The structural dynamics of proteins is crucial to their biological functions. A precise and convenient method to determine the structural changes of a protein is still urgently needed. Herein, we employ fluorescence correlation spectroscopy (FCS) to track the structural transition of bovine serum albumin (BSA) in low concentrated cationic (cetyltrimethylammonium chloride, CTAC), anionic (sodium dodecyl sulfate, SDS), and nonionic (pentaethylene glycol monododecyl ether, C₁₂E₅ and octaethylene glycol monododecyl ether, C₁₂E₈) surfactant solutions. BSA is labelled with the fluorescence dye called ATTO-488 (ATTO-BSA) to obtain steady fluorescence signals for measurements. We find that the diffusion coefficient of BSA decreases abruptly with the surfactant concentration in ionic surfactant solutions at concentrations below the critical micelle concentration (CMC), while it is constant in nonionic surfactant solutions. According to the Stokes–Sutherland–Einstein equation, the hydrodynamic radius of BSA in ionic surfactant solutions amounts to ∼6.5 nm, which is 1.7 times larger than in pure water or in nonionic surfactant solutions (3.9 nm). The interaction between BSA and ionic surfactant monomers is believed to cause the structural transition of BSA. We confirm this proposal by observing a sudden shift of the fluorescence lifetime of ATTO-BSA, from 2.3 ns to ∼3.0 ns, in ionic surfactant solutions at the concentration below CMC. No change in the fluorescence lifetime is detected in nonionic surfactant solutions. Moreover, by using FCS we are also able to identify whether the structural change of protein results from its self-aggregation or unfolding.

This paper demonstrates a renewed procedure for the quantification of surface-enhanced Raman scattering (SERS) enhancement factors with improved precision. The principle of this method relies on deducting the resonance Raman scattering (RRS) contribution from surface-enhanced resonance Raman scattering (SERRS) to end up with the surface enhancement (SERS) effect alone. We employed 1,8,15,22-tetraaminophthalocyanato-cobalt(II) (4α-Co^IITAPc), a resonance Raman- and electrochemically redox-active chromophore, as a probe molecule for RRS and SERRS experiments. The number of 4α-Co^IITAPc molecules contributing to RRS and SERRS phenomena on plasmon inactive glassy carbon (GC) and plasmon active GC/Au surfaces, respectively, has been precisely estimated by cyclic voltammetry experiments. Furthermore, the SERS substrate enhancement factor (SSEF) quantified by our approach is compared with the traditionally employed methods. We also demonstrate that the present approach of SSEF quantification can be applied for any kind of different SERS substrates by choosing an appropriate laser line and probe molecule.

We discuss a quantitative influence of macromolecular crowding on biological processes: motion, bimolecular reactions, and gene expression in prokaryotic and eukaryotic cells. We present scaling laws relating diffusion coefficient of an object moving in a cytoplasm of cells to a size of this object and degree of crowding. Such description leads to the notion of the length scale dependent viscosity characteristic for all living cells. We present an application of the length-scale dependent viscosity model to the description of motion in the cytoplasm of both eukaryotic and prokaryotic living cells. We compare the model with all recent data on diffusion of nanoscopic objects in HeLa, and E. coli cells. Additionally a description of the mobility of molecules in cell nucleus is presented. Finally we discuss the influence of crowding on the bimolecular association rates and gene expression in living cells.

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS M_w = 12.91 kDa) and 1550 s (e.g. for PepA₆ of M_w = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between  for large proteins up to  for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.

We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10⁻³–0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data.

The mobility of segments of the polymer mesh in a solution determines the dynamic response of the depletion layer (DL) to mechanical stimuli. This phenomenon can be used to vastly decrease the local viscosity experienced by any device performing periodic motion at the nano- and microscale in complex liquids. We refined the vibrating quartz tuning fork (QTF) method to probe the viscosity of model aqueous solutions of polyethylene glycol, covering a broad range of molecular weights (3 kDa to 1 MDa) and QTF oscillation amplitudes (50 pm to 100 nm). For semidilute solutions of PEGs of high molecular weight, we found a drop of local viscosity, up to two orders of magnitude below the bulk value. We propose a simple explanation based on the motion of the depletion layer, strongly supported by rheometry and dynamic light scattering results. We show that it is possible to directly probe the viscosity of the DL and increase its thickness far above the equilibrium value. The key role is played by the rate of relaxation of the entangled system. The relevance of this paradigm ranges from the basic research on dynamics of entangled systems to design of energy-efficient nanomachines operating in a crowded environment.

We developed a laser-based method to quantify the double labeling efficiency of double-stranded DNA (dsDNA) in a fluorescent dsDNA pool with fluorescence correlation spectroscopy (FCS). Though, for quantitative biochemistry, accurate measurement of this parameter is of critical importance, before our work it was almost impossible to quantify what percentage of DNA is doubly labeled with the same dye. The dsDNA is produced by annealing complementary single-stranded DNA (ssDNA) labeled with the same dye at 5′ end. Due to imperfect ssDNA labeling, the resulting dsDNA is a mixture of doubly labeled dsDNA, singly labeled dsDNA and unlabeled dsDNA. Our method allows the percentage of doubly labeled dsDNA in the total fluorescent dsDNA pool to be measured. In this method, we excite the imperfectly labeled dsDNA sample in a focal volume of <1 fL with a laser beam and correlate the fluctuations of the fluorescence signal to get the FCS autocorrelation curves; we express the amplitudes of the autocorrelation function as a function of the DNA labeling efficiency; we perform a comparative analysis of a dsDNA sample and a reference dsDNA sample, which is prepared by increasing the total dsDNA concentration c (c > 1) times by adding unlabeled ssDNA during the annealing process. The method is flexible in that it allows for the selection of the reference sample and the c value can be adjusted as needed for a specific study. We express the precision of the method as a function of the ssDNA labeling efficiency or the dsDNA double labeling efficiency. The measurement precision can be controlled by changing the c value.

We postulate an empirical scaling equation, which accurately describes flow of polymer solutions, complimenting the paradigm of length-scale-dependent viscosity. We investigated poly(ethylene glycol) aqueous solutions and observed an exponential dependence of viscosity on the hydrodynamic radius of a single coil R_h divided by the correlation length ξ. Properties of the system changed abruptly with the onset of chain entanglement at concentration corresponding to ξ = R_h. We propose a single equation valid for all the investigated systems, analyze the physical meaning of parameters appearing therein and discuss the impact of chain entanglement. Viscous flow is treated as an activated process, following the Eyring rate theory. We show that the difference of activation energy for flow between pure solvent and polymer solution, ΔE_a, is a function of concentration, whose derivative has a discontinuity at the crossover concentration. For dilute PEG solutions ΔE_a takes values of up to several kJ/mol and is proportional to the intrinsic viscosity. We successfully apply the scaling approach to the diffusive motion of a protein (aldolase) in solutions of 25 kg/mol PEO (concentrations of 2–20%), investigated by fluorescence correlation spectroscopy (FCS). A significant difference in the influence of crowding on translational and rotational motion of the protein is revealed.

This communication presents a new pathway for the more precise quantification of surface-enhanced Raman scattering (SERS) enhancement factor via deducing resonance Raman scattering (RRS) effect from surface-enhanced resonance Raman scattering (SERRS). To achieve this, a self-assembled monolayer of 1,8,15,22-tetraaminophthalocyanatocobalt(II) (4α-Co^IITAPc) is formed on plasmon inactive glassy carbon (GC) and plasmon active GC/AuNP surface. The surfaces are subsequently used as common probes for electrochemical and Raman (RRS and SERRS) studies. The most crucial parameters required for the quantification of SERS substrate enhancement factor (SSEF) such as real surface area of GC/AuNPs substarte and the number of 4α-Co^IITAPc molecules contributing to RRS (on GC) and SERRS (on GC/AuNPs) are precisely estimated by cyclic voltammetry experiments. The present approach of SSEF quantification can be applied to varieties of surfaces by choosing an appropriate laser line and probe molecule for each surface.

We have investigated the oxidation of ferrocene at a flowing organic solvent|aqueous electrolyte|solid electrode junction in a microfluidic setup using cyclic voltammetry and fluorescent laser scanning confocal microscopy. At low flow rates the oxidation current decreases with increasing flow, contrary to the Levich equation, but at higher flow rates the current increases linearly with the cube root of the flow rate. This behavior is explained using a simple model postulating a smallest effective width of the three-phase junction, which after fitting to the data comes to be ca. 20 μm. The fluorescence microscopy reveals mixing of the two phases close to the PDMS cover, but the liquid|liquid junction is stable close to the glass support. This study shows the importance of the solid|liquid|liquid junctions for the behavior of multiphase systems under microfluidic conditions.

Photosystem II has been purified from a transplastomic strain of Nicotiana tabacum according to two different protocols. Using the procedure described in Piano et al. (Photosynth Res 106:221–226, 2010) it was possible to isolate highly active PSII composed of monomers and dimers but depleted in their PsbS protein content. A “milder” procedure than the protocol reported by Fey et al. (Biochim Biophys Acta 1777:1501–1509, 2008) led to almost exclusively monomeric PSII complexes which in part still bind the PsbS protein. This finding might support a role for PSII monomers in higher plants.

We present a method of prediction of in vivo association rate constants between proteins from in vitro rate constants. This model accounts for the changes in length-scale dependent viscosity of the cytoplasm of a living cell and interaction potential between proteins. We explain the unexpected results obtained for protein–protein association rate constants in the cytoplasm of HeLa cells determined by Phillip et al. Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 1461.

We use molecular dynamics (MD) simulations of a two-component Lennard-Jones (LJ) fluid to analyze the energy flux from an inert gas to the interface of an evaporating liquid droplet. Using this analysis we derive an analytical equation for the radius of the droplet, R(t), as a function of time, t. The formula is valid for evaporation of droplets of any material or size into the gas characterized by the mean free path, λ, much larger than the molecular diameter, σ. We find linear dependence R(t) ∼ t, for high λ/R(t) ratios and standard law R²(t) ∼ t for small λ/R(t) ratios. We apply equation for R(t) to experimental results of evaporation of water micro-droplets into air and glycerol, diethylene glycol and triethylene glycol micro-droplets into the nitrogen gas evaporating in time from seconds to tens of minutes. The experimental results together with computer simulations span 12 orders of magnitude of evaporation times and more than 3 orders of magnitude of droplets’ radii. In the experiments the evaporation rate is governed by a very small difference in temperatures (from one tenth of mK to a few K) between the gas far from the droplet and evaporating liquid. From MD simulations we also obtain suitable boundary conditions for the energy flux at the interface, used in irreversible thermodynamics, and the accommodation coefficients used in kinetic models of evaporation.

We identified a mechanism of fluorescence quenching of CdSe/ZnS quantum dots (QDs) coated with two organic layers, octadecylamine and an amphiphilic polymer containing COOH groups, by nonionic polyoxyethylene-based (C₁₂E_n) surfactants. The surfactant molecules by themselves do not affect the fluorescence of the QDs. For the quenching to occur, “wrapping” of the QDs by a bilayer of the surfactant molecules is necessary. The formation of the bilayer causes an irreversible detachment (“wresting”) of the ligand molecules, accompanied by the creation of quenching sites on the QD surface. Due to its two-stage nature, we refer to the quenching mechanism as the “wrap-and-wrest” mechanism. The adsorption of the surfactant on the QD surface is a relatively slow process, occurring within minutes or hours. Such long quenching times allowed monitoring surfactant adsorption progress in real time. The fluorescence signal decays exponentially, and the decay time is inversely proportional to the surfactant concentration in solution.

We measure the frequency of collective molecular precession as a function of temperature in the ferroelectric liquid crystalline monolayer at the water–air interface. This movement is driven by the unidirectional flux of evaporating water molecules. The collective rotation in the monolayer with angular velocities ω ∼ 1 s⁻¹ (at T = 312 K) to 10⁻² s⁻¹ (at T = 285.8 K) is 9 to 14 orders of magnitude slower than rotation of a single molecule (typically ω ∼ 10⁹ to 10¹² s⁻¹). The angular velocity reaches 0 upon approach to the two dimensional liquid-to-solid transition in the monolayer at T = 285.8 K. We estimate the rotational viscosity, γ₁, in the monolayer and the torque, Γ, driving this rotation. The torque per molecule equals Γ = 5.7 × 10⁻⁸ pN nm at 310 K (γ₁ = 0.081 Pa s, ω = 0.87 s⁻¹). The energy generated during one turn of the molecule at the same temperature is W = 3.5 × 10⁻²⁸ J. Surprisingly, although this energy is 7 orders of magnitude smaller than the thermal energy, k_BT (310 K) = 4.3 × 10⁻²¹ J, the rotation is very stable. The potential of the studied effect lies in the collective motion of many (>10¹²) “nano-windmills” acting “in concerto” at the scale of millimetres. Therefore, such systems are candidates for construction of artificial molecular engines, despite the small energy density per molecular volume (5 orders of magnitude smaller than for a single ATPase).