Jeongho Kim

The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal mode analysis

The vibrational properties of the hydrated proton and deuteron in bulk phase water and deuterated water are investigated spectroscopically and computationally. Mid-infrared spectra of aqueous acid solutions are measured by attenuated total reflectance-Fourier transform IR spectroscopy and compared with pure water and salt/counterion spectra to extract high-quality hydrated proton spectra at a series of concentrations. Multistate empirical valence bond simulations of the excess proton in bulk phase water are also performed, allowing the autocorrelation function of the time derivative of the dipole moment, and hence the power spectrum of the hydrated proton, to be evaluated. The experimental and theoretical spectra are found to be in very good agreement. Normal mode analysis of the bulk phase simulation data allows definitive assignment of the spectrum. The associated motions are found to be represented by both Eigen and Zundel forms of the hydrated proton.

Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump-probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 μs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.

Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules

Recent years have witnessed the birth of picosecond pump-probe X-ray diffraction and scattering techniques, thanks to the technological developments in the third generation synchrotron beamlines and advances in theory and data analysis by combining quantum calculations, molecular dynamics simulations and global fitting analysis. Our laboratories have employed this technique to study structural dynamics and spatiotemporal kinetics of many molecular systems in solution including diatomic molecules, haloalkanes, organometallic complexes and protein molecules over timescales from picoseconds (ps) to milliseconds. The visualising power and unbiased sensitivity of X-ray scattering proved to be instrumental in identifying global reaction pathways and in some cases capturing detailed three-dimensional structures of reaction intermediates. Many results have accumulated from which we have selected some interesting examples to be reviewed here. The structural dynamics of Br2 and I2 are compared and the reaction pathways for HgBr2 and HgI2 are compared. Solvents may affect the reaction pathways as illustrated in the photolysis of CH2I2 in two different solvents. How does the excitation wavelength affect the reaction pathways is another important aspect in photochemistry as shown for Ru3(CO)12. Applications to the folding of cytochrome-c and the structural dynamics of myoglobin and bacteriorhodopsin are also reviewed. The time resolution is currently limited to about 100 ps, the X-ray pulse width available from synchrotron sources. In the near future, X-ray free electron lasers (XFELs) will deliver 100 fs or shorter X-ray pulses. In femtosecond (fs) X-ray scattering experiments with this higher resolution, real-time observation of ultrafast chemical events, such as bond-breaking and bond-making will be possible. So far, gas-phase reactions, which are the main targets for ultrafast electron diffraction due to the high scattering power of electrons, have not yet been studied with time-resolved X-ray scattering, but in principle this discipline will become feasible with the coming XFEL sources. We thus discuss potential fs X-ray scattering experiments for gas phase as well as solution phase reactions. In addition, the high photon flux and the coherence of XFEL-generated X-ray pulses might open up new research areas, such as single-molecule diffraction.

Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering.

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I1, I2, and I3) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme–heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I1 intermediate is generated within 100 ps and transforms to the R-like I2 intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I3 intermediate is formed via subunit rotation, a decrease in the heme–heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I3 intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme–heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.

Clinical Performance Evaluation of Four Automated Chemiluminescence Immunoassays for Hepatitis C Virus Antibody Detection

ABSTRACT Various automated chemiluminescence immunoassay (CLIA) analyzers for the detection of antibodies to hepatitis C virus (HCV) are now commercially available in clinical laboratories and are replacing conventional enzyme immunoassays. We investigated the performance of four anti-HCV CLIAs (the Architect Anti-HCV assay on the Architect i2000 system, the Vitros Anti-HCV assay on the Vitros ECiQ Immunodiagnostic System, the Access HCV Ab PLUS assay on the UniCel DxI 800 analyzer, and the newly developed Elecsys Anti-HCV assay on the Cobas e 411 analyzer). The total percent coefficient of variation values of imprecision were 3.5 to 5.7% with positive control materials and 7.2 to 10.2% with negative control materials. The agreement between the results of the Elecsys, Architect, Vitros, and Access CLIAs ranged from 94.5 to 98.1%. The clinical sensitivity of all CLIAs was 100%. Each CLIA showed excellent reproducibility and clinical sensitivity. The Elecsys, Architect, Vitros, and Access CLIAs showed clinical specificities of 98.2, 98.8, 96.5, and 98.2%.

Protein Tertiary Structural Changes Visualized by Time-Resolved X-ray Solution Scattering

We obtained a solution structural model of myoglobin (Mb) formed upon the CO photolysis of MbCO by analyzing time-resolved X-ray solution scattering data. An experiment-restrained rigid-body molecular dynamics simulation was used to find the best model whose theoretical difference scattering curve gives a satisfactory agreement with the experimental data at the time delay of 10 ns. The obtained solution model shows structural changes similar to crystallographic models for MbCO --> Mb but also displays a noticeable difference in that the N-terminus and F helix show larger structural changes.

Clinical Features and Outcomes of IgA Nephropathy with Nephrotic Syndrome

BACKGROUND AND OBJECTIVES Nephrotic syndrome (NS) is a rare manifestation of IgA nephropathy (IgAN). Clinical characteristics and long-term outcomes of this condition have not yet been explored. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A multicenter observational study was conducted between January 2000 and September 2010 in 1076 patients with biopsy-proven IgAN from four medical centers in Korea. The primary outcome was a doubling of the baseline serum creatinine concentration. RESULTS Of the 1076 patients, 100 (10.2%) presented with NS; complete remission (CR), partial remission (PR), and no response (NR) occurred in 48 (48%), 32 (32%), and 20 (20%) patients, respectively. During the median follow-up of 45.2 months, 24 patients (24%) in the NS group reached the primary endpoint compared with 63 (7.1%) in the non-NS group (P<0.001). The risk of reaching the primary endpoint was significantly higher in the PR (P=0.04) and NR groups (P<0.001) than in the CR group. Among patients with NS, 24 (24%) underwent spontaneous remission (SR). SR occurred more frequently in female patients and in patients with serum creatinine levels ≤1.2 mg/dl and a >50% decrease in proteinuria within 3 months after NS onset. None of the patients with SR reached the primary endpoint and they had fewer relapses during follow-up. CONCLUSIONS This study demonstrated that the prognosis of NS in IgAN was not favorable unless PR or CR was achieved. In addition, SR was more common than expected, particularly in patients with preserved kidney function and spontaneous decrease in proteinuria shortly after NS onset.

Exciton Fine Structure and Spin Relaxation in Semiconductor Colloidal Quantum Dots

Quantum dots (QDs) have discrete quantum states isolated from the environment, making QDs well suited for quantum information processing. In semiconductor QDs, the electron spins can be coherently oriented by photoexcitation using circularly polarized light, creating optical orientation. The optically induced spin orientation could serve as a unit for data storage and processing. Carrier spin orientation is also envisioned to be a key component in a related, though parallel, field of semiconductor spintronics. However, the oriented spin population rapidly loses its coherence by interaction with the environment, thereby erasing the prepared information. Since long-lasting spin orientation is desirable in both areas of investigation, spin relaxation is the central focus of investigation for optimization of device performance. In this Account, we discuss a topic peripherally related to these emerging areas of investigation: exciton fine structure relaxation (EFSR). The radiationless transition occurring in the exciton fine structure not only highlights a novel aspect of QD exciton relaxation but also has implications for carrier spin relaxation in QDs. We focus on examining the EFSR in connection with optical spin orientation and subsequent ultrafast relaxation of electron and hole spin densities in the framework of the exciton fine structure basis. Despite its significance, the study of exciton fine structure in colloidal QDs has been hampered by the experimental challenge arising from inhomogeneous line broadening that obscures the details of closely spaced fine structure states in the frequency domain. In this Account, we show that spin relaxation occurring in the fine structure of CdSe QDs can be probed by a time-domain nonlinear polarization spectroscopy, circumventing the obstacles confronted in the frequency-domain spectroscopy. In particular, by combining polarization sequences of multiple optical pulses with the unique optical selection rules of semiconductors, fast energy relaxation among the QD exciton fine structure states is selectively measured. The measured exciton fine structure relaxation, which is a nanoscale analogue of molecular radiationless transitions, contains direct information on the relaxation of spin densities of electron and hole carriers, that is, spin relaxation in QDs. From the exciton fine structure relaxation rates measured for CdSe nanorods and complex-shaped nanocrystals using nonlinear polarization spectroscopy, we elucidated the implications of QD size and shape on the QD exciton properties as well, for example, size- and shape-scaling laws governing exciton spin flips and how an exciton is delocalized in a QD. We envision that the experimental development and the discoveries of QD exciton properties presented in this Account will inspire further studies toward revealing the characteristics of QD excitons and spin relaxation therein, for example, spin relaxation in QDs made of various materials with different electronic structures, spin relaxation under an external perturbation of QD electronic states using magnetic fields, and spin relaxation of separated electrons and holes in type-II QD heterostructures.

Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer

Optoelectronic properties of a polyphenylenevinylene-based oligomer and its paracylophane-linked dimer are studied using a variety of experimental and theoretical techniques. Despite the symmetrical structure and redshifted absorption of the dimer versus the monomer, an exciton picture is not the most appropriate. Electronic structure calculations establish changes in charge density upon optical excitation and show localized excitations that cannot be accounted for by a simple Frenkel exciton model. Visible frequency pump-probe anisotropy measurements suggest that the dimer should be considered as a three-level system with a fast, approximately 130 fs, internal conversion from the higher to lower energy excited electronic state. Signatures of nuclear relaxation processes are compared for electric field-resolved transient grating and two-dimensional photon echo spectra. These measurements reveal that nuclear relaxation occurs on similar time scales for the monomer and dimer. The connection between the spectral phase of four-wave mixing signals and the time dependent width of a nuclear wave packet is discussed. Semiempirical electronic structure and metropolis Monte Carlo calculations show that the dominant line broadening mechanisms for the monomer and dimer are associated with inter-ring torsional coordinates. Together, the theoretical calculations and electric field-resolved four-wave mixing experiments suggest that while the structure of dimer is more rigid than that of monomer, the difference in their rigidities is not sufficient to slow down excited state relaxation of dimer with respect to the monomer.

Control of Exciton Spin Relaxation by Electron−Hole Decoupling in Type-II Nanocrystal Heterostructures

The electron spin flip relaxation dynamics in type II CdSe/CdTe nanorod heterostructures are investigated by an ultrafast polarization transient grating technique. Photoexcited charge separation in the heterostructures suppresses the electron-hole exchange interaction and their recombination, which reduces the electron spin relaxation rate in CdSe nanocrystals by 1 order of magnitude compared to exciton relaxation. The electron orientation is preserved during charge transfer from CdTe to CdSe, and its relaxation time constant is found to be approximately 5 ps at 293 K in the CdSe part of these nanorods. This finding suggests that hole spin relaxation determines the exciton fine structure relaxation rate and therefore control of exciton spin relaxation in semiconductor nanostructures is possible by delocalizing or translating the hole density relative to the electron.