Probing single-molecule by surface-enhanced resonance Raman scattering with linearly and circularly polarized laser

Rhodamine 6G (R6G) was incubated in silver sols with different low concentrations and its surface-enhanced resonance Raman scattering (SERRS) spectra, excited by linearly and circularly polarized light, respectively, were studied. At the single-molecule level the SERRS spectra were recorded in 10(-13) M dye colloidal solution. Spectral inhomogeneous behaviors from single-molecule were observed such as spectral polarization, spectral diffusion and intensity fluctuations of vibrational lines. Difference between SERRS spectra of R6G excited by linearly and circularly polarized light and the effect of the polarizing angle of Raman signal relative to the slit of spectrograph on the Raman spectral polarization were analyzed and measured experimentally. Circularly polarized laser and the correction of the polarizing angle of Raman signal are necessary to avoid fake results in the measuring of Raman spectral of single-molecule, which was not noticed in initial papers. (c) 2005 Elsevier B.V. All rights reserved.

Constitutive plasma membrane targeting and microdomain localization of Dok5 studied by single-molecule microscopy

In the present study, single-molecule fluorescence microscopy was used to examine the characteristics of plasma membrane targeting and microdomain localization of enhanced yellow fluorescent protein (eYFP)-tagged wild-type Dok5 and its variants in living Chinese hamster ovary (CHO) cells. We found that Dok5 can target constitutively to the plasma membrane, and the PH domain is essential for this process. Furthermore, single-molecule trajectories analysis revealed that Dok5 can constitutively partition into microdomain on the plasma membrane. Finally, the potential mechanism of microdomain localization of Dok5 was discussed. This study provided insights into the characteristics of plasma membrane targeting and microdomain localization of Dok5 in living CHO cells. (C) 2008 Elsevier B.V. All rights reserved.

Heterodimerization of integrin Mac-1 subunits studied by single-molecule imaging

Heterodimerization of integrin Mac-1 (alpha(M) beta(2)) Subunits plays important role on regulating leukocytes adhesion to extracellular matrix or endothelial cells. Here, using total internal reflection microscopy, we investigated the heterodimerization of integrin Mac-1 subunits at the single-molecule level in live cells. Individual alpha(M) subunit fused to the enhanced yellow fluorescent protein (eYFP) was imaged at the basal plasma membrane of live Chinese hamster ovary (CHO) cells. Through analysis of mean square displacement (MSD), diffusion coefficient, the size of restricted domain and fraction of molecules undergoing restricted diffusion, we found that as compared with the diffusion in the absence of beta(2) subunit, the diffusion of single-molecule of alpha(M)-YFP was suppressed significantly in the presence of beta(2) subunit. Thus, based on the oligomerization-induced trapping model, we suggested that in the presence of beta(2) subunit, the am subunit may form heterodimer with it. (C) 2008 Elsevier Inc. All rights reserved.

Single-molecule detection in a liquid by surface-enhanced resonance Raman scattering

Surface-enhanced resonance Raman scattering (SERRS) of Rhodamine 6G (R6G) adsorbed on colloidal silver clusters in a liquid has been studied. The first observation of single molecule resonance Raman scattering in a liquid in a probed volume of 10 pL was achieved. Anisotropy of SERRS spectra of single R6G molecule and huge SERRS spectra were observed and compared with that of single molecule fixed in the dried films of sols, which revealed the intricate complex interaction between R6G molecules and the environment in a liquid.

Exploring the Origin of Power Law Distribution in Single-Molecule Conformation Dynamics: Energy Landscape Perspectives

We explored the origin of power law distribution observed in single-molecule conformational dynamics experiments. By establishing a kinetic master equation approach to study statistically the microscopic state dynamics, we show that the underlying landscape with exponentially distributed density of states leads to power law distribution of kinetics. The exponential density of states emerges when the system becomes glassy and landscape becomes rough with significant trapping.

Probing Charge Transport of Ruthenium-Complex-Based Molecular Wires at the Single-Molecule Level

A ruthenium(II) bis(sigma-arylacetylide)-complex-based molecular wire functionalized with thiolacetyl alligator clips at both ends (OPERu) was used to fabricate gold substrate-molecular wire-conductive tip junctions. To elucidate the ruthenium-complex-enhanced charge transport, we conducted a single-molecule level investigation using the technique-combination method, where electronic delay constant, single-molecular conductance, and barrier height were obtained by scanning tunneling microscopy (STM) apparent height measurements, STM break junction measurements, and conductive probe-atomic force microscopy (CP-AFM) measurements, respectively.

Full View of Single-Molecule Force Spectroscopy of Polyaniline in Oxidized, Reduced, and Doped States

The macroscopic mechanical properties of polyaniline (PANI) lie mainly on two factors, the structure of molecular aggregations of polymers and the mechanical properties of a single polymer chain. The former factor is swell revealed; however, the latter is rarely studied. In this article, we have employed atomic force microscopy-based single-molecule force spectroscopy to investigate the mechanical properties of a kind of water-soluble PANI at a single-molecular level. We have carried out the study comparatively on single-chain-stretching experiments of oxidized, reduced, and doped PANI and obtained a full view of the single-chain elasticity of PANI in all these states. It is found that oxidized and reduced PANI chains are rigid, and the oxidized PANI is more rigid than the reduced PANI. Such a difference in single-chain elasticity can be rationalized by the molecular structures that are composed of benzenoid diamine and quinoid diimine its different proportions. The doped PANI has been found to be more flexible than the oxidized and reduced PANI, and the modified freely jointed chain parameters of doped PANI are similar with those of a common flexible-chain polymer.

Four New Lanthanide-Nitronyl Nitroxide (Ln(III)=Pr-III, Sm-III, Eu-III, Tm-III) Complexes and a Tb-III Complex Exhibiting Single-Molecule Magnet Behavior

Five new complexes based on rare-earth-radical [Ln(hfac)(3)(NIT-5-Br-3py)](2) (Ln=Pr (1), Sm (2), Eu (3), Tb (4), Tm (5); hfac = hexafluoroacetylacetonate; NIT-5-Br-3py = 2-(4,4,5,5-tetramethyl-3-oxylimidazoline-1-oxide)-5-bromo-3-pyridine) have been synthesized and characterized by X-ray crystal diffraction. The single-crystal structures show that these complexes have similar structures, in which a NIT-5-Br-3py molecule acts as a bridging ligand linking two Ln(III) ions through the oxygen atom of the N-O group and nitrogen atom from the pyridine ring to form a four-spin system. Both static and dynamic magnetic properties were measured for complex 4, which exhibits single-molecule magnetism behavior.

A monometallic tri-spin single-molecule magnet based on rare earth radicals

A mononuclear tri-spin single-molecule magnet based on the rare earth radical [Tb(hfac)(3)(NITPhOEt)(2)] (NITPhOEt = 4'-ethoxy-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) has been synthesized, structurally characterized and the alternating current signals show a slow relaxation of magnetization and frequency-dependent signals.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Single molecule dynamics and statistical fluctuations of gene regulatory networks: A repressilator

The authors developed a time dependent method to study the single molecule dynamics of a simple gene regulatory network: a repressilator with three genes mutually repressing each other. They quantitatively characterize the time evolution dynamics of the repressilator. Furthermore, they study purely dynamical issues such as statistical fluctuations and noise evolution. They illustrated some important features of the biological network such as monostability, spirals, and limit cycle oscillation. Explicit time dependent Fano factors which describe noise evolution and show statistical fluctuations out of equilibrium can be significant and far from the Poisson distribution. They explore the phase space and the interrelationships among fluctuations, order, amplitude, and period of oscillations of the repressilators. The authors found that repressilators follow ordered limit cycle orbits and are more likely to appear in the lower fluctuating regions. The amplitude of the repressilators increases as the suppressing of the genes decreases and production of proteins increases. The oscillation period of the repressilators decreases as the suppressing of the genes decreases and production of proteins increases.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.