Interaction between the VDAC channel and a polyanionic effector. An electron microscopic study.

The conductance of the voltage-dependent mitochondrial outer membrane channel is modulated by a synthetic anionic polymer. When added to suspensions of membrane crystals of the channel, the polyanion caused disordering of the usual parallelogram array and increased occurrence of a contracted form of the array. Correlation averages obtained from electron microscopic images of the channel crystals indicated a narrowing of the projected channel lumen in the presence of the polyanion and the appearance of new, narrow zones of stain exclusion on the outside of the channel. These effects are interpreted in terms of possible conformational changes induced in the channel by binding of the polyanion.     

Correlation analysis of gap junction lattice images.

Fourier averages of connexon images computed from low-irradiation electron micrographs of isolated negatively stained gap junction domains exhibited differences in stain distribution and connexon orientation. To analyze these polymorphic structures, correlation averaging methods were applied to images from negatively stained and frozen-hydrated specimens. For the negatively stained specimens, separate averages over two subsets of connexons with differing degrees of stain accumulation in the axial channel were obtained. Two populations of connexons with opposite skew orientations were distinguishable within a single junctional domain of a frozen-hydrated specimen. Correlation maps calculated using the left- and right-skewed references showed that the selected connexons tend to locally cluster. Using correlation methods to analyze packing disorder in a typical connexon lattice, we estimated the root-mean-square variation in the nearest neighbor pair separation to be approximately 11% of the lattice constant. Displacements of the connexons relative to each other increased with increasing pair separation in the lattice, rather like a liquid, although long-range orientation order was conserved as in a crystal. These results support the hypothesis that the hexagonal ordering of the connexons results from short-range repulsive forces.     

Structure of functional single AQP0 channels in phospholipid membranes

Aquaporin-0 (AQP0) is the most prevalent intrinsic protein in the plasma membrane of lens fiber cells where it functions as a water selective channel and also participates in fiber-fiber adhesion. We report the 3D envelope of purified AQP0 reconstituted with random orientation in phospholipid bilayers as single particles. The envelope was obtained by combining freeze-fracture, shadowing and random conical tilt electron microscopy followed by single particle image processing. Two-dimensional analysis of 2547 untilted images produced eight class averages exhibiting "square" and "octagonal" shapes with a continuum of variation. We reconstructed in 3D five class averages that best described the data set. The reconstructions ("molds") appeared as metal cups exhibiting external and internal surfaces. We used the internal surface of the mold to calculate the "imprints" that represent the AQP0 particles protruding from the hydrophobic core of the phospholipid bilayer. The complete envelope of the channel, formed by joining the square and octagonal imprints, described accurately the size, shape, oligomeric state, orientation, and molecular weight of the AQP0 channel inserted in the phospholipid bilayer. Rigid body docking of the atomic model of the aquaporin-1 (AQP1) tetramer showed that the freeze-fracture envelope accounted for the conserved transmembrane domain (approximately 73% similarity between AQP0 and AQP1) but not for the amino and carboxyl termini. We suggest that the discrepancy might reflect differences in the location of the amino and carboxyl termini in the crystal and in the phospholipid bilayer.     

Correlated ion flux through parallel pores: Application to channel subconductance states

Summary Many ion channels that normally gate fully open or shut have recently been observed occasionally to display well-defined subconductance states with conductances much less than those of the fully open channel. One model of this behavior is a channel consisting of several parallel pores with a strong correlation between the flux in each pore such that, normally, they all conduct together but, under special circumstances, the pores may transfer to a state in which only some of them conduct. This paper introduces a general technique for modeling correlated pores, and explores in detail by computer simulation a particular model based upon electric interaction between the pores. Correlation is obtained when the transient electric field of ions passing through the pores acts upon a common set of ionizable residues of the channel protein, causing transient changes in their effective pK and hence in their charged state. The computed properties of such a correlated parallel pore channel with single occupation of each pore are derived and compared to those predicted for a single pore that can contain more than one ion at a time and also to those predicted for a model pore with fluctuating barriers. Experiments that could distinguish between the present and previous models are listed.R.M.B. is grateful to the S.E.R.C. for the award of a graduate studentship.     

Multivariate statistical analysis of ribosome electron micrographs. L and R lateral views of the 40 S subunit from HeLa cells

The morphology of the small (40 S) subunit of the eukaryotic ribosome from HeLa cells has been examined by single-particle averaging and multivariate image analysis applied to electron micrographs of negatively stained specimens. The use of multivariate image analysis allows different, independent components of the structural variation within the particles to be identified and separately studied. The largest component of variance for both lateral views (termed L and R) was the variation in the peripheral stain intensity. The second largest component of interparticle variation is due to changes in the particle appearance most likely associated with a change of orientation on the specimen film.Averages formed from particles falling within a small range of peripheral stain intensity allowed the changes in the projected structure to be studied as a function of local stain level. Visual observations of stain variation could be confirmed quantitatively.Significant differences were found between averages of particles in the L view and those in the R view. Multivariate image analysis of a mixed population of L and mirrored R particles showed that the differences consistently affect all particles. However, the R view increasingly resembles the L view as the overall level of stain is increased, in agreement with a model of partial stain immersion.     

Electron microscopy and computer image averaging of ice-embedded large ribosomal subunits from Escherichia coli

Electron micrographs of frozen-hydrated, large ribosomal subunits from Escherichia coli have been analyzed by computer image processing. Images of subunits in the so-called "crown" orientation were analyzed by correlation alignment procedures developed for negatively stained specimens. Averages of the aligned images showed both similarities and differences to averages determined for negatively stained specimens. The L1 ridge is more dense and stalk-like in frozen-hydrated as compared with negatively stained subunits, possibly because it is associated with ribosomal RNA. The results show that it should be feasible to determine the three-dimensional structure of the large ribosomal subunit from micrographs of individual, frozen-hydrated subunits that have been tilted in the electron microscope.     

A patch clamp study on the electro-permeabilization of higher plant cells: Supra-physiological voltages induce a high-conductance, K+ selective state of the plasma membrane

Permeabilization of biological membranes by pulsed electric fields ("electroporation") is frequently used as a tool in biotechnology. However, the electrical properties of cellular membranes at supra-physiological voltages are still a topic of intensive research efforts. Here, the patch clamp technique in the whole cell and the outside out configuration was employed to monitor current-voltage relations of protoplasts derived from the tobacco culture cell line "Bright yellow-2". Cells were exposed to a sequence of voltage pulses including supra-physiological voltages. A transition from a low-conductance (~0.1 nS/pF) to a high-conductance state (~5 nS/pF) was observed when the membrane was either hyperpolarized or depolarized beyond threshold values of around -250 to -300 mV and +200 to +250 mV, respectively. Current-voltage curves obtained with ramp protocols revealed that the electro-permeabilized membrane was 5-10 times more permeable to K+ than to gluconate. The K+ channel blocker tetraethylammonium (25 mM) did not affect currents elicited by 10 ms-pulses, suggesting that the electro-permeabilization was not caused by a non-physiological activation of K+ channels. Supra-physiological voltage pulses even reduced "regular" K+ channel activity, probably due to an increase of cytosolic Ca2+ that is known to inhibit outward-rectifying K+ channels in Bright yellow-2 cells. Our data are consistent with a reversible formation of aqueous membrane pores at supra-physiological voltages.     

Voltage-dependent synchronization of gating of syringomycin E ion channels

Antifungal lipodepsipeptide syringomycin E (SRE) forms two major conductive states in lipid bilayers: "small" and "large". Large SRE channels are cluster of several small ones, demonstrating synchronous opening and closure. To get insight into the mechanism of such synchronization we investigated how transmembrane potential, membrane surface charge, and ionic strength affect the number of small SRE channels synchronously functioning in the cluster. Here, we report that the large SRE channels can be presented as 3-8 simultaneously gating small channels. The increase in the absolute value of the transmembrane potential (from 50 to 200 mV) decreases the number of synchronously gated channels in the clusters. Voltage-dependence of channel synchronization was influenced by the ionic strength of the bathing solution, but not by membrane surface charge. We propose a mechanism for the voltage-dependent cluster behavior that involves a voltage-induced reorientation of lipid dipoles associated with the channel pores.     

Structure of paracrystalline arrays on outer membranes of rat-liver and rat-heart mitochondria.

Crystalline arrays are induced in outer membranes of rat-liver and rat-heart mitochondria by phosphotungstate and silicotungstate. The basic structure of the arrays has been determined by correlation averaging of electron microscopic images of side views of tubular arrays and en face views of planar arrays. The arrays consist of rows of bilobed projecting subunits and are similar (in lattice parameters and projected subunit dimensions) to periodic arrays of ion transport ATPases, e.g., arrays of Ca(2+)-ATPase induced by vanadate in sarcoplasmic reticulum. Hexokinase-labeled colloidal gold particles do not specifically decorate the arrays, suggesting that the hexokinase receptor (VDAC channel) is not a component of the arrays.     

Densely packed beta-structure at the protein-lipid interface of porin is revealed by high-resolution cryo-electron microscopy

Porin is an integral membrane protein that forms channels across the outer membrane of Escherichia coli. Electron microscopic studies of negatively stained two-dimensional porin crystals have shown three stain accumulations per porin trimer, revealing the locations of pores spanning the membrane. In this study, reconstituted porin lattices embedded in glucose were investigated using the low-dose technique on a cryo-electron microscope equipped with a helium-cooled superconducting objective lens. The specimen temperature was maintained at 5 K to yield an improved microscopic and specimen stability. Under these conditions, we obtained for the first time electron diffraction patterns from porin lattices to a resolution of 3.2 A and images showing optical diffraction up to a resolution of 4.9 A. Applying correlation averaging techniques to the digitized micrographs, we were able to reconstruct projected images of the porin trimer to a resolution of up to 3.5 A. In the final projection maps, amplitudes from electron diffraction and phases from these images were combined. The predominant feature is a high-density narrow band (about 6 A in thickness) that delineates the outer perimeter of the trimer. Since the molecule consists of almost exclusively beta-sheet structure, as revealed by spectroscopic data, we conclude that this band is a cylindrical beta-pleated sheet crossing the membrane nearly perpendicularly to its plane. Another intriguing finding is a low-density area (about 70 A2) situated in the centre of the trimer.     

Amino acid residues 4425-4621 localized on the three-dimensional structure of the skeletal muscle ryanodine receptor

We have localized a region contained within the sequence of amino acid residues 4425-4621 on the three-dimensional structure of the skeletal muscle ryanodine receptor (RyR). Mouse monoclonal antibodies raised against a peptide comprising these residues have been complexed with ryanodine receptors and imaged in the frozen-hydrated state by cryoelectron microscopy. These images, along with images of antibody-free ryanodine receptor, were used to compute two-dimensional averaged images and three-dimensional reconstructions. Two-dimensional averages of immunocomplexes in which the ryanodine receptor was in the fourfold symmetrical orientation disclosed four symmetrical regions of density located on the edges of the receptor's cytoplasmic assembly that were absent from control averages of receptor without added antibody. Three-dimensional reconstructions revealed the antibody-binding sites to be on the so-called handle domains of the ryanodine receptor's cytoplasmic assembly, near their junction with the transmembrane assembly. This study is the first to demonstrate epitope mapping on the three-dimensional structure of the ryanodine receptor.     

Defining the physical gate of a mechanosensitive channel, MscL, by engineering metal-binding sites

The mechanosensitive channel of large conductance, MscL, of Escherichia coli is one of the best-studied mechanosensitive proteins. Although the structure of the closed or "nearly-closed" state of the Mycobacterium tuberculosis ortholog has been solved and mechanisms of gating have been proposed, the transition from the closed to the open states remains controversial. Here, we probe the relative position of specific residues predicted to line the pore of MscL in either the closed state or during the closed-to-open transition by engineering single-site histidine substitutions and assessing the ability of Ni2+, Cd2+ or Zn2+ ions to affect channel activity. All residues predicted to be within the pore led to a change in channel threshold pressure, although the direction and extent of this change were dependent upon the mutation and metal used. One of the MscL mutants, L19H, exhibited gating that was inhibited by Cd2+ but stimulated by Ni2+, suggesting that these metals bind to and influence different states of the channel. Together, the results derived from this study support the hypotheses that the crystal structure depicts a "nearly closed" rather than a "fully closed" state of MscL, and that a clockwise rotation of transmembrane domain 1 occurs early in the gating process.     

Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra

Three-dimensional electron cryomicroscopy of randomly oriented single particles is a method that is suitable for the determination of three-dimensional structures of macromolecular complexes at molecular resolution. However, the electron-microscopical projection images are modulated by a contrast transfer function (CTF) that prevents the calculation of three-dimensional reconstructions of biological complexes at high resolution from uncorrected images. We describe here an automated method for the accurate determination and correction of the CTF parameters defocus, twofold astigmatism and amplitude-contrast proportion from single-particle images. At the same time, the method allows the frequency-dependent signal decrease (B factor) and the non-convoluted background signal to be estimated. The method involves the classification of the power spectra of single-particle images into groups with similar CTF parameters; this is done by multivariate statistical analysis (MSA) and hierarchically ascending classification (HAC). Averaging over several power spectra generates class averages with enhanced signal-to-noise ratios. The correct CTF parameters can be deduced from these class averages by applying an iterative correlation procedure with theoretical CTF functions; they are then used to correct the raw images. Furthermore, the method enables the tilt axis of the sample holder to be determined and allows the elimination of individual poor-quality images that show high drift or charging effects.     

Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations

Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insights into the metabolic mechanisms underlying complex biological systems. However, because mRNA and protein abundance are affected by many cellular and physical processes, there have been conflicting results on their correlation. Using whole-genome microarray and LC-MS/MS proteomic data collected from Desulfovibrio vulgaris grown under three different conditions, we systematically investigate the relationship between mRNA and protein abundance by a multiple regression approach, in which some of the key covariates that may affect mRNA-protein relationship were included. The results showed that mRNA abundance alone can explain only 20-28% of the total variation of protein abundance, suggesting mRNA-protein correlation can not be determined by mRNA abundance alone. Among various covariates, analytic variation of protein abundance is the major source for the variation of mRNA-protein correlation, which contributes to 34-44% of the total variation of mRNA-protein correlation. The cellular functional category of genes/proteins contributes 10-15% of the total variation of mRNA-protein correlation, with a more pronounced correlation of the two properties was observed for "central intermediary metabolism" and "energy metabolism" categories. In addition, protein stability also contributes 5% of the total variation of mRNA-protein correlation. The study presents the first quantitative analysis of the contributions of various biochemical and physical sources to the correlation of mRNA and protein abundance in D. vulgaris.     

Transport of maltodextrins through maltoporin: a single-channel study.

Transport of sugars through maltoporin channels reconstituted into planar lipid membranes has traditionally been addressed using multichannel preparations. Here we show that single-channel experiments offer new possibilities to reveal molecular details of the interaction between the sugar and the channel. We analyze time-resolved transient interruptions in the maltoporin ionic current in the presence of differently sized maltodextrins. We find for all studied sugars, from maltotriose to maltoheptaose, that only one sugar molecule is required to completely block one of the pores in the maltoporin trimer. The probability of simultaneous blockage of different pores increases with sugar concentration in a manner that demonstrates their mutual independence. The maltoporin channel is asymmetric and, added from one side only, predominantly inserts in an oriented manner. The asymmetry of the channel structure manifests itself in two ways. First, it is seen as an asymmetrical response to applied voltage at otherwise symmetrical conditions; second, as asymmetrical rates of sugar entry into the channel with asymmetrical (one-sided) sugar addition. Importantly, we find that the sugar residence time in the pore does not depend on which side the sugar is added. This voltage-dependent time is the same for symmetrical, cis, or trans sugar addition. This observation suggests that once a sugar molecule is captured by the "greasy slide" of the channel, it spends enough time there to "forget" from what entrance it was captured. This also means that the blockage events studied here represent sugar translocation events, and not just binding at and release from the same entrance of the channel.     

Plasticity of Escherichia coli porin channels. Dependence of their conductance on strain and lipid environment.

The conductance properties of three members of the porin family which form channels across the outer membrane of Gram-negative bacteria were compared. With their endogenous lipopolysaccharide (LPS) bound, the closely related porins F and C from Escherichia coli reveal significantly different conductance steps and closing potentials, with values of 0.82 nS (nanosiemens) and 89 mV for F-type channels, and 0.49 nS and 158 mV for C-type pores (1 M NaCl), respectively. On the basis of their closing potentials, the two channel types can be distinguished unequivocally. If reconstituted in asolectin and extraneous LPS, porin C forms F-type in addition to C-type channels. Substitution of asolectin by mitochondrial lipids yields the native C-type pores only. Both channel types can be induced to assume the mutually other channel configuration by variation of ionic strength. A multiplicity of channel subtypes is observed by variation of the pH of the medium. The three channels within a trimer are, however, consistently of the same type. Since structural studies have revealed a single channel per monomer, the several conductance steps observed are likely to reflect distinct configurations of the same channel. Best channel recoveries were observed if endogenous LPS remained associated to porin during purification. Significant yields could nevertheless be obtained also if LPS was removed from porin and replaced with various precursors or chemically synthesized analogues. As function requires the presence of glycolipids, yet crystallization is perturbed by heterodisperse endogenous LPS, the smallest monodisperse analogues yielding good channel recovery were determined. The minimal synthetic moiety is a monoglucosaminetetraacyl compound. The characteristics of porin B from E. coli BE are shown to be indistinguishable from those of porin F. The conductance properties of this porin, refolded from random coil configuration, are indistinguishable from those exhibited by native protein. The formation of channels is thus encoded by the sequence of the mature polypeptide alone.     

Molecular dynamics simulations of water within models of ion channels.

The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.     

Dihydropyridine-sensitive skeletal muscle Ca channels in polarized planar bilayers. 1. Kinetics and voltage dependence of gating.

Rabbit skeletal muscle transverse tubule (T) membranes were fused with planar bilayers. Ca channel activity was studied with a "cellular" approach, using solutions that were closer to physiological than in previous studies, including asymmetric extracellular divalent ions as current carriers. The bilayer was kept polarized at -80 mV and depolarizing pulses were applied under voltage clamp. Upon depolarization the channels opened in a steeply voltage-dependent manner, and closed rapidly at the end of the pulses. The activity was characterized at the single-channel level and on macroscopic ensemble averages of test-minus-control records, using as controls the null sweeps. The open channel events had one predominant current corresponding to a conductance of 9 pS (100 mM Ba2+). The open time histogram was fitted with two exponentials, with time constants of 5.8 and 30 ms (23 degrees C). Both types of events were virtually absent at -80 mV. The average open probability (fractional open time) increased sigmoidally from 0 to a saturation level of 0.08, following a Boltzmann function centered at -25 mV and with a steepness factor of 7 mV. Ensemble averages of test-minus-control currents showed a sigmoidal activation followed by inactivation during the pulse and deactivation (closing) after the pulse. The ON time course was well fitted with "m3h" kinetics, with tau m = 120 ms and tau h = 1.2 s. Deactivation was exponential with tau = 8 ms. This study demonstrates a technique for obtaining Ca channel events in lipid bilayers that are strictly voltage dependent and exhibit most of the features of the macroscopic ICa. The technique provides a useful approach for further characterization of channel properties, as exemplified in the accompanying paper, that describes the consequences on channel properties of phosphorylation by cAMP dependent protein kinase.     

Voltage-Gated Lipid Ion Channels

Synthetic lipid membranes can display channel-like ion conduction events even in the absence of proteins. We show here that these events are voltage-gated with a quadratic voltage dependence as expected from electrostatic theory of capacitors. To this end, we recorded channel traces and current histograms in patch-experiments on lipid membranes. We derived a theoretical current-voltage relationship for pores in lipid membranes that describes the experimental data very well when assuming an asymmetric membrane. We determined the equilibrium constant between closed and open state and the open probability as a function of voltage. The voltage-dependence of the lipid pores is found comparable to that of protein channels. Lifetime distributions of open and closed events indicate that the channel open distribution does not follow exponential statistics but rather power law behavior for long open times.     

Issues of resolution and polymorphism in single-particle reconstruction

Three-dimensional reconstruction from electron microscopic (EM) images of isolated macromolecular complexes is being employed by many laboratories. This approach is extremely powerful and continues to improve in resolution. In the absence of stereochemical constraints that can be used to assess the quality of a reconstruction, as exist in X-ray crystallography, several other measures have typically been used. A very useful assessment of quality can be made in the comparison between the projections of the three-dimensional reconstruction and averages generated from classes of images. The main quantitative measure has been that of resolution statistics, typically based upon Fourier shell correlations. We show, using only simulated noise for images, that impressive resolution statistics are generated that can even extend the apparent resolution of the starting model. When truly independent reconstructions are generated starting from different initial models, however, such artefacts are not possible. We also show, using real images of DnaB rings, that in the presence of polymorphism artefactual reconstructions can be generated whose projections match class averages. These averages, however, are themselves artefactual as they involve heterogeneous images. The issues presented here need to be considered when single-particle EM reconstructions are evaluated.