that well-dissolved poly(3-hexyl thiophene) (P3HT) chains in good solvent (chloroform) form long rectangular parallelepipeds (RPs) via nucleation and growth processes upon increasing the volume fraction of poor solvent (hexane) above a certain critical point. The growth of the RPs is due to the π–π stacking of the P3HT main backbone occurring along the long axis of the RPs. P3HT solutions prepared with different poor solvent volume fractions were drop-cast onto Si-wafers to prepare thin films, which were examined using 2D grazing-incidence X-ray scattering and 1D X-ray diffraction. The results indicate that the RPs grown in solution preferentially orient on the substrate with their two longer axes parallel to the surface after solvent evaporation, and give rise to much improved crystallinity and crystal orientation compared to the disordered chains.

Formation of kinetically trapped nanoscopic unilamellar vesicles from metastable nanodiscs.

Zwitterionic long-chain lipids (e.g., dimyristoyl phosphatidylcholine, DMPC) spontaneously form onion-like, thermodynamically stable structures in aqueous solutions (commonly known as multilamellar vesicles, or MLVs). It has also been reported that the addition of zwitterionic short-chain (i.e., dihexanoyl phosphatidylcholine, DHPC) and charged long-chain (i.e., dimyristoyl phosphatidylglycerol, DMPG) lipids to zwitterionic long-chain lipid solutions results in the formation of unilamellar vesicles (ULVs). Here, we report a kinetic study on lipid mixtures composed of DMPC, DHPC, and DMPG. Two membrane charge densities (i.e., [DMPG]/[DMPC] = 0.01 and 0.001) and two solution salinities (i.e., [NaCl] = 0 and 0.2 M) are investigated. Upon dilution of the high-concentration samples at 50 °C, thermodynamically stable MLVs are formed, in the case of both weakly charged and high salinity solution mixtures, implying that the electrostatic interactions between bilayers are insufficient to cause MLVs to unbind. Importantly, in the case of these samples small angle neutron scattering (SANS) data show that, initially, nanodiscs (also known as bicelles) or bilayered ribbons form at low temperatures (i.e., 10 °C), but transform into uniform size, nanoscopic ULVs after incubation at 10 °C for 20 h, indicating that the nanodisc is a metastable structure. The instability of nanodiscs may be attributed to low membrane rigidity due to a reduced charge density and high salinity. Moreover, the uniform-sized ULVs persist even after being heated to 50 °C, where thermodynamically stable MLVs are observed. This result clearly demonstrates that these ULVs are kinetically trapped, and that the mechanical properties (e.g., bending rigidity) of 10 °C nanodiscs favor the formation of nanoscopic ULVs over that of MLVs. From a practical point of view, this method of forming uniform-sized ULVs may lend itself to their mass production, thus making them economically feasible for medical applications that depend on monodisperse lipid-based systems for therapeutic and diagnostic purposes.

Self-organization of OPV-PEG diblock copolymers in THF/water

Oligo(phenylenevinylene)-poly(ethyleneglycol) (OPV-PEG) diblock copolymers in tetrahydrofuran (THF) solution at concentrations of 5 to 25 gl self-assemble into rod-like structures with a radius of about 80 {angstrom} for an OPV-PEG diblock copolymer comprising 13 PV and 45 EG monomers. These aggregates consist of a liquid crystalline OPV core and a PEG shell. Addition of about 10% water to the solution induces the formation of a phase of packed rods, as revealed by a sudden and dramatic transition of the scattering pattern. Further addition of water leads to swelling and at about 30% ultimately to disruption of the packed-rod phase.

Small-angle neutron scattering study of shearing effects on drag-reducing surfactant solutions

Drag-reducing surfactant solutions are very sensitive to shear. Shear can induce nanostructural transitions which affect drag reduction effectiveness and rheological properties. Literature reports on the effects of shear on different micellar solutions are inconsistent. In this paper, the effects of shear on three cationic drag-reducing surfactant solutions each with very different nanostructures and rheological behaviors, Arquad 16-50/sodium salicylate (NaSal) (5 mM/5 mM) (has thread-like micelles, shear-induced structure and large first normal stress (N(1))), Arquad S-50/NaSal (5 mM/12.5 mM) (has branched micelles, no shear-induced structure and first normal stress is about zero) and Arquad 16-50/sodium 3,4-dimethyl-benzoate (5 mM/5 mM) (has vesicles and thread-like micelles, shear-induced structure and high first normal stress (N(1))) are studied by small-angle neutron scattering (SANS), together with their rheological properties, drag reduction behavior and nanostructures by cryogenic-temperature transmission electron microscopy(cryo-TEM). The differences in the rheological behavior and the SANS data of the solutions are explained by the different responses of the nanostructures to shear based on a two-step response to shear.

Unrivaled combination of surface area and pore volume in micelle-templated carbon for supercapacitor energy storage

We created Immense Surface Area Carbons (ISACs) by a novel heat treatment that stabilized the micelle structure in a biological based precursor prior to high temperature combined activation – pyrolysis. While displaying a morphology akin to that of commercial activated carbon, ISACs contain an unparalleled combination of electrochemically active surface area and pore volume (up to 4051 m2 g−1, total pore volume 2.60 cm3 g−1, 76% small mesopores). The carbons also possess the benefit of being quite pure (combined O and N: 2.6–4.1 at%), thus allowing for a capacitive response that is primarily EDLC. Tested at commercial mass loadings (∼10 mg cm−2) ISACs demonstrate exceptional specific capacitance values throughout the entire relevant current density regime, with superior rate capability primarily due to the large fraction of mesopores. In the optimized ISAC, the specific capacitance (Cg) is 540 F g−1 at 0.2 A g−1, 409 F g−1 at 1 A g−1 and 226 F g−1 at a very high current density of 300 A g−1 (∼0.15 second charge time). At intermediate and high currents, such capacitance values have not been previously reported for any carbon. Tested with a stable 1.8 V window in a 1 M Li2SO4 electrolyte, a symmetric supercapacitor cell yields a flat energy–power profile that is fully competitive with those of organic electrolyte systems: 29 W h kg−1 at 442 W kg−1 and 17 W h kg−1 at 3940 W kg−1. The cyclability of symmetric ISAC cells is also exceptional due to the minimization of faradaic reactions on the carbon surface, with 80% capacitance retention over 100 000 cycles in 1 M Li2SO4 and 75 000 cycles in 6 M KOH.