Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Study on polymer micelles of hydrophobically modified ethyl hydroxyethyl cellulose using single-molecule force spectroscopy

Individual hydrophobically modified ethyl hydroxyethyl cellulose (HM-EHEC) molecules under different conditions were elongated using a new atomic force microscope (AFM) based technique-single-molecule force spectroscopy (SMFS). The critical concentration of HM-EHEC for micelle-like clusters at a solid/liquid interface was around 0.8 wt %, which is lower than that in solution. The different mechanical properties of HM-EHEC below and above the critical concentration were displayed on force-extension curves. Through a comparison with unmodified hydroxyethyl cellulose, substituent-induced effects on nanomechanical features of HM-EHEC were investigated. Because of hydrophobic interactions and cooperative binding with the polymer, surfactants such as sodium dodecyl sulfate (SDS) dramatically influence the elastic properties of HM-EHEC below the critical concentration, and further addition of SDS reduces the interactions between the hydrophobic groups and the surfactant.

Ethanol-induced formation of silver nanoparticle aggregates for highly active SERS substrates and application in DNA detection

A controllable silver nanoparticle aggregate system has been synthesized by adding different amounts of ethanol to cetyltrimethylammonium bromide (CTAB) capped silver nanoparticles (Ag-nps), which could be used as highly efficient surface-enhanced Raman scattering (SERS) active substrates. This ethanol-induced aggregation can be attributed to preferential dissolution of CTAB into ethanol, which leads a partial removal of the protective CTAB layer on Ag-nps. The optical and morphological properties of these aggregates under various volumes of ethanol were explored via UV-vis spectroscopy and atomic force microscopy.

表面增强拉曼光谱术在生命科学及单分子研究中的应用与进展

本文介绍了表面增强拉曼散射的基本原理及其在生命科学研究中的应用；综述了最近十年来利用表面增强拉曼散射进行单分子和活细胞检测的研究进展以及在活体检测中的应用；对表面增强拉曼光谱术在生命科学研究中的独特优势及发展前景进行了介绍。

R6G单分子表面增强共振拉曼散射光谱探测研究

以共焦显微系统为平台，研究了不同浓度的R6G银溶胶的表面增强共振拉曼散射（SERRS）光谱，结果表明不同浓度溶液中的R6G分子表现出了不同的光谱特性。在浓度为10^-13mol·L^-1的R6G银溶胶中得到了R6G单分子的表面增强共振拉曼散射光谱，观察到了一些光谱非均匀变化现象，如谱色散、谱线的强度起伏、拉曼谱的偏振化以及分子的闪烁等，并对这些现象进行了分析，证明得到的是R6G单分子的SERRS光谱。文章还对单分子检测中的一些关键问题进行了分析与讨论，确定了单分子SERRS光谱检测的适当条件。

Surface-enhanced resonance Raman scattering spectroscopy of single R6G molecules

Surface-enhanced resonance Raman scattering (SERRS) of Rhodamine 6G (R6G) adsorbed on colloidal silver clusters has been studied. Based on the great enhancement of the Raman signal and the quench of the fluorescence, the SERRS spectra of R6G were recorded for the samples of dye colloidal solution with different concentrations. Spectral inhomogeneity behaviours from single molecules in the dried sample films were observed with complementary evidences, such as spectral polarization, spectral diffusion, intensity fluctuation of vibrational lines and even "breathing" of the molecules. Sequential spectra observed from a liquid sample with an average of 0.3 dye molecules in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1 or 2 molecules. Difference between the SERRS spectra of R6G excited by linearly and circularly polarized light were experimentally measured.

Imaging and tracking single fluorescent nanobeads in solution

In single-particle tracking (SPT), fluorescence video microscopy is used to record the motion images of single particle or single molecule. Here, by using a total-internal-reflection microscope equipped with an argon ion laser and a charge-coupled device (CCD) camera with high-speed and high-sensitivity, video images of single nanobeads in solutions were obtained. From the trajectories, the diffusion coefficient of individual nanobead was determined by the mean square displacements as a function of time. The sizes of nanobeads were calculated by Stokes-Einstein equation, and the results were compared with the actual values.

Interaction between single molecules of Mac-1 and ICAM-1 in living cells: An atomic force microscopy study

The interaction between integrin macrophage differentiation antigen associated with complement three receptor function (Mac-1) and intercellular adhesion molecule-1 (ICAM-1), which is controlled tightly by the ligand-binding activity of Mac-1, is central to the regulation of neutrophil adhesion in host defense. Several "inside-out" signals and extracellular metal ions or antibodies have been found to activate Mac-1, resulting in an increased adhesiveness of Mac-1 to its ligands. However, the molecular basis for Mac-1 activation is not well understood yet. In this work, we have carried out a single-molecule study of Mac-1/ICAM-1 interaction force in living cells by atomic force microscopy (AFM). Our results showed that the binding probability and adhesion force of Mac-1 with ICAM-1 increased upon Mac-1 activation. Moreover, by comparing the dynamic force spectra of different Mac-1 mutants, we expected that Mac-1 activation is governed by the downward movement of its alpha 7 helix. (c) 2007 Elsevier Inc. All rights reserved.

A New Method to Investigate InGaAsP Single-Photon Avalanche Diodes Using a Digital Sampling Oscilloscope

A near-infrared single-photon detection system is established by using pigtailed InGaAs/InP avalanche photodiodes. With a 50GHz digital sampling oscilloscope, the function and process of gated-mode (Geiger-mode) single-photon detection are intuitionally demonstrated for the first time. The performance of the detector as a gated-mode single-photon counter at wavelengths of 1310 and 1550nm is investigated. At the operation temperature of 203K,a quantum efficiency of 52% with a dark count probability per gate of 2. 4 * 10~(-3), and a gate pulse repetition rate of 50kHz are obtained at 1550nm. The corresponding parameters are 43% , 8. 5 * 10~(-3), and 200kHz at 238K.

Surface enhanced Raman scattering of brilliant green on ag nanoparticles and applications in living cells as optical probes

In this article, surface enhanced Raman scattering (SERS) of different concentrations of brilliant green (13G) on Ag nanoparticles (AgNPs) has been investigated. The results indicate that only 10(-12) M BG can be detected on AgNPs while as low as 10(-11) M BG can be detected upon the activation of AgNPs by chloride ions. The additional improvement of the detection of BG mainly derives from the increase of the electromagnetic field around AgNPs and partially from the reorientation of BG on AgNPs induced by chloride ions, which was proved by the different spectra feature in the two systems. Adsorption of BG on AgNPs has also been demonstrated in applications of living cells as optical probes based on SERS, indicating that dye-AgNPs can probe the local environment in the living cells. The related cytotoxicity measurements demonstrated that BG-AgNPs produced little cytotoxicity to the cells, which shows great potential in biornedical applications of BG labeled-AgNPs for SERS nanosensors in cells as optical probes. Meanwhile, SERS spectra of BG on AgNPs in the presence chloride ions are expected to be used in living cells as more sensitive optical probes.

Surface enhanced Raman scattering of brilliant green on ag nanoparticles and applications in living cells as optical probes

In this article, surface enhanced Raman scattering (SERS) of different concentrations of brilliant green (13G) on Ag nanoparticles (AgNPs) has been investigated. The results indicate that only 10(-12) M BG can be detected on AgNPs while as low as 10(-11) M BG can be detected upon the activation of AgNPs by chloride ions. The additional improvement of the detection of BG mainly derives from the increase of the electromagnetic field around AgNPs and partially from the reorientation of BG on AgNPs induced by chloride ions, which was proved by the different spectra feature in the two systems. Adsorption of BG on AgNPs has also been demonstrated in applications of living cells as optical probes based on SERS, indicating that dye-AgNPs can probe the local environment in the living cells. The related cytotoxicity measurements demonstrated that BG-AgNPs produced little cytotoxicity to the cells, which shows great potential in biornedical applications of BG labeled-AgNPs for SERS nanosensors in cells as optical probes. Meanwhile, SERS spectra of BG on AgNPs in the presence chloride ions are expected to be used in living cells as more sensitive optical probes.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

AMPEROMETRIC DETECTION OF CATECHOLAMINES WITH LIQUID-CHROMATOGRAPHY AT A NOVELLY CONSTRUCTED PRUSSIAN BLUE CHEMICALLY MODIFIED ELECTRODE

A novel Prussian blue chemically modified electrode (CME) was constructed and characterized for liquid chromatography electrochemical detection (LCEC) of catecholamines. Both anodic and cathodic peaks could be obtained by monitoring at constant applied potential at anodic and slightly cathodic potential ranges (0.3-0.7 and -0.2-0.1 V vs. SCE), respectively. When arranged in a series configuration, using the modified electrodes as generating and collecting detectors, extremely high effective collection efficiencies of 0.91 (for norepinephrine) and 0.58 (for dihydroxyphenylacetic acid) were achieved in dual-electrode LCEC for catecholamines; and a linear response range over 3 orders of magnitude and a detection limit of 10 pg were obtained with a downstream CME as the indicating detector.

AMPEROMETRIC DETECTION AT A CARBON-FIBER ARRAY RING GLASSY-CARBON DISK ELECTRODE IN A WALL-JET CELL

A wall-jet cell incorporating a carbon fibre array ring/glassy-carbon disk electrode has been constructed, and characterized by the cyclic voltammetry and flow-injection techniques. The ring (composed of several microdisks) and glassy-carbon disk electrode, can be used separately for different purposes, e.g., detection in solution without a supporting electrolyte, collection/shielding detection with dual-electrode and voltammetric/amperometric detection with series dual-electrode. The electrode shows better collection and shielding effects than usual ring-disk electrode in quiescent solution and the series dual-electrode in a thin-layer flow-through cell. The detection limit at the ring electrode is comparable with that at a conventional-size electrode, and has been used in the mobile phase without a supporting electrolyte, proving to be a promising detector for normal-phase liquid chromatography.

Direct observation of adsorption sites of protein impurities and their effects on step advancement of protein crystals

We measured noninvasively step velocities of elementary two-dimensional (2D) islands on {110} faces of tetragonal lysozyme crystals, under various supersaturations, by laser confocal microscopy combined with differential interference contrast microscopy. We studied the correlation between the effects of protein impurities on the growth of elementary steps and their adsorption sites on a crystal surface, using three kinds of proteins: fluorescent-labeled lysozyme (F-lysozyme), covalently bonded dimers of lysozyme (dimer), and a 18 kDa polypeptide (18 kDa). These three protein impurities suppressed the advancement of the steps. However, they exhibited different supersaturation dependencies of the suppression of the step velocities. To clarify the cause of this difference, we observed in situ the adsorption sites of individual molecules of F-lysozyme and fluorescent-labeled dimer (F-dimer) on the crystal surface by single-molecule visualization. We found that F-lysozyme adsorbed preferentially on steps (i.e., kinks), whereas F-dimer adsorbed randomly on terraces. Taking into account the different adsorption sites of F-lysozyme and F-dimer, we could successfully explain the different effects of the impurities on the step velocities. These observations strongly suggest that 18 kDa also adsorbs randomly on terraces. Seikagaku lysozyme exhibited a complex effect that could not alone be explained by the two major impurities (dimer and 18 kDa) present in Seikagaku lysozyme, indicating that trace amounts of other impurities significantly affect the step advancement.