Nanoparticle-amplified Surface Plasmon Resonance Study of Protein Conformational Change at Interface

This paper reports the study of protein conformational change by Au nanoparticles (AUNPs)-amplified surface plasmon resonance (SPR) spectroscopy. Taking cytochrome c (Cyt c) as an example, this paper gives a detailed description of the construction of metal-protein-metal sandwich nanostructure consisting of an Au film underlayer, a cytochrome c intermediate layer and an AuNPs upper layer. The incorporation of AuNPs into SPR biosensing results in increased SPR sensitivity to protein conformational change as demonstrated by acid denaturation of Cyt c. It suggests the conformational change of surface-confined Cyt c leads to the distance and electromagnetic coupling variations of Au film-AuNPs.

Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments.

Surface-enhanced resonance Raman spectroscopy and spectroscopy study of redox-induced conformational equilibrium of cytochrome c adsorbed on DNA-modified metal electrode

The redox-induced conformational equilibrium of cytochrome c (cyt c) adsorbed on DNA-modified metal electrode and the interaction mechanism of DNA with cyt c have been studied by electrochemical, spectroscopic and spectroelectrochemical techniques. The results indicate that the external electric field induces potential-dependent coordination equilibrium of the adsorbed cyt c between its oxidized state (with native six-coordinate low-spin and non-native five-coordinate high-spin heme configuration) and its reduced state (with native six-coordinate low-spin heme configuration) on DNA-modified metal electrode. The strong interactions between DNA and cyt c induce the self-aggregation of cyt c adsorbed on DNA. The orientational distribution of cyt c adsorbed on DNA-modified metal electrode is potential-dependent, which results in the deviation from an ideal Nernstian behavior of the adsorbed cyt c at high electrode potentials. The electric-field-induced increase in the activation barrier of proton-transfer steps attributed to the rearrangement of the hydrogen bond network and the self-aggregation of cyt c upon adsorption on DNA-modified electrode strongly decrease the interfacial electron transfer rate.

Numerical study of bluff body flow structures

Our recent progress in numerical studies of bluff body flow structures and a new method for the numerical analysis of near wake flow field for high Reynolds number flow are introduced. The paper consists of three parts. In part one, the evolution of wake vortex structure and variation of forces on a flat plate in harmonic oscillatory flows and in in-line steady-harmonic combined flows are presented by an improved discrete vortex method, as the Keulegan-Carpenter number (KC) varies from 2 to 40 and ratios of U-m to U-0 are of O(10(-1)), O(10) and O(10), respectively. In part 2, a domain decomposition hybrid method, combining the finite-difference and vortex methods for numerical simulation of unsteady viscous separated flow around a bluff body, is introduced. By the new method, some high resolution numerical visualization on near wake evolution behind a circular cylinder at Re = 10(2), 10(3) and 3 x 10(3) are shown. In part 3, the mechanism and the dynamic process for the three-dimensional evolution of the Karman vortex and vortex filaments in braid regions as well as the early features of turbulent structure in the wake behind a circular cylinder are presented numerically by the vortex dynamics method.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

In situ study of nanostructure and morphological development during the crystal-mesophase transition of poly(di-n-hexylsilane) and poly(di-n-butylsilane) by X-ray and hot-stage AFM

Nanostructure and morphology and their development of poly(di-n-hexylsilane) (PDHS) and poly(di-n-butylsilane) (PDBS) during the crystal-mesophase transition are investigated using small angle X-ray scattering (SAXS), wide angle X-ray diffraction and hot-stage atomic force microscopy. At room temperature, PDHS consists of stacks of lamellae separated by mesophase layers, which can be well accounted using an ideal two-phase model. During the crystal-mesophase transition, obvious morphological changes are observed due to the marked changes in main chain conformation and intermolecular distances between crystalline phase and mesophase. In contrast to PDHS, the lamellae in PDBS barely show anisotropy in dimensions at room temperature. The nonperiodic structure and rather small electronic density fluctuation in PDBS lead to the much weak SAXS. The nonperiodic structure is preserved during the crystal-mesophase transition because of the similarity of main chain conformation and intermolecular distances between crystalline phase and mesophase.

Surface-enhanced resonance Raman spectroscopic study of yeast iso-1-cytochrome c and its mutant

The structural stability and redox properties of yeast iso-1-cytochrome c and its mutant, F82H, were studied by surface-enhanced resonance Raman scattering (SERRS) spectroscopy. Phenylalanine, which exists at the position-82 in yeast iso-1-cytochrome c, is replaced by histidine in the mutant. The SERRS spectra of the proteins on the bare silver electrodes indicate that the mutant possesses a more stable global structure with regard to the adsorption-induced conformational alteration. The redox potential of the mutant negatively shifts by about 400 mV, relative to that of yeast iso-1-cytochrome c. This is ascribed to axial ligand switching and higher solvent accessibility of the heme iron in the mutant during the redox reactions.

Resonance Raman spectroscopic study of cytochrome c mutants

The spectroscopic characteristics of cytochrome c(WT) and its mutants(Y67F and N521) in the low frequency region were studied by Resonance Raman technique. The results show that the replacement of phenylalanine for Tyr 67 in WT had a very slight effect on the hydrogen-bonding and conformation of the amino acid residues around propionic acid side chains of heme group. However, large effects on the hydrogen-bonding of internal water with its surrounding amino acid residues and hydrophobility of the home cavity were observed as Asn 52 was substituted with isoleucine, which resulted in conformational regulations of home group and surrounding amino acid residues.

AN INFRARED SPECTROSCOPIC STUDY OF THE STRUCTURAL PHASE-TRANSITION IN THE PEROVSKITE-TYPE LAYER COMPOUND [N-C16H33NH3]2COCL4

The solid-solid phase transitions in the perovskite-type layer compound [n- C16H33NH3]2CoCl4 have been studied by infrared spectroscopy. A new phase transition at 340 K was found by comparison with differential scanning calorimetry results. A temperature dependence study of the infrared spectra provides evidence of the occurrence of structural phase transitions related to the dynamics of the alkylammonium ions and hydrogen bonds. The main transition at 374 K corresponds to the conformational order-disorder change in the chain, which probably couples with reorientational motions of the NH3 polar heads. GTG or GTG' defects appear in the high temperature disordered phase.