Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center.

Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Šfrom the Cu. For CuII , PET from label to Cu occurs at a rate of (4.8±0.3)×104  s-1 and back at (0.7±0.1)×103  s-1 . With CuI the numbers are (3.3±0.7)×106  s-1 and (1.0±0.1)×104  s-1 . Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm-1 , respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label.

Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells.

Aggregation of α-synuclein has been linked to both familial and sporadic Parkinson's disease. Recent studies suggest that α-synuclein aggregates may spread from cell to cell and raise questions about the propagation of neurodegeneration. While continuous progress has been made characterizing α-synuclein aggregates in vitro, there is a lack of information regarding the structure of these species inside the cells. Here, we use confocal fluorescence microscopy in combination with direct stochastic optical reconstruction microscopy, dSTORM, to investigate α-synuclein uptake when added exogenously to SH-SY5Y neuroblastoma cells, and to probe in situ morphological features of α-synuclein aggregates with near nanometer resolution. We demonstrate that using dSTORM, it is possible to follow noninvasively the uptake of extracellularly added α-synuclein aggregates by the cells. Once the aggregates are internalized, they move through the endosomal pathway and accumulate in lysosomes to be degraded. Our dSTORM data show that α-synuclein aggregates remain assembled after internalization and they are shortened as they move through the endosomal pathway. No further aggregation was observed inside the lysosomes as speculated in the literature, nor in the cytoplasm of the cells. Our study thus highlights the super-resolution capability of dSTORM to follow directly the endocytotic uptake of extracellularly added amyloid aggregates and to probe the morphology of in situ protein aggregates even when they accumulate in small vesicular compartments.

Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit.

Photosynthetic reaction centres show promise for biomolecular electronics as nanoscale solar-powered batteries and molecular diodes that are amenable to atomic-level re-engineering. In this work the mechanism of electron conduction across the highly tractable Rhodobacter sphaeroides reaction centre is characterized by conductive atomic force microscopy. We find, using engineered proteins of known structure, that only one of the two cofactor wires connecting the positive and negative termini of this reaction centre is capable of conducting unidirectional current under a suitably oriented bias, irrespective of the magnitude of the bias or the applied force at the tunnelling junction. This behaviour, strong functional asymmetry in a largely symmetrical protein-cofactor matrix, recapitulates the strong functional asymmetry characteristic of natural photochemical charge separation, but it is surprising given that the stimulus for electron flow is simply an externally applied bias. Reasons for the electrical resistance displayed by the so-called B-wire of cofactors are explored.

Tracking electrons in biological macromolecules: from ensemble to single molecule.

Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level.

Nanoscale methods for single-molecule electrochemistry.

The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.

Photosynthetic protein complexes as bio-photovoltaic building blocks retaining a high internal quantum efficiency.

Photosynthetic compounds have been a paradigm for biosolar cells and biosensors and for application in photovoltaic and photocatalytic devices. However, the interconnection of proteins and protein complexes with electrodes, in terms of electronic contact, structure, alignment and orientation, remains a challenge. Here we report on a deposition method that relies on the self-organizing properties of these biological protein complexes to produce a densely packed monolayer by using Langmuir-Blodgett technology. The monolayer is deposited onto a gold electrode with defined orientation and produces the highest light-induced photocurrents per protein complex to date, 45 µA/cm(2) (with illumination power of 23 mW/cm(2) at 880 nm), under ambient conditions. Our work shows for the first time that a significant portion of the intrinsic quantum efficiency of primary photosynthesis can be retained outside the biological cell, leading to an internal quantum efficiency (absorbed photon to electron injected into the electrode) of the metal electrode-protein complex system of 32%.

Insights into the excitonic states of individual chlorosomes from Chlorobaculum tepidum.

Green-sulfur bacteria have evolved a unique light-harvesting apparatus, the chlorosome, by which it is perfectly adapted to thrive photosynthetically under extremely low light conditions. We have used single-particle, optical spectroscopy to study the structure-function relationship of chlorosomes each of which incorporates hundreds of thousands of self-assembled bacteriochlorophyll (BChl) molecules. The electronically excited states of these molecular assemblies are described as Frenkel excitons whose photophysical properties depend crucially on the mutual arrangement of the pigments. The signature of these Frenkel excitons and its relation to the supramolecular organization of the chlorosome becomes accessible by optical spectroscopy. Because subtle spectral features get obscured by ensemble averaging, we have studied individual chlorosomes from wild-type Chlorobaculum tepidum by polarization-resolved fluorescence-excitation spectroscopy. This approach minimizes the inherent sample heterogeneity and allows us to reveal properties of the exciton states without ensemble averaging. The results are compared with predictions from computer simulations of various models of the supramolecular organization of the BChl monomers. We find that the photophysical properties of individual chlorosomes from wild-type Chlorobaculum tepidum are consistent with a (multiwall) helical arrangement of syn-anti stacked BChl molecules in cylinders and/or spirals of different size.

One at a time: intramolecular electron-transfer kinetics in small laccase observed during turnover.

Single-molecule enzymology provides an unprecedented level of detail about aspects of enzyme mechanisms which have been very difficult to probe in bulk. One such aspect is intramolecular electron transfer (ET), which is a recurring theme in the research on oxidoreductases containing multiple redox-active sites. We measure the intramolecular ET rates between the copper centers of the small laccase from Streptomyces coelicolor at room temperature and pH 7.4, one molecule at a time, during turnover. The forward and backward rates across many molecules follow a log-normal distribution with means of 460 and 85 s(-1), respectively, corresponding to activation energies of 347 and 390 meV for the forward and backward rates. The driving force and the reorganization energy amount to 0.043 and 1.5 eV, respectively. The spread in rates corresponds to a spread of ∼30 meV in the activation energy. The second-order rate constant for reduction of the T1 site amounts to 2.9 × 10(4) M(-1) s(-1). The mean of the distribution of forward ET rates is higher than the turnover rate from ensemble steady-state measurements and, thus, is not rate limiting.

Bi-enzyme sensor for phenolic compounds with fluorescent read-out.

In this paper, the use of tyrosinase (Ty) from Streptomyces antibioticus, labeled with a fluorescent tag, in combination with soluble quinoprotein (PQQ-containing) glucose dehydrogenase (s-GDH) to measure trace amounts of phenols is explored. Proof of concept is provided by a series of experiments, which show a clear quantitative dependence of the response on the phenol concentration. One of the advantages of the detection system is that apart from a standard fluorimeter no further instrumentation is required.

Probing redox proteins on a gold surface by single molecule fluorescence spectroscopy.

The interaction between the fluorescently labeled redox protein, azurin, and a thin gold film is characterized using single-molecule fluorescence intensity and lifetime measurements. Fluorescence quenching starts at distances below 2.3 nm from the gold surface. At shorter distances the quantum yield may decrease down to fourfold for direct attachment of the protein to bare gold. Outside of the quenching range, up to fivefold enhancement of the fluorescence is observed on average with increasing roughness of the gold layer. Fluorescence-detected redox activity of individual azurin molecules, with a lifetime switching ratio of 0.4, is demonstrated for the first time close to a gold surface.

Fluorescence Excitation Spectra from Individual Chlorosomes of the Green Sulfur Bacterium Chlorobaculum tepidum.

We performed polarization-resolved fluorescence excitation spectroscopy on individual chlorosomes from the photosynthetic green sulfur bacterium Chlorobaculum tepidum. The experiments were conducted at room temperature and under cryogenic conditions. All spectra showed a strong intensity modulation as a function of the polarization of the incident radiation, and we determined the modulation ratio as a function of the excitation energy. Under ambient conditions this ratio shows only little variation across the absorption band, whereas the low-temperature experiments clearly revealed that the broad absorption band around 740 nm consists of several spectral contributions.

Sensitive detection of histamine using fluorescently labeled oxido-reductases.

A detection scheme is described by which the histamine contents of biological samples can be established. The scheme is based on the use of methylamine dehydrogenase (MADH) which converts primary amines into the corresponding aldehydes and ammonia. The generated reducing equivalents are subsequently transferred to the physiological partner of MADH, amicyanin, which thereby is converted from the oxidized blue-colored form into the reduced colorless form. The change in absorption is detected by monitoring the fluorescence of a covalently attached Cy5 dye label whose fluorescence is (partly) quenched by Förster resonance energy transfer (FRET) to the Cu-site of the amicyanin. The quenching efficiency and, thereby, the label fluorescence, depends on the oxidation state of the amicyanin. When adding histamine to the assay mixture the proportionality between the substrate concentration and the observed rate of the fluorescence increase has enabled this assay as a sensor method with high sensitivity. The MADH and amicyanin composition can be tuned so that the sensor can be adapted over a broad range of histamine concentrations (13 nM-225 µM). The lowest concentration detected so far is 13 nM of histamine. The sensor retained its linearity up to 225 µM with a coefficient of variation of 11% for 10 measurements of 100nM histamine in a 100 µL sample volume. The use of a label fluorescing around 660 nm helps circumventing the interference from background fluorescence in biological samples. The sensor has been tested to detect histamine in biological fluids such as fish extracts and blood serum.

Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase.

Single-molecule measurements are a valuable tool for revealing details of enzyme mechanisms by enabling observation of unsynchronized behavior. However, this approach often requires immobilizing the enzyme on a substrate, a process which may alter enzyme behavior. We apply a microfluidic trapping device to allow, for the first time, prolonged solution-phase measurement of single enzymes in solution. Individual redox events are observed for single molecules of a blue nitrite reductase and are used to extract the microscopic kinetic parameters of the proposed catalytic cycle. Changes in parameters as a function of substrate concentration are consistent with a random sequential substrate binding mechanism.

Orientational control over nitrite reductase on modified gold electrode and its effects on the interfacial electron transfer.

Recently, studies have been reported in which fluorescently labeled redox proteins have been studied with a combination of spectroscopy and electrochemistry. In order to understand the effect of the dye on the protein-electrode interaction, voltammetry and surface analysis have been performed on protein films of dye-labeled and unlabeled forms of a cysteine-surface variant (L93C) and the wild type (wt) of the copper containing nitrite reductase (NiR) from Alcaligenes faecalis S6. The protein has been adsorbed onto gold electrodes modified with self-assembled monolayers (SAMs) made up of 6-mercaptohexanol (6-OH) and mixtures of various octanethiols. Electrochemical and surface-analytical techniques were utilized to explore the influence of the SAM composition on wt and L93C NiR enzyme activity and the orientation of the enzyme molecules with respect to the electrode/SAM. The unlabeled L93C NiR enzyme is only electroactive on mixed SAMs composed of positive 8-aminooctanethiol (8-NH(2)) and 8-mercaptooctanol (8-OH). No enzymatic activity is observed on SAMs consisting of pure 6-OH, 8-OH, or pure 8-NH(2). Modification of L93C NiR with the ATTO 565 dye resulted in enzymatic activity on SAMs of 6-OH, but not on SAMs of 8-OH. Quartz crystal microbalance with dissipation measurements show that well-ordered and rigid protein films (single orientation of the protein) are formed when NiR is electroactive. By contrast, electrode-NiR combinations for which no electrochemical activity is observed still have NiR adsorbed on the surfaces, but a less-structured and water-rich film is formed. For the unlabeled L93C NiR, bilayer formation is observed, suggesting that the Cys93 residue is orientated away from the surface and able to form disulfide bridges to a second layer of L93C NiR. The results indicate that interfacial electron transfer is only possible if the negatively charged surface patch surrounding the electron-entry site of NiR is directed toward the electrode. This can be achieved either by introducing positive charges in the SAM or, when the SAM does not carry a charge, by labeling the enzyme with an ATTO 565 dye, which has some hydrophobic character, close to the electron entry site of the NiR.

Spectroelectrochemical investigation of intramolecular and interfacial electron-transfer rates reveals differences between nitrite reductase at rest and during turnover.

A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Förster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (≥520 µM), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer.

Enhanced photocurrent generation by photosynthetic bacterial reaction centers through molecular relays, light-harvesting complexes, and direct protein-gold interactions.

The utilization of proteins as nanodevices for solar cells, bioelectronics, and sensors generally necessitates the transfer of electrons to or from a conducting material. Here we report on efforts to maximize photocurrent generation by bacterial photosynthetic reaction center pigment-protein complexes (RCs) interfaced with a metal electrode. The possibility of adhering RCs to a bare gold electrode was investigated with a view to minimizing the distance for electron tunneling between the protein-embedded electron-transfer cofactors and the metal surface. Substantial photocurrents were achieved despite the absence of coating layers on the electrode or engineered linkers to achieve the oriented deposition of RCs on the surface. Comparison with SAM-covered gold electrodes indicating enhanced photocurrent densities was achieved because of the absence of an insulating layer between the photoactive pigments and the metal. Utilizing RCs surrounded by light-harvesting 1 complex resulted in higher photocurrents, surprisingly not due to enhanced photoabsorption but likely due to better surface coverage of uniformly oriented RC-LH1 complexes and the presence of a tetraheme cytochrome that could act as a connecting wire. The introduction of cytochrome-c (cyt-c) as a molecular relay also produced increases in current, probably by intercalating between the adhered RCs or RC-LH1 complexes and the electrode to mediate electron transfer. Varying the order in which components were introduced to the electrode indicated that dynamic rearrangements of RCs and cyt-c occurred at the bare metal surface. An upper limit for current generation could not be detected within the range of the illumination power available, with the maximum current density achieved by RC-LH1 complexes being on the order of 25 µA/cm(2). High currents could be generated consecutively for several hours or days under ambient conditions.

Use of engineered unique cysteine residues to facilitate oriented coupling of proteins directly to a gold substrate.

A prerequisite for any "lab on a chip" device that utilizes an electrical signal from the sensor protein is the ability to attach the protein in a specific orientation onto a conducting substrate. Here, we demonstrate the covalent attachment to a gold surface of light-harvesting membrane proteins, from Rhodobacter sphaeroides, via cysteine (Cys) residues engineered on either the cytoplasmic or periplasmic face. This simple directed attachment is superior in its ability to retain light-harvesting complex (LHC) function, when compared to a similar attachment procedure utilizing a self-assembled monolayer on gold. LH 1 has previously been observed to have superior photostability over LH 2 (Magis et al. [2010] Biochim. Biophys. Acta, 1798, 637-645); this characteristic is maintained even with the introduction of Cys residues.

Channeling of electrons within SLAC, the small laccase from Streptomyces coelicolor.

The reduction kinetics of the fluorescently labeled small laccase (SLAC) from Streptomyces coelicolor was studied by stopped flow kinetic measurements. The tryptophan fluorescence and the emission from a covalently attached label were used to selectively follow the progress of the reduction of the trinuclear copper center (TNC) and the type-1 (T1) Cu site in the enzyme as a function of time. A numerical analysis of the kinetic traces provided new insight into the midpoint potential difference between the T1 and the TNC site as the TNC becomes stepwise charged with electrons. The change in fluorescence of the TNC as the reduction of the TNC proceeds provided evidence that the type-3 dinuclear part of the TNC becomes charged prior to the reduction of the type-2 (T2) center of the TNC. The rate of reduction of the enzyme by dithionite (DT) appeared proportional to the square root of the DT concentration with a rate constant of k(red) = 0.28 +/- 0.02 microM(-1/2) s(-1).