Protein Conformation-Controlled Rebinding Barrier of NO and Its Binding Trajectories in Myoglobin and Hemoglobin at Room Temperature

Kim, Seongheun,Lim, Manho American Chemical Society 2012 The journal of physical chemistry. B, Condensed ma Vol.116 No.20

<P>The effect of the solvent viscosity on the dynamics of NO rebinding to myoglobin (Mb) and hemoglobin (Hb) was examined by femtosecond (fs) time-resolved vibrational spectroscopy after photodeligation of NO from MbNO and HbNO in various viscous solutions at 283 K using a 580 nm excitation pulse. The rebinding kinetics of NO to both Mb and Hb were nonexponential, but their dependence on the solvent viscosity was different. The rate of NO rebinding to Mb increased with increasing solution viscosity, which was achieved by increasing the glycerol content in glycerol/water mixture. In contrast, the rate of NO rebinding to Hb was independent of the solution viscosity but faster than the fastest rate of NO rebinding observed in Mb. The dynamics of conformational relaxation of the protein after deligation were also measured by probing the evolution of the amide band. The effect of the solvent viscosity on the kinetics of conformational relaxation in both proteins was also quite different. The conformational relaxation of Mb became slower with increasing solution viscosity. On the other hand, the conformational relaxation of Hb was independent of the solution viscosity but slower than the slowest kinetics of Mb. The inverse correlation in the kinetics of conformational relaxation and NO rebinding suggests that the barrier of NO rebinding increases as the conformation of the protein relaxes toward the deligated structure after NO dissociation. The rebinding kinetics of NO to both proteins was well described by a kinetic model incorporating a time-dependent barrier for rebinding and exponential translocations between three states for dissociated NO.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2012/jpcbfk.2012.116.issue-20/jp300176q/production/images/medium/jp-2012-00176q_0010.gif'></P>

Ion aggregation in high salt solutions: Ion network versus ion cluster

Kim, Seongheun,Kim, Heejae,Choi, Jun-Ho,Cho, Minhaeng American Institute of Physics 2014 The Journal of chemical physics Vol.141 No.12

<P>The critical aggregation phenomena are ubiquitous in many self-assembling systems. Ions in high salt solutions could also spontaneously form larger ion aggregates, but their effects on hydrogen-bond structures in water have long been controversial. Here, carrying out molecular dynamics (MD) simulation studies of high salt solutions and comparing the MD simulation results with infrared absorption and pump-probe spectroscopy of O-D stretch mode of HDO in highly concentrated salt solutions and (13)C-NMR chemical shift of S(13)CN(-) in KSCN solutions, we find evidence on the onset of ion aggregate and large-scale ion-ion network formation that concomitantly breaks water hydrogen-bond structure in certain salt solutions. Despite that these experimental results cannot provide direct evidence on the three-dimensional morphological structures of ion aggregates, they serve as reference data for verifying MD simulation methods. The MD results suggest that disrupted water hydrogen-bond network is intricately intertwined with ion-ion network. This further shows morphological variation of ion aggregate structures from ion cluster to ion network in high salt solutions that are interrelated to the onset of macroscopic aggregate formation and the water hydrogen-bond structure making and breaking processes induced by Hofmeister ions.</P>

Direct Observation of Ligand Rebinding Pathways in Hemoglobin Using Femtosecond Mid-IR Spectroscopy

Kim, Seongheun,Park, Jaeheung,Lee, Taegon,Lim, Manho American Chemical Society 2012 The Journal of physical chemistry B Vol.116 No.22

<P>The dynamics of NO rebinding in hemoglobin (Hb) was directly observed using femtosecond mid-IR spectroscopy after photodeligation of NO from HbNO in D<SUB>2</SUB>O at 283 K. Time-resolved spectra of bound NO appeared to have a single feature peaked at 1616 cm<SUP>–1</SUP> but were much better described by two Gaussians with equal intensities but different rebinding kinetics, where the feature at 1617 cm<SUP>–1</SUP> rebinds faster than the one at 1614 cm<SUP>–1</SUP>. It is possible that the two bands each correspond to one of two subunit constituents of the tetrameric Hb. Transient absorption spectra of photodeligated NO revealed three evolving bands near 1858 cm<SUP>–1</SUP> and their red-shifted replicas. The red-shifted replicas arise from photodeligated NO in the vibrationally excited <I>v</I> = 1 state. More than 10% of the NO was dissociated into the vibrationally excited <I>v</I> = 1 state when photolyzed by a 580 nm pulse. The three absorption bands for the deligated NO could be attributed to three NO sites in or near the heme pocket. The kinetics of the three transient bands for the deligated NO, as well as the recovery of the bound NO population, was most consistent with a kinetics scheme that incorporates time-dependent rebinding from one site that rapidly equilibrates with the other two sites. The time dependence results from a time-dependent rebinding barrier due to conformational relaxation of protein after deligation. By assigning each absorption band to a site in the heme pocket of Hb, a pathway for rebinding of NO to Hb was proposed.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2012/jpcbfk.2012.116.issue-22/jp3026495/production/images/medium/jp-2012-026495_0001.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp3026495'>ACS Electronic Supporting Info</A></P>

Observation of magnetoconductivity with terahertz probes for ferromagnetic Fe films

Huang Lin,Zhao Yunxiu,Le Thi Nguyen,Lee Sang-Hyuk,Peng Zhi,Kim Seongheun,Shin Hee Jun,Park Jaehun,Kim Hyun-Joong,Hong Jung-Il,Bang Junhyeok,Lee Hyun Seok,Kim Kyung Wan,Kim Dong-Hyun 한국물리학회 2022 Current Applied Physics Vol.41 No.-

Ultrafast characterization of spin-dependent transport behavior in ferromagnetic systems without contact probes has been of strong demand, recently. We have experimentally investigated spin-dependent complex conductivity for ferromagnetic Fe films of various thickness by means of terahertz time-domain transmission spectroscopy. Comparison of the transmitted terahertz wave amplitude and the spin-dependent conductivity reveals that the magnetization state of films effectively determines the complex conductivity. Non-invasive observation of spin-dependent conductivity by contact-free terahertz probe method is proven to be promising in further investigating spintronic materials, particularly on an ultrafast timescale.

Disulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopy.

Ishikawa, Haruto,Kim, Seongheun,Kwak, Kyungwon,Wakasugi, Keisuke,Fayer, Michael D National Academy of Sciences 2007 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.104 No.49

<P>Intramolecular disulfide bonds are understood to play a role in regulating protein stability and activity. Because disulfide bonds covalently link different components of a protein, they influence protein structure. However, the effects of disulfide bonds on fast (subpicosecond to approximately 100 ps) protein equilibrium structural fluctuations have not been characterized experimentally. Here, ultrafast 2D-IR vibrational echo spectroscopy is used to examine the constraints an intramolecular disulfide bond places on the structural fluctuations of the protein neuroglobin (Ngb). Ngb is a globin family protein found in vertebrate brains that binds oxygen reversibly. Like myoglobin (Mb), Ngb has the classical globin fold and key residues around the heme are conserved. Furthermore, the heme-ligated CO vibrational spectra of Mb (Mb-CO) and Ngb (Ngb-CO) are virtually identical. However, in contrast to Mb, human Ngb has an intramolecular disulfide bond that affects its oxygen affinity and protein stability. By using 2D-IR vibrational echo spectroscopy, we investigated the equilibrium protein dynamics of Ngb-CO by observing the CO spectral diffusion (time dependence of the 2D-IR line shapes) with and without the disulfide bond. Despite the similarity of the linear FTIR spectra of Ngb-CO with and without the disulfide bond, 2D-IR measurements reveal that the equilibrium sampling of different protein configurations is accelerated by disruption of the disulfide bond. The observations indicate that the intramolecular disulfide bond in Ngb acts as an inhibitor of fast protein dynamics even though eliminating it does not produce significant conformational change in the protein's structure.</P>

Ion aggregation in high salt solutions. III. Computational vibrational spectroscopy of HDO in aqueous salt solutions

Choi, Jun-Ho,Kim, Heejae,Kim, Seongheun,Lim, Sohee,Chon, Bonghwan,Cho, Minhaeng American Institute of Physics 2015 The Journal of chemical physics Vol.142 No.20

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

Feng, Yuan,Huang, Jing,Kim, Seongheun,Shim, Ji Hyun,MacKerell, Alexander D.,Ge, Nien-Hui American Chemical Society 2016 The Journal of physical chemistry B Vol.120 No.24

<P>We have studied the structure of (Ala)(5), a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with C-13=O and C-13=O-18, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR. spectra taken under the double-crossed <pi/4, -pi/4, Y, Z > polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for alpha(+), beta, and ppII, and the polarizable Drude-2013 predicted dominating beta structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.</P>

Dielectric Response of Nonpolar a-plane (1120) ZnO Crystals in the Terahertz Frequency

Jang, Soohwan,Park, Jaehun,Kim, Seongheun,Baik, Kwang Hyeon American Scientific Publishers 2016 Journal of nanoscience and nanotechnology Vol.16 No.11

<P>We investigated the dielectric response of nonpolar a-plane (11 (2) over bar0) ZnO (a-ZnO) bulk crystals in the terahertz (THz) frequency using femto-second THz time-domain spectroscopy. The peak amplitude of the transmitted output pulse for nonpolar a-ZnO crystal decreased down to about 25% of c-plane ZnO (c-ZnO), showing strong absorptions in a-ZnO when compared with polar c-ZnO. While the polar c-ZnO did not show any azimuthal angle dependence, nonpolar a-ZnO crystals exhibited significant variation as a function of azimuthal angle, presumably due to the birefringence in a-ZnO crystal. We believe that the discrepancy in the refractive index originates from the difference of the transverse-optical and the longitudinal optical phonon splitting between the optical phonon branches.</P>

Delayed auger recombination in silicon measured by time-resolved X-ray scattering

Jo, Wonhyuk,Landahl, Eric C.,Kim, Seongheun,Lee, Dong Ryeol,Lee, Sooheyong ELSEVIER 2018 CURRENT APPLIED PHYSICS Vol.18 No.11

<P>We report a new method of measuring the non-radiative recombination rate in bulk Silicon. Synchrotron time-resolved x-ray scattering (TRXS) combines femtometer spatial sensitivity with nanosecond time resolution to record the temporal evolution of a crystal lattice following intense ultrafast laser excitation. Modeling this data requires an Auger recombination time that is considerably slower than previous measurements, which were made at lower laser intensifies while probing only a relatively shallow surface depth. We attribute this difference to an enhanced Coulomb interaction that has been predicted to occur in bulk materials with high densities of photoexcited charge carriers.</P>

Ultrafast transient photocarrier dynamics of the bulk-insulating topological insulator <tex> $ \mathrm{B}\mathrm{i}_{1.5}\mathrm{S}\mathrm{b}_{0.5}\mathrm{T}\mathrm{e}_{1.7}\mathrm{S}\mathrm{e}_{1.3}$</tex>

Choi, Young Gwan,Zhung, Chan June,Park, Sun-Hee,Park, Joonbum,Kim, Jun Sung,Kim, Seongheun,Park, Jaehun,Lee, J. S. American Physical Society 2018 Physical review. B Vol.97 No.7

<P>Using optical-pump terahertz-probe spectroscopy, we investigated an ultrafast photocarrier relaxation behavior in a Bi1.5Sb0.5Te1.7Se1.3 (BSTS) single crystal, which is one of the most bulk-insulating topological insulators. Compared to n-type bulk-metallic Bi2Se3, we found that BSTS endows distinct behaviors in its photocarrier dynamics; the relaxation time turns out to be an order of magnitude longer, and the transient conductance spectrum exhibits a nonlinear increase as a function of the pumping power. Also, we observed an abrupt reduction of the photocarrier scattering rate in several picoseconds after the initial photoexcitation. We discuss these intriguing experimental observations based on a bulk-to-surface carrier injection assisted by the built-in electric field near the surface and electron-phonon scattering.</P>