Acceptor Fluorophores Research Articles

On the Origin of Multi-Exponential Kinetics in Peptide Binding to Phospholipid Vesicles

Binding kinetics of amphipathic peptides to phospholipid bilayer vesicles are generally well described by a single exponential function. However, closer inspection of the data sometimes reveals the presence of additional exponential phases. These usually depend on the exact experimental conditions and on the peptide studied, but are indicative of other processes that contribute to the binding kinetics. We investigated the binding of a model amphipathic peptide, Lysette-26, to unilamellar lipid vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a function of lipid and peptide concentration. Lysette-26 is a 22 residue peptide with the sequence IISTIGDLVKWIIDTVKWIIDTVNKFTKK. The peptide binds well to zwitterionic lipid bilayer membranes and forms an amphipathic α-helix when bound at the membrane-water interface. Peptide binding was measured through fluorescence energy transfer from the intrinsic tryptophan residue in the peptide to an acceptor fluorophore embedded in the membrane at low concentrations. A series of exact kinetic models was developed to describe the experimental data. We found that the kinetics of peptide binding to POPC vesicles depended strongly on peptide concentration in solution. The model that best described the experimental data included the presence of peptide monomers and aggregates in solution that bind independently and with different rate constants to the lipid vesicles. Peptide aggregation is favored at higher peptide concentrations, leading to the appearance of an additional exponential phase. Based on the kinetic models, other processes, such as peptide insertion or translocation across the bilayer, could be excluded as the source of the second exponential phase in the binding kinetics.

Plasmon-Enhanced Resonance Energy Transfer from a Conjugated Polymer to Fluorescent Multilayer Core−Shell Nanoparticles: A Photophysical Study

The influence of metallic silver nanoparticles on Forster resonance energy transfer (FRET) between a water-soluble cationic conjugated polymer and fluorescent multilayer Ag@SiO2@SiO2+FiTC core−shell nanoparticles was characterized using a combination of light scattering and luminescence techniques. Positioning the fluorescent polymer 7 nm away from the surface of a 45 nm silver nanoparticle with a silica spacing layer increases its quantum yield to 77%, as compared to 3% when measured as an isolated emitter. In the presence of the metallic core, the luminescence of the nanoparticle-bound acceptor fluorophore is increased at the expense of the polymer donor luminescence, and time-resolved fluorescence measurements indicate an enhancement of FRET efficiency from 4 to 50%, an increase in the Forster distance from 50 to 85 A, and a resonant transfer rate between donors and acceptors more than 2 orders of magnitude higher than that measured in the absence of the metal core. The strong influence of plasmonic co...

Ultra-Sensitive Fluorescent Sensor for Hg2+ Based on a Donor−Acceptor−Donor Framework

A new fluoroionophore [E-4,4'-di(N-(2-pyridyl)amino)stilbene, E1] with a donor-acceptor-donor framework, which features a central stilbene (acceptor) fluorophore and two terminal pyridylamino (donor) ionophores, is reported. The probe displays an ultrasensitive fluorescence quenching response toward Hg(2+) in H(2)O/THF. Coordination of Hg(2+) to E1 affords a 2:1 complex, enabling the detection of Hg(2+) at a concentration as low as 4.4 × 10(-14) M. The interactions between the two species have been thoroughly characterized with UV-vis absorption spectroscopy, fluorescence spectroscopy, and nuclear magnetic resonance spectroscopy. Density functional theory calculations provide further insights into the nature of the fluorescence quenching response. In contrast, a fluorescent molecule with the donor-acceptor architecture, E-4-(N-(2-pyridyl)amino)stilbene (E4), exhibits a greatly attenuated fluorescence quenching response toward Hg(2+).

Dual-Channel Single-Molecule Fluorescence Resonance Energy Transfer to Establish Distance Parameters for RNA Nanoparticles

The increasing interest in RNA nanotechnology and the demonstrated feasibility of using RNA nanoparticles as therapeutics have prompted the need for imaging systems with nanometer-scale resolution for RNA studies. Phi29 dimeric pRNAs can serve as building blocks in assembly into the hexameric ring of the nanomotors, as modules of RNA nanoparciles, and as vehicles for specific delivery of therapeutics to cancers or viral infected cells. The understanding of the 3D structure of this novel RNA dimeric particle is fundamentally and practically important. Although a 3D model of pRNA dimer has been proposed based on biochemical analysis, no distance measurements or X-ray diffraction data have been reported. Here we evaluated the application of our customized single-molecule dual-viewing system for distance measurement within pRNA dimers using single-molecule Fluorescence Resonance Energy Transfer (smFRET). Ten pRNA monomers labeled with single donor or acceptor fluorophores at various locations were constructed and eight dimers were assembled. smFRET signals were detected for six dimers. The tethered arm sizes of the fluorophores were estimated empirically from dual-labeled RNA/DNA standards. The distances between donor and acceptor were calculated and used as distance parameters to assess and refine the previously reported 3D model of the pRNA dimer. Distances between nucleotides in pRNA dimers were found to be different from those of the dimers bound to procapsid, suggesting a conformational change of the pRNA dimer upon binding to the procapsid.

Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer

Many biological processes, such as gene transcription and replication, involve opening and closing of short regions of double-stranded DNA (dsDNA). Few techniques, however, can study these processes in real time or at the single-molecule level. Here, we present a Förster resonance energy transfer (FRET) assay that monitors the state of DNA (double- vs single-stranded) at a specific region within a DNA fragment, at both the ensemble level and the single-molecule level. The assay utilizes two closely spaced fluorophores: a FRET donor fluorophore (Cy3B) on the first DNA strand and a FRET acceptor fluorophore (ATTO647N) on the complementary strand. Because our assay is based on quenching and dequenching FRET processes, i.e., the presence or absence of contact-induced fluorescence quenching, we have named it a "quenchable FRET" assay or "quFRET". Using lac promoter DNA fragments, quFRET allowed us to sense transcription bubble expansion and compaction during abortive initiation by bacterial RNA polymerase. We also used quFRET to confirm the mode of action of gp2 (a phage-encoded protein that acts as a potent inhibitor of Escherichia coli transcription) and rifampicin (an antibiotic that blocks transcription initiation). Our results demonstrate that quFRET should find numerous applications in many processes involving DNA opening and closing, as well as in the development of new antibacterial therapies involving transcription.

Signal/Noise Analysis of FRET-Based Sensors

Molecular sensors based on intramolecular Förster resonance energy transfer (FRET) have become versatile tools to monitor regulatory molecules in living tissue. However, their use is often compromised by low signal strength and excessive noise. We analyzed signal/noise (SNR) aspects of spectral FRET analysis methods, with the following conclusions: The most commonly used method (measurement of the emission ratio after a single short wavelength excitation) is optimal in terms of signal/noise, if only relative changes of this uncalibrated ratio are of interest. In the case that quantitative data on FRET efficiencies are required, these can be calculated from the emission ratio and some calibration parameters, but at reduced SNR. Lux-FRET, a recently described method for spectral analysis of FRET data, allows one to do so in three different ways, each based on a ratio of two out of three measured fluorescence signals (the donor and acceptor signal during a short-wavelength excitation and the acceptor signal during long wavelength excitation). Lux-FRET also allows for calculation of the total abundance of donor and acceptor fluorophores. The SNR for all these quantities is lower than that of the plain emission ratio due to unfavorable error propagation. However, if ligand concentration is calculated either from lux-FRET values or else, after its calibration, from the emission ratio, SNR for both analysis modes is very similar. Likewise, SNR values are similar, if the noise of these quantities is related to the expected dynamic range. We demonstrate these relationships based on data from an Epac-based cAMP sensor and discuss how the SNR changes with the FRET efficiency and the number of photons collected.

ChemInform Abstract: Design, Synthesis and Biological Application of Chemical Probes for Bio‐Imaging

AbstractReview: 29 refs.

A20 Interaction of huntingtin and the ryanodine receptor

BackgroundAlterations in cellular calcium homeostasis have been recognised as one of several pathogenic mechanisms in Huntington's disease (HD). The discovery of a direct interaction between the C terminal extremity (C-ter)...

Actin cytoskeleton-dependent Rab GTPase-regulated angiotensin type I receptor lysosomal degradation studied by fluorescence lifetime imaging microscopy

The dynamic regulation of the cellular trafficking of human angiotensin (Ang) type 1 receptor (AT1R) is not well understood. Therefore, we investigated the cellular trafficking of AT1R-enhanced green fluorescent protein (EGFP) (AT1R-EGFP) heterologously expressed in HEK293 cells by determining the change in donor lifetime (AT1R-EGFP) in the presence or absence of acceptor(s) using fluorescence lifetime imaging-fluorescence resonance energy transfer (FRET) microscopy. The average lifetime of AT1R-EGFP in our donor-alone samples was ∼2.33 ns. The basal state lifetime was shortened slightly in the presence of Rab5 (2.01±0.10 ns) or Rab7 (2.11±0.11 ns) labeled with Alexa 555, as the acceptor fluorophore. A 5-min Ang II treatment markedly shortened the lifetime of AT1R-EGFP in the presence of Rab5-Alexa 555 (1.78±0.31 ns) but was affected minimally in the presence of Rab7-Alexa 555 (2.09±0.37 ns). A 30-min Ang II treatment further decreased the AT1R-EGFP lifetime in the presence of both Rab5- and Rab7-Alexa 555. Latrunculin A but not nocodazole pretreatment blocked the ability of Ang II to shorten the AT1R-EGFP lifetime. The occurrence of FRET between AT1R-EGFP (donor) and LAMP1-Alexa 555 (acceptor) with Ang II stimulation was impaired by photobleaching the acceptor. These studies demonstrate that Ang II-induced AT1R lysosomal degradation through its association with LAMP1 is regulated by Rab5/7 via mechanisms that are dependent on intact actin cytoskeletons.

Optimizing Methods to Recover Absolute FRET Efficiency from Immobilized Single Molecules

Microscopy-based fluorescence resonance energy transfer (FRET) experiments measure donor and acceptor intensities by isolating these signals with a series of optical elements. Because this filtering discards portions of the spectrum, the observed FRET efficiency is dependent on the set of filters in use. Similarly, observed FRET efficiency is also affected by differences in fluorophore quantum yield. Recovering the absolute FRET efficiency requires normalization for these effects to account for differences between the donor and acceptor fluorophores in their quantum yield and detection efficiency. Without this correction, FRET is consistent across multiple experiments only if the photophysical and instrument properties remain unchanged. Here we present what is, to our knowledge, the first systematic study of methods to recover the true FRET efficiency using DNA rulers with known fluorophore separations. We varied optical elements to purposefully alter observed FRET and examined protein samples to achieve quantum yields distinct from those in the DNA samples. Correction for calculated instrument transmission reduced FRET deviations, which can facilitate comparison of results from different instruments. Empirical normalization was more effective but required significant effort. Normalization based on single-molecule photobleaching was the most effective depending on how it is applied. Surprisingly, per-molecule γ-normalization reduced the peak width in the DNA FRET distribution because anomalous γ-values correspond to FRET outliers. Thus, molecule-to-molecule variation in gamma has an unrecognized effect on the FRET distribution that must be considered to extract information on sample dynamics from the distribution width.

Distance Variations between Active Sites of H+-Pyrophosphatase Determined by Fluorescence Resonance Energy Transfer

Homodimeric H(+)-pyrophosphatase (H(+)-PPase; EC 3.6.1.1) is a unique enzyme playing a pivotal physiological role in pH homeostasis of organisms. This novel H(+)-PPase supplies energy at the expense of hydrolyzing metabolic byproduct, pyrophosphate (PP(i)), for H(+) translocation across membrane. The functional unit for the translocation is considered to be a homodimer. Its putative active site on each subunit consists of PP(i) binding motif, Acidic I and II motifs, and several essential residues. In this investigation structural mapping of these vital regions was primarily determined utilizing single molecule fluorescence resonance energy transfer. Distances between two C termini and also two N termini on homodimeric subunits of H(+)-PPase are 49.3 + or - 4.0 and 67.2 + or - 5.7 A, respectively. Furthermore, putative PP(i) binding motifs on individual subunits are found to be relatively far away from each other (70.8 + or - 4.8 A), whereas binding of potassium and substrate analogue led them to closer proximity. Moreover, substrate analogue but not potassium elicits significant distance variations between two Acidic I motifs and two His-622 residues on homodimeric subunits. Taken together, this study provides the first quantitative measurements of distances between various essential motifs, residues, and putative active sites on homodimeric subunits of H(+)-PPase. A working model is accordingly proposed elucidating the distance variations of dimeric H(+)-PPase upon substrate binding.

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Extracting Rate Coefficients from Single-Molecule Photon Trajectories and FRET Efficiency Histograms for a Fast-Folding Protein

Recently developed statistical methods by Gopich and Szabo were used to extract folding and unfolding rate coefficients from single-molecule Förster resonance energy transfer (FRET) data for proteins with kinetics too fast to measure waiting time distributions. Two types of experiments and two different analyses were performed. In one experiment bursts of photons were collected from donor and acceptor fluorophores attached to a 73-residue protein, α(3)D, freely diffusing through the illuminated volume of a confocal microscope system. In the second, the protein was immobilized by linkage to a surface, and photons were collected until one of the fluorophores bleached. Folding and unfolding rate coefficients and mean FRET efficiencies for the folded and unfolded subpopulations were obtained from a photon by photon analysis of the trajectories using a maximum likelihood method. The ability of the method to describe the data in terms of a two-state model was checked by recoloring the photon trajectories with the extracted parameters and comparing the calculated FRET efficiency histograms with the measured histograms. The sum of the rate coefficients for the two-state model agreed to within 30% with the relaxation rate obtained from the decay of the donor-acceptor cross-correlation function, confirming the high accuracy of the method. Interestingly, apparently reliable rate coefficients could be extracted using the maximum likelihood method, even at low (<10%) population of the minor component where the cross-correlation function was too noisy to obtain any useful information. The rate coefficients and mean FRET efficiencies were also obtained in an approximate procedure by simply fitting the FRET efficiency histograms, calculated by binning the donor and acceptor photons, with a sum of three-Gaussian functions. The kinetics are exposed in these histograms by the growth of a FRET efficiency peak at values intermediate between the folded and unfolded peaks as the bin size increases, a phenomenon with similarities to NMR exchange broadening. When comparable populations of folded and unfolded molecules are present, this method yields rate coefficients in very good agreement with those obtained with the maximum likelihood method. As a first step toward characterizing transition paths, the Viterbi algorithm was used to locate the most probable transition points in the photon trajectories.

A Divalent Cation Stabilizes the Active Conformation of the B. subtilis RNase P·Pre-tRNA Complex: A Role for an Inner-Sphere Metal Ion in RNase P

Metal ions interact with RNA to enhance folding, stabilize structure, and, in some cases, facilitate catalysis. Assigning functional roles to specifically bound metal ions presents a major challenge in analyzing the catalytic mechanisms of ribozymes. Bacillus subtilis ribonuclease P (RNase P), composed of a catalytically active RNA subunit (PRNA) and a small protein subunit (P protein), catalyzes the 5′-end maturation of precursor tRNAs (pre-tRNAs). Inner-sphere coordination of divalent metal ions to PRNA is essential for catalytic activity but not for the formation of the RNase P·pre-tRNA (enzyme–substrate, ES) complex. Previous studies have demonstrated that this ES complex undergoes an essential conformational change (to the ES ⁎ conformer) before the cleavage step. Here, we show that the ES ⁎ conformer is stabilized by a high-affinity divalent cation capable of inner-sphere coordination, such as Ca(II) or Mg(II). Additionally, a second, lower-affinity Mg(II) activates cleavage catalyzed by RNase P. Structural changes that occur upon binding Ca(II) to the ES complex were determined by time-resolved Förster resonance energy transfer measurements of the distances between donor–acceptor fluorophores introduced at specific locations on the P protein and pre-tRNA 5′ leader. These data demonstrate that the 5′ leader of pre-tRNA moves 4 to 6 Å closer to the PRNA·P protein interface during the ES-to-ES ⁎ transition and suggest that the metal-dependent conformational change reorganizes the bound substrate in the active site to form a catalytically competent ES ⁎ complex.

Control of the orientation of ATF2‐Jun binding and the efficiency of IFNβ gene expression

A heterodimer containing activating transcription factor 2 and c-jun (ATF2-Jun) is an essential component of the multi-protein enhancer complex that regulates the expression of interferon beta (IFNβ) in response to viral infection. Our objectives were to (1) identify factors that influence the orientation of DNA-binding by ATF2-Jun at the IFNβ enhancer using gel-based fluorescence resonance energy transfer (gelFRET) analysis and (2) determine the role of ATF2-Jun orientation in gene expression. In gelFRET, protein-DNA complexes are isolated in a native gel and heterodimer orientation is determined using energy transfer measurements of complexes labeled with donor and acceptor fluorophores. We find that interferon regulatory factor 3 (IRF3) does not influence ATF2-Jun orientation but has dramatic effects when charged residues in either ATF2 or Jun are substituted with alanine. Alanine substitution of symmetrically located charged residues in both ATF2 and Jun restores the effect of IRF3 on wild-type ATF2-Jun orientation and reduces the effect of specific alanine substitutions in IRF3 on IRF3 binding. Alanine substitutions that orient Jun downstream of ATF2 in vitro significantly increase IFNβ mRNA levels in vivo. We conclude that competing alternative interactions between residues in IRF3 and residues in ATF2 and Jun influence ATF2-Jun orientation and the efficiency of endogenous IFNβ gene expression. Supported by NIH Molecular Biophysics Training Grant

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5' and 3' splice sites. During splicing in vitro, we observed a multitude of generally reversible time- and ATP-dependent conformational transitions of individual pre-mRNAs. The conformational dynamics of branchpoint and 3'-splice site mutants differ from one another and from wild type. Because all transitions are reversible, spliceosome assembly appears to be occurring close to thermal equilibrium.

Monitoring a coordinated exchange process in a four-component biological interaction system: development of a time-resolved terbium-based one-donor/three-acceptor multicolor FRET system.

Hormonal regulation of cellular function involves the binding of small molecules with receptors that then coordinate subsequent interactions with other signal transduction proteins. These dynamic, multicomponent processes are difficult to track in cells and even in reconstituted in vitro systems, and most methods can monitor only two-component interactions, often with limited capacity to follow dynamic changes. Through a judicious choice of three organic acceptor fluorophores paired with a terbium donor fluorophore, we have developed the first example of a one-donor/three-acceptor multicolor time-resolved fluorescence energy transfer (TR-FRET) system, and we have exemplified its use by monitoring a ligand-regulated protein-protein exchange process in a four-component biological system. By careful quantification of the emission from each of the three acceptors at the four channels for terbium donor emission, we demonstrate that any of these donor channels can be used to estimate the magnitude of the three FRET signals in this terbium-donor triple-acceptor system with minimal bleedthrough. Using this three-channel terbium-based, TR-FRET assay system, we show in one experiment that the addition of a fluorescein-labeled estrogen agonist displaces a SNAPFL-labeled antiestrogen from the ligand binding pocket of a terbium-labeled estrogen receptor, at the same time causing a Cy5-labeled coactivator to be recruited to the estrogen receptor. This experiment demonstrates the power of a four-color TR-FRET experiment, and it shows that the overall process of estrogen receptor ligand exchange and coactivator binding is a dynamic but precisely coordinated process.

FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry

As the smallest and simplest motor enzymes, kinesins have served as the prototype for understanding the relationship between protein structure and mechanochemical function of enzymes in this class. Conventional kinesin (kinesin-1) is a motor enzyme that transports cargo toward the plus end of microtubules by a processive, asymmetric hand-over-hand mechanism. The coiled-coil neck domain, which connects the two kinesin motor domains, contributes to kinesin processivity (the ability to take many steps in a row) and is proposed to be a key determinant of the asymmetry in the kinesin mechanism. While previous studies have defined the orientation and position of microtubule-bound kinesin motor domains, the disposition of the neck coiled-coil remains uncertain. We determined the neck coiled-coil orientation using a multidonor fluorescence resonance energy transfer (FRET) technique to measure distances between microtubules and bound kinesin molecules. Microtubules were labeled with a new fluorescent taxol donor, TAMRA-X-taxol, and kinesin derivatives with an acceptor fluorophore attached at positions on the motor and neck coiled-coil domains were used to reconstruct the positions and orientations of the domains. FRET measurements to positions on the motor domain were largely consistent with the domain orientation determined in previous studies, validating the technique. Measurements to positions on the neck coiled-coil were inconsistent with a radial orientation and instead demonstrated that the neck coiled-coil is parallel to the microtubule surface. The measured orientation provides a structural explanation for how neck surface residues enhance processivity and suggests a simple hypothesis for the origin of kinesin step asymmetry and "limping."

Gαi and Gβγ Jointly Regulate the Conformations of a Gβγ Effector, the Neuronal G Protein-activated K+ Channel (GIRK)

Stable complexes among G proteins and effectors are an emerging concept in cell signaling. The prototypical G betagamma effector G protein-activated K(+) channel (GIRK; Kir3) physically interacts with G betagamma but also with G alpha(i/o). Whether and how G alpha(i/o) subunits regulate GIRK in vivo is unclear. We studied triple interactions among GIRK subunits 1 and 2, G alpha(i3) and G betagamma. We used in vitro protein interaction assays and in vivo intramolecular Förster resonance energy transfer (i-FRET) between fluorophores attached to N and C termini of either GIRK1 or GIRK2 subunit. We demonstrate, for the first time, that G betagamma and G alpha(i3) distinctly and interdependently alter the conformational states of the heterotetrameric GIRK1/2 channel. Biochemical experiments show that G betagamma greatly enhances the binding of GIRK1 subunit to G alpha(i3)(GDP) and, unexpectedly, to G alpha(i3)(GTP). i-FRET showed that both G alpha(i3) and G betagamma induced distinct conformational changes in GIRK1 and GIRK2. Moreover, GIRK1 and GIRK2 subunits assumed unique, distinct conformations when coexpressed with a "constitutively active" G alpha(i3) mutant and G betagamma together. These conformations differ from those assumed by GIRK1 or GIRK2 after separate coexpression of either G alpha(i3) or G betagamma. Both biochemical and i-FRET data suggest that GIRK acts as the nucleator of the GIRK-G alpha-G betagamma signaling complex and mediates allosteric interactions between G alpha(i)(GTP) and G betagamma. Our findings imply that G alpha(i/o) and the G alpha(i) betagamma heterotrimer can regulate a G betagamma effector both before and after activation by neurotransmitters.

Mapping of the Signal Peptide-Binding Domain of Escherichia coli SecA Using Förster Resonance Energy Transfer

Identification of the signal peptide-binding domain within SecA ATPase is an important goal for understanding the molecular basis of SecA preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. In this study, Forster resonance energy transfer methodology was employed to map the location of the SecA signal peptide-binding domain using a collection of functional monocysteine SecA mutants and alkaline phosphatase signal peptides labeled with appropriate donor-acceptor fluorophores. Fluorescence anisotropy measurements yielded an equilibrium binding constant of 1.4 or 10.7 muM for the alkaline phosphatase signal peptide labeled at residue 22 or 2, respectively, with SecA, and a binding stoichiometry of one signal peptide bound per SecA monomer. Binding affinity measurements performed with a monomer-biased mutant indicate that the signal peptide binds equally well to SecA monomer or dimer. Distance measurements determined for 13 SecA mutants show that the SecA signal peptide-binding domain encompasses a portion of the preprotein cross-linking domain but also includes regions of nucleotide-binding domain 1 and particularly the helical scaffold domain. The identified region lies at a multidomain interface within the heart of SecA, surrounded by and potentially responsive to domains important for binding nucleotide, mature portions of the preprotein, and the SecYEG channel. Our FRET-mapped binding domain, in contrast to the domain identified by NMR spectroscopy, includes the two-helix finger that has been shown to interact with the preprotein during translocation and lies at the entrance to the protein-conducting channel in the recently determined SecA-SecYEG structure.