Yecheol Rho

pH-dependent structures of ferritin and apoferritin in solution: disassembly and reassembly.

The pH-dependent structures of the ferritin shell (apoferritin, 24-mer) and the ferrihydrite core, under physiological conditions that permit enzymatic activity, were investigated by synchrotron small-angle X-ray scattering (SAXS). The solution structure of apoferritin was found to be nearly identical to the crystal structure. The shell thickness and hollow core volumes were estimated. The intact hollow spherical apoferritin was stable over a wide pH range, 3.40-10.0, and the ferrihydrite core was stable over the pH range 2.10-10.0. The apoferritin subunits underwent aggregation below pH 0.80, whereas the ferrihydrite cores aggregated below pH 2.10 as a result of the disassembly of the ferritin shell under the strongly acidic conditions. As the pH decreased from 3.40 to 0.80, apoferritin underwent stepwise disassembly by first forming a hollow sphere with two holes, then a headset-shaped structure, and, finally, rodlike oligomers. As the pH was increased from pH 1.96, the disassembled rodlike oligomers recovered only to the headset-shaped structure, and the disassembled headset-shaped intermediates recovered only to the hollow spherical structure with two hole defects. The apoferritin hole defects that formed during the disassembly process did not heal as the pH was increased to neutral or slightly basic conditions. The pH-induced apoferritin disassembly and reassembly processes were not fully reversible, although they were pseudoreversible over a limited pH range, between 10.0 and 2.66.

pH-Dependent Structures of an i-Motif DNA in Solution

We have investigated for the first time the structure of i-motif DNA in solution at various pH conditions by using synchrotron small-angle X-ray scattering technique. To facilitate direct structural comparison between solution structures of i-motif DNA at various pH values, we created atomic coordinates of i-motif DNA from a fully folded to unfolded atomic model. Under mild acidic conditions, the conformations for i-motif DNA appeared to be similar to that of the partially unfolded i-motif atomic model in overall shape, rather than the fully folded i-motif atomic model. Collectively, our observations indicate that i-motif DNA molecule is structurally dynamic over a wide pH range, adopting multiple conformations ranging from the folded i-motif structure to a random coil conformation. As the i-motif structure has been used as an important component in nanomachines, we can therefore believe that the structural evidence presented herein will promote the development of future DNA-based molecular-actuator devices.

Synchrotron Small-Angle X-ray Scattering Studies of the Structure of Porcine Pepsin under Various pH Conditions

Structural characteristics of various conformational states of porcine pepsin in solution under different pH conditions were investigated in terms of size and shape by small-angle X-ray scattering (SAXS). Low-resolution structural models of porcine pepsin were reconstructed from SAXS data, which were made inside the search volume of maximum dimension (Dmax), calculated from the pair distance distribution function p(r). The reconstructed structural models were obtained without imposing any restrictions on the symmetry or anisometry of the pepsin molecule. Under conditions emulating those for physiological activity of the enzyme, the reconstructed structural models exhibited a more extended C-terminal domain compared to the crystal structure. The differences between the solution and crystal structures of pepsin can be explained by inherent conformations of the flexible subdomain in the C-terminal domain under the solution pH conditions. Under mild acidic conditions where the enzyme is inactive, the reconstructed structural models revealed a compact globular conformation similar in overall shape to the crystal structure. These results indicate that the changes in fluorescence and circular dichroism curves observed under acidic conditions could also arise from the inherent conformation of the flexible subdomain, which has a tendency to roll into a sphere in the overall structure, but without affecting the stability of internal structure. Furthermore, the conformational changes in the subdomain might explain the inactivity of pepsin under mildly acidic conditions. Finally, compared to neutral denaturing conditions, pepsin under alkaline denaturing conditions had a larger expanded vertical conformation in the reconstructed model, as a consequence of alkaline denaturation of the N-terminal domain and a fully extended conformation of the C-terminal domain. The structural evidence presented here may have important implications for understanding the relationship between the structure of porcine pepsin and enzymatic function.

Biaxially extended quaterthiophene-thiophene and -selenophene conjugated polymers for optoelectronic device applications

New biaxially extended quaterthiophene (4T) conjugated polymers, including poly(5,5′′′-di-(2-ethylhexyl)[2,3′;5′,2′′4′′,2′′′]quaterthiophene) (P4T) and their copolymers with thiophene(P4TT), bithiophene (P4T2T), selenophene(P4TSe) and biselenophene (P4T2Se) were synthesized by Stille coupling reactions under microwave heating. The effects of the ring number of thiophene and selenophene moieties on the physical properties and polymer structures were systematically investigated experimentally and theoretically. With the increased ring number of the unsubstituted thiophene and selenophene moieties, the band gaps and the main-chain torsional angles were reduced. However, the side-chain torsional angles were increased with increasing the ring number, and thus significantly affected the carrier transporting characteristics. Among these studied conjugated polymers, the field-effect transistor (FET) based on P4TSe showed the highest hole mobility of up to 4.28 × 10−2 cm2 V−1 s−1 and an on/off ratio of 1.12 × 104. The photovoltaic device prepared from P4TSe/PC71BM exhibited the highest power conversion efficiency (PCE) of 2.6%, which resulted from more balanced hole/electron mobility and a smaller band gap. The above results revealed that the conformation, charge-transporting and optoelectronic device characteristics of biaxially extended 4T-based conjugated copolymers could be manipulated by incorporating the heteroaromatic ring spacer.

Well-defined DNA-mimic brush polymers bearing adenine moieties: synthesis, layer-by-layer self-assembly, and biocompatibility.

Two new DNA-mimicking brush polymers were synthesized: poly[oxy(11-(3-(9-adeninyl)propionato)-undecanyl-1-thiomethyl)ethylene] (PECH-AP) and poly[oxy(11-(5-(9-adenylethyloxy)-4-oxopentanoato)undecanyl-1-thiomethyl)ethylene] (PECH-AS). These polymers were found to be thermally stable up to 220 °C and could be applied easily by conventional coating processes to produce good quality films. Interestingly, both brush polymers formed molecular multibilayer structures to provide an adenine-rich surface. Despite the structural similarities, PECH-AS surprisingly exhibited higher hydrophilicity and better water sorption properties than PECH-AP. These differences were attributed to the chemical structures in the bristles of the polymers. The adenine-rich surfaces of the polymer films demonstrated selective protein adsorption, suppressed bacterial adherence, facilitated HEp-2 cell adhesion, and exhibited good biocompatibility in mice. However, the high hydrophilicity and good water sorption characteristics of the PECH-AS film suggest that this brush polymer is better suited to applications requiring good biocompatibility and reduced chance of bacterial infection compared with the PECH-AP film.

The biocompatibility of self-assembled brush polymers bearing glycine derivatives

We have synthesized brush polymers with various glycine derivatives as the end groups of their long alkyl bristles. The polymers are thermally stable up to 170-210 degrees C and form good quality films through conventional spin- or dip-coating and subsequent drying. Interestingly, the thin films of these brush polymers exhibit different molecular multi-layer structures that arise through the efficient self-assembly of the bristles with glycine derivative end groups. These brush polymer films have hydrophilic surfaces and exhibit some water sorption. The extent of the water sorption by these films depends upon the nature of the glycine derivatives in the bristle end. These films not only repel fibrinogen molecules and platelets from their surfaces, but also have high resistance to bacterial adherence. Moreover, the films were found to provide conducive surface environments for the successful anchoring and growth of HEp-2 cells, and to exhibit excellent biocompatibility in mice. These brush polymers have potential uses in biomedical applications including medical devices, especially blood contacting devices such as catheters, stents, blood vessels, and biosensors, due to their enhanced biocompatibility and the reduced possibility of post-operative infection.

Effect of C60 Fullerene on the Duplex Formation of i-Motif DNA with Complementary DNA in Solution

The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.

Comprehensive synchrotron grazing-incidence X-ray scattering analysis of nanostructures in porous polymethylsilsesquioxane dielectric thin films

A complete grazing-incidence X-ray scattering (GIXS) formula has been derived for nanopores buried in a polymer dielectric thin film supported by a substrate. Using the full power of the scattering formula, GIXS data from nanoporous polymethylsilsesquioxane dielectric thin films, a model nanoporous system, have successfully been analysed. The nanopores were found to be spherical and to have a certain degree of size distribution but were randomly dispersed in the film. In the film, GIXS was confirmed to arise predominantly via the first scattering process in which the incident X-ray beam scatters without reflection; the other scattering processes and their contributions were significantly dependent on the grazing angle. This study also confirmed that GIXS scattering can be analysed using only independent scattering terms, but this simple approach can only provide structural parameters. The cross terms were found to make a relatively small contribution to the intensity of the overall scattering but were required for the complete characterization of the measured two-dimensional scattering data, in particular the extracted out-of-plane scattering data, and their inclusion in the analysis enabled film properties such as film thickness, critical angle (i.e. electron density), refractive index and the absorption term to be determined.

Molecular layer-by-layer self-assembly and mercury sensing characteristics of novel brush polymers bearing thymine moieties.

Two new brush polyoxyethylenes bearing thymine moieties at the bristle ends have been synthesized as model polymers in which the chemical loading of the thymine functional group into the polymer is maximized: poly(oxy(11-thyminoacetyloxyundecylthiomethyl)ethylene) (PECH(S)-T) and poly(oxy(11-thyminoacetyloxyundecylsulfonylmethyl)ethylene) (PECH(SO(2))-T). These brush polymers are thermally stable up to around 225 °C, and their glass transitions occur in the range 23-27 °C, but they have significantly different properties despite the similarity of their chemical structures. In particular, PECH(SO(2))-T films exhibit better performance in sensing mercury ions than PECH(S)-T films. These differences were found to originate in the differences between their morphological structures. The PECH(SO(2))-T film has a multi-bilayer structure without interdigitation, in which the layers stack along the out-of-plane of the film and provide a thymine-rich surface. In contrast, the PECH(S)-T film is amorphous with a relatively low population of thymine moieties at the surface. This study demonstrated that a thymine-rich surface is required for recyclable thymine-based polymers to provide highly improved sensitivity and selectivity as well as full reversibility in the sensing of mercury ions. A thymine-rich surface can be achieved with a brush polymer bearing thymine moieties that can self-assemble into a multi-bilayer structure. Because of the thymine-rich surface, the PECH(SO(2))-T thin films even in only 6 nm thickness demonstrate the detection of mercury ions in aqueous solutions with a detection limit of 10(-6) M.

Synchrotron X-ray scattering characterization of the molecular structures of star polystyrenes with varying numbers of arms.

We have synthesized well-defined multiarmed star polystyrenes, with 6, 9, 17, 33, and 57 arms, and studied their molecular shapes and structural characteristics in a good solvent (tetrahydrofuran at 25 degrees C) and in a theta (Theta) solvent (cyclohexane at 35 degrees C) by small-angle X-ray scattering (SAXS) using a synchrotron radiation source. Analysis of the SAXS data provided a detailed characterization of the molecular shapes, including the contributions of the blob morphology of the arms, the radius of gyration, the paired distance distribution, the radial electron density distribution, and the Zimm-Stockmayer and Roovers g-factor, for the multiarmed star polystyrenes. In particular, the molecular shapes of the star polystyrenes were found to change from a fuzzy ellipsoid, for the 6-armed polystyrene, to a fuzzy sphere, for the 57-armed polystyrene, with an increasing number of arms. The ellipsoidal character of the star polystyrenes with fewer arms may originate from the extended anisotropically branched architecture at the center of the molecule. The arms of the star polystyrenes were found to be more extended than those of the linear polystyrenes. Furthermore, the degree of chain extension in the arms increased with the number of arms.