Characterization of the first planctomycetal outer membrane protein identifies a channel in the outer membrane of the anammox bacterium Kuenenia stuttgartiensis.

Planctomycetes are a bacterial phylum known for their complex intracellular compartmentalization. While most Planctomycetes have two compartments, the anaerobic ammonium oxidizing (anammox) bacteria contain three membrane-enclosed compartments. In contrast to a long-standing consensus, recent insights suggested the outermost Planctomycete membrane to be similar to a Gram-negative outer membrane (OM). One characteristic component that differentiates OMs from cytoplasmic membranes (CMs) is the presence of outer membrane proteins (OMPs) featuring a ß-barrel structure that facilitates passage of molecules through the OM. Although proteomic and genomic evidence suggested the presence of OMPs in several Planctomycetes, no experimental verification existed of the pore-forming function and localization of these proteins in the outermost membrane of these exceptional microorganisms. Here, we show via lipid bilayer assays that at least two typical OMP-like channel-forming proteins are present in membrane preparations of the anammox bacterium Kuenenia stuttgartiensis. One of these channel-forming proteins, the highly abundant putative OMP Kustd1878, was purified to homogeneity. Analysis of the channel characteristics via lipid bilayer assays showed that Kustd1878 forms a moderately cation-selective channel with a high current noise and an average single-channel conductance of about 170-190pS in 1M KCl. Antibodies were raised against the purified protein and immunogold localization indicated Kustd1878 to be present in the outermost membrane. Therefore, this work clearly demonstrates the presence of OMPs in anammox Planctomycetes and thus firmly adds to the emerging view that Planctomycetes have a Gram-negative cell envelope.

Identification and characterization of a bacterial hydrosulphide ion channel.

The hydrosulphide ion (HS(-)) and its undissociated form, hydrogen sulphide (H(2)S), which are believed to have been critical to the origin of life on Earth, remain important in physiology and cellular signalling. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H(2)S (ref. 4). The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD(+), which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite. Above a certain concentration threshold, both H(2)S and HS(-) inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase, necessitating a release mechanism for the export of this toxic metabolite from the cell. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS(-) channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate (FocA) and for nitrite (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS(-) ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel's crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.

Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin.

Uncoupling protein 1 (UCP1) catalyzes fatty acid-activated, purine nucleotide-sensitive proton leak across the mitochondrial inner membrane of brown adipose tissue to produce heat, and could help combat obesity and metabolic disease in humans. Studies over the last 30 years conclude that the protein is a dimer, binding one nucleotide molecule per two proteins, and unlike the related mitochondrial ADP/ATP carrier, does not bind cardiolipin. Here, we have developed novel methods to purify milligram amounts of UCP1 from native sources by using covalent chromatography that, unlike past methods, allows the protein to be prepared in defined conditions, free of excess detergent and lipid. Assessment of purified preparations by TLC reveal that UCP1 retains tightly bound cardiolipin, with a lipid phosphorus content equating to three molecules per protein, like the ADP/ATP carrier. Cardiolipin stabilizes UCP1, as demonstrated by reconstitution experiments and thermostability assays, indicating that the lipid has an integral role in the functioning of the protein, similar to other mitochondrial carriers. Furthermore, we find that UCP1 is not dimeric but monomeric, as indicated by size exclusion analysis, and has a ligand titration profile in isothermal calorimetric measurements that clearly shows that one nucleotide binds per monomer. These findings reveal the fundamental composition of UCP1, which is essential for understanding the mechanism of the protein. Our assessment of the properties of UCP1 indicate that it is not unique among mitochondrial carriers and so is likely to use a common exchange mechanism in its primary function in brown adipose tissue mitochondria.

Expression and purification of native and functional influenza A virus matrix 2 proton selective ion channel.

Influenza A virus displays one of the highest infection rates of all human viruses and therefore represents a severe human health threat associated with an important economical challenge. Influenza matrix protein 2 (M2) is a membrane protein of the viral envelope that forms a proton selective ion channel. Here we report the expression and native isolation of full length active M2 without mutations or fusions. The ability of the influenza virus to efficiently infect MDCK cells was used to express native M2 protein. Using a Calixarene detergents/surfactants based approach; we were able to solubilize most of M2 from the plasma membrane and purify it. The tetrameric form of native M2 was maintained during the protein preparation. Mass spectrometry shows that M2 was phosphorylated in its cytoplasmic tail (serine 64) and newly identifies an acetylation of the highly conserved Lysine 60. ELISA shows that solubilized and purified M2 was specifically recognized by M2 antibody MAB65 and was able to displace the antibody from M2 MDCK membranes. Using a bilayer voltage clamp measurement assay, we demonstrate a pH dependent proton selective ion channel activity. The addition of the M2 ion channel blocker amantadine allows a total inhibition of the channel activity, illustrating therefore the specificity of purified M2 activity. Taken together, this work shows the production and isolation of a tetrameric and functional native M2 ion channel that will pave the way to structural and functional characterization of native M2, conformational antibody development, small molecules compounds screening towards vaccine treatment.

A Low-Noise Transimpedance Amplifier for BLM-Based Ion Channel Recording.

High-throughput screening (HTS) using ion channel recording is a powerful drug discovery technique in pharmacology. Ion channel recording with planar bilayer lipid membranes (BLM) is scalable and has very high sensitivity. A HTS system based on BLM ion channel recording faces three main challenges: (i) design of scalable microfluidic devices; (ii) design of compact ultra-low-noise transimpedance amplifiers able to detect currents in the pA range with bandwidth >10 kHz; (iii) design of compact, robust and scalable systems that integrate these two elements. This paper presents a low-noise transimpedance amplifier with integrated A/D conversion realized in CMOS 0.35 µm technology. The CMOS amplifier acquires currents in the range ±200 pA and ±20 nA, with 100 kHz bandwidth while dissipating 41 mW. An integrated digital offset compensation loop balances any voltage offsets from Ag/AgCl electrodes. The measured open-input input-referred noise current is as low as 4 fA/√Hz at ±200 pA range. The current amplifier is embedded in an integrated platform, together with a microfluidic device, for current recording from ion channels. Gramicidin-A, α-haemolysin and KcsA potassium channels have been used to prove both the platform and the current-to-digital converter.

CHEXVIS: a tool for molecular channel extraction and visualization.

BACKGROUND: Understanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for extracting, storing, and analyzing protein channels are required to support such studies. Further, there is a need for an integrated framework that supports computation of the channels, interactive exploration of their structure, and detailed visual analysis of their properties. RESULTS: We describe a method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. We describe methods for effective visualization of the channels and their profiles. These methods and the visual analysis framework are implemented in a software tool, CHEXVIS. We apply the method on a number of known channel containing proteins to extract pore features. Results from these experiments on several proteins show that CHEXVIS performance is comparable to, and in some cases, better than existing channel extraction techniques. Using several case studies, we demonstrate how CHEXVIS can be used to study channels, extract their properties and gain insights into molecular function. CONCLUSION: CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels. The CHEXVIS web-server is freely available at http://vgl.serc.iisc.ernet.in/chexvis/ . The web-server is supported on all modern browsers with latest Java plug-in.

Bacteriophage membrane protein P9 as a fusion partner for the efficient expression of membrane proteins in Escherichia coli.

Despite their important roles and economic values, studies of membrane proteins have been hampered by the difficulties associated with obtaining sufficient amounts of protein. Here, we report a novel membrane protein expression system that uses the major envelope protein (P9) of phage φ6 as an N-terminal fusion partner. Phage membrane protein P9 facilitated the synthesis of target proteins and their integration into the Escherichia coli cell membrane. This system was used to produce various multi-pass transmembrane proteins, including G-protein-coupled receptors, transporters, and ion channels of human origin. Green fluorescent protein fusion was used to confirm the correct folding of the expressed proteins. Of the 14 membrane proteins tested, eight were highly expressed, three were moderately expressed, and three were barely expressed in E. coli. Seven of the eight highly expressed proteins could be purified after extraction with the mild detergent lauryldimethylamine-oxide. Although a few proteins have previously been developed as fusion partners to augment membrane protein production, we believe that the major envelope protein P9 described here is better suited to the efficient expression of eukaryotic transmembrane proteins in E. coli.

Hydrophobic gating of mechanosensitive channel of large conductance evidenced by single-subunit resolution.

Mechanosensitive (MS) ion channels are membrane proteins that detect and respond to membrane tension in all branches of life. In bacteria, MS channels prevent cells from lysing upon sudden hypoosmotic shock by opening and releasing solutes and water. Despite the importance of MS channels and ongoing efforts to explain their functioning, the molecular mechanism of MS channel gating remains elusive and controversial. Here we report a method that allows single-subunit resolution for manipulating and monitoring "mechanosensitive channel of large conductance" from Escherichia coli. We gradually changed the hydrophobicity of the pore constriction in this homopentameric protein by modifying a critical pore residue one subunit at a time. Our experimental results suggest that both channel opening and closing are initiated by the transmembrane 1 helix of a single subunit and that the participation of each of the five identical subunits in the structural transitions between the closed and open states is asymmetrical. Such a minimal change in the pore environment seems ideal for a fast and energy-efficient response to changes in the membrane tension.

Ion channels and their molecular environments--glimpses and insights from functional proteomics.

There is emerging evidence from functional analyses and molecular research that the role of ion channels in cell physiology is not only determined by the pore-forming subunits but also depends on their molecular environment. Accordingly, the local and temporal specificity of channel-mediated signal transduction is thought to result from association of these integral membrane proteins with distinct sets of partner proteins or from their assembly into stable macromolecular complexes. As yet, however, the molecular environments of most ion channels have escaped direct investigation, mostly because of technical limitations that precluded their comprehensive molecular analysis. Recent advances in proteomic technologies promoted an experimental workflow that combines affinity purification of readily solubilized protein complexes with quantitative high-resolution mass spectrometry and that offers access to channel-associated protein environments. We will discuss advantages and limitations of this proteomic approach, as well as the results obtained from its application to several types of ion channels including Cav channels, Kv channels, HCN channels, AMPA-type glutamate receptors and GABA(B) receptors. The respective results indicate that the approach provides unbiased and comprehensive information on (i) the subunit composition of channel cores including identification of auxiliary subunits, on (ii) the assembly of channel cores into 'signaling entities' and on (iii) integration of channels into extended protein networks. Thus, quantitative proteomics opens a new window for the investigation of ion channels and their function in the context of various types of cell.

Production of UCP1 a membrane protein from the inner mitochondrial membrane using the cell free expression system in the presence of a fluorinated surfactant.

Structural studies of membrane protein are still challenging due to several severe bottlenecks, the first being the overproduction of well-folded proteins. Several expression systems are often explored in parallel to fulfil this task, or alternately prokaryotic analogues are considered. Although, mitochondrial carriers play key roles in several metabolic pathways, only the structure of the ADP/ATP carrier purified from bovine heart mitochondria was determined so far. More generally, characterisations at the molecular level are restricted to ADP/ATP carrier or the uncoupling protein UCP1, another member of the mitochondrial carrier family, which is abundant in brown adipose tissues. Indeed, mitochondrial carriers have no prokaryotic homologues and very few efficient expression systems were described so far for these proteins. We succeeded in producing UCP1 using a cell free expression system based on E. coli extracts, in quantities that are compatible with structural approaches. The protein was synthesised in the presence of a fluorinated surfactant, which maintains the protein in a soluble form. Further biochemical and biophysical analysis such as size exclusion chromatography, circular dichroism and thermal stability, of the purified protein showed that the protein is non-aggregated, monodisperse and well-folded.

TRIC channels are essential for Ca2+ handling in intracellular stores.

Cell signalling requires efficient Ca2+ mobilization from intracellular stores through Ca2+ release channels, as well as predicted counter-movement of ions across the sarcoplasmic/endoplasmic reticulum membrane to balance the transient negative potential generated by Ca2+ release. Ca2+ release channels were cloned more than 15 years ago, whereas the molecular identity of putative counter-ion channels remains unknown. Here we report two TRIC (trimeric intracellular cation) channel subtypes that are differentially expressed on intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel. In TRIC-knockout mice suffering embryonic cardiac failure, mutant cardiac myocytes show severe dysfunction in intracellular Ca2+ handling. The TRIC-deficient skeletal muscle sarcoplasmic reticulum shows reduced K+ permeability, as well as altered Ca2+ 'spark' signalling and voltage-induced Ca2+ release. Therefore, TRIC channels are likely to act as counter-ion channels that function in synchronization with Ca2+ release from intracellular stores.

Mitsugumin 23 forms a massive bowl-shaped assembly and cation-conducting channel.

Mitsugumin 23 (MG23) is a 23 kDa transmembrane protein localized to the sarcoplasmic/endoplasmic reticulum and nuclear membranes in a wide variety of cells. Although the characteristics imply the participation in a fundamental function in intracellular membrane systems, the physiological role of MG23 is unknown. Here we report the biochemical and biophysical characterization of MG23. Hydropathicity profile and limited proteolytic analysis proposed three transmembrane segments in the MG23 primary structure. Chemical cross-linking analysis suggested a homo-oligomeric assembly of MG23. Ultrastructural observations detected a large symmetrical particle as the predominant component and a small asymmetric assembly as the second major component in highly purified MG23 preparations. Single-particle three-dimensional reconstruction revealed that MG23 forms a large bowl-shaped complex equipped with a putative central pore, which is considered an assembly of the small asymmetric subunit. After reconstitution into planar phospholipid bilayers, purified MG23 behaved as a voltage-dependent, cation-conducting channel, permeable to both K(+) and Ca(2+). A feature of MG23 gating was that multiple channels always appeared to be gating together in the bilayer. Our observations suggest that the bowl-shaped MG23 can transiently assemble and disassemble. These building transitions may underlie the unusual channel gating behavior of MG23 and allow rapid cationic flux across intracellular membrane systems.

Identification and characterization of uncoupling protein 4 in fat body and muscle mitochondria from the cockroach Gromphadorhina cocquereliana.

We have identified and characterized an uncoupling protein in mitochondria isolated from leg muscle and from fat body, an insect analogue tissue of mammalian liver and adipose tissue, of the cockroach Gromphadorhina coquereliana (GcUCP). This is the first functional characterization of UCP activity in isolated insect mitochondria. Bioenergetic studies clearly indicate UCP function in both insect tissues. In resting (non-phosphorylating) mitochondria, cockroach GcUCP activity was stimulated by the addition of micromolar concentrations of palmitic acid and inhibited by the purine nucleotide GTP. Moreover, in phosphorylating mitochondria, GcUCP activity was able to divert energy from oxidative phosphorylation. Functional studies indicate a higher activity of GcUCP-mediated uncoupling in cockroach muscle mitochondria compared to fat body mitochondria. GcUCP activation by palmitic acid resulted in a decrease in superoxide anion production, suggesting that protection against mitochondrial oxidative stress may be a physiological role of UCPs in insects. GcUCP protein was immunodetected using antibodies raised against human UCP4 as a single band of around 36 kDa. GcUCP protein expression in cockroach muscle mitochondria was significantly higher compared to mitochondria isolated from fat body. LC-MS/MS analyses revealed 100% sequence identities for peptides obtained from GcUCP to UCP4 isoforms from D. melanogaster (the highest homology), human, rat or other insect mitochondria. Therefore, it can be proposed that cockroach GcUCP corresponds to the UCP4 isoforms of other animals.

OTRPC4, a nonselective cation channel that confers sensitivity to extracellular osmolarity.

Ca2+-permeable channels that are involved in the responses of mammalian cells to changes in extracellular osmolarity have not been characterized at the molecular level. Here we identify a new TRP (transient receptor potential)-like channel protein, OTRPC4, that is expressed at high levels in the kidney, liver and heart. OTRPC4 forms Ca2+-permeable, nonselective cation channels that exhibit spontaneous activity in isotonic media and are rapidly activated by decreases in, and are inhibited by increases in, extracellular osmolarity. Changes in osmolarity of as little as 10% result in significant changes in intracellular Ca2+ concentration. We propose that OTRPC4 is a candidate for a molecular sensor that confers osmosensitivity on mammalian cells.

Supramolecular complexes of the Agrobacterium tumefaciens virulence protein VirE2.

Virulence protein VirE2 from Agrobacterium tumefaciens is involved in plant infection by transferring a fragment of agrobacterial Ti plasmid ssT-DNA in complex with VirE2-VirD2 proteins into the plant cell nucleus. The VirE2 protein interactions with ssDNA and formation of VirE2 protein complexes in vitro and in silico have been studied. Using dynamic light scattering we found that purified recombinant protein VirE2 exists in buffer solution in the form of complexes of 2-4 protein molecules of 12-18 nm size. We used computer methods to design models of complexes consisting of two and four individual VirE2 proteins, and their dimensions were estimated. Dimensions of VirE2 complexes with ssDNA (550 and 700 nucleotide residues) were determined using transmission electron microscopy and dynamic light scattering. We found that in vitro, upon interaction with ssDNA recombinant protein, VirE2 is able to alter conformation of the latter by shortening the initial length of the ssDNA.

Role of the transmembrane potential in the membrane proton leak.

The molecular mechanism responsible for the regulation of the mitochondrial membrane proton conductance (G) is not clearly understood. This study investigates the role of the transmembrane potential (DeltaPsim) using planar membranes, reconstituted with purified uncoupling proteins (UCP1 and UCP2) and/or unsaturated FA. We show that high DeltaPsim (similar to DeltaPsim in mitochondrial State IV) significantly activates the protonophoric function of UCPs in the presence of FA. The proton conductance increases nonlinearly with DeltaPsim. The application of DeltaPsim up to 220 mV leads to the overriding of the protein inhibition at a constant ATP concentration. Both, the exposure of FA-containing bilayers to high DeltaPsim and the increase of FA membrane concentration bring about the significant exponential Gm increase, implying the contribution of FA in proton leak. Quantitative analysis of the energy barrier for the transport of FA anions in the presence and absence of protein suggests that FA- remain exposed to membrane lipids while crossing the UCP-containing membrane. We believe this study shows that UCPs and FA decrease DeltaPsim more effectively if it is sufficiently high. Thus, the tight regulation of proton conductance and/or FA concentration by DeltaPsim may be key in mitochondrial respiration and metabolism.

Removal of starch granule-associated proteins affects amyloglucosidase hydrolysis of rice starch granules.

Starch granule-associated proteins (SGAPs) include granule-surface proteins (SGSPs) and granule-channel proteins (SGCPs). To investigate impacts of SGAPs on amyloglucosidase (AMG) hydrolysis, waxy and non-waxy rice starches had their SGCPs or SGAPs removed. Removal of SGAPs or SGCPs did not affect morphology and amylopectin chain distribution but decreased relative crystallinity. Removal of SGAPs increased the digestion rate, AMG binding ability and pore diameter of hydrolyzed granules, and accelerated changes in relative crystallinity and destruction of crystalline region on hydrolysis. However, after removing SGCPs, AMG only bound to surface and attacked of the fingerprint of protein bodies on granules, with decreased hydrolysis rate. The degree of change in hydrolysis rate was not determined by SGCPs content of rice starch. These results implied that SGCPs had a more dominant role in AMG hydrolysis of rice starch than did SGSPs. This study provides novel information about the role of SGAPs in AMG hydrolysis mechanisms.

Evidence for the amphipathic nature and tilted topology of helices 4 and 5 in the closed state of the colicin E1 channel.

The membrane-bound closed channel structure of helices 4 and 5 (Lys-406-Asp-446) of the colicin E1 channel domain was investigated by using a site-directed fluorescence labeling technique. A bimane probe was covalently attached to a cysteine residue in a series of single-cysteine mutant proteins to scan each helix in a residue-by-residue fashion. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. The fluorescence properties were collated for construction of a membrane-bound topology model of helices 4 and 5 of the channel domain. Finally, the data reveal that both helices 4 and 5 are two separate amphipathic alpha-helices that are situated parallel to the membrane surface. Dual fluorescence quencher analysis shows that helix 4 adopts a tilted topology in which its C-terminus is more buried than its N-terminus within the bilayer. In contrast, helix 5 is relatively solvent-exposed and located parallel to the interfacial region of the membrane surface. However, the loop region of both helices 4 and 5 was shown to be relatively buried within the bilayer. In addition, a least-squares fit of the data to a harmonic wave function indicated that both periodicity and frequency are typical for an amphipathic alpha-helix (3.75 +/- 0.1 residues per turn for helix 4 and 3.70 +/- 0.1 residues per turn for helix 5). Squared residual plots of the harmonic wave function also reveal that the N-terminus of helix 4 is elongated by two residues from Lys-406 to Phe-404, while the C-terminus of helix 5 is elongated by three residues from Tyr-434 to Ile-437 upon membrane association.

Mass spectrometry of full-length integral membrane proteins to define functionally relevant structural features.

The crystallization and structure determination of integral membrane proteins remains a difficult task relying on a good understanding of the behavior of the protein for success. To date, membrane protein structures are still far outnumbered by soluble protein structures. Mass spectrometry is a powerful and versatile tool offering deep insights into the state of the integral membrane protein the structuralist intends to crystallize. With appropriate sample preparation methods, it provides information that can sometimes prove critical at various stages of the structure determination process, from protein expression to model building. Moreover, valuable knowledge is gained when the identified structural features underlie important functional aspects. Electrospray and matrix assisted laser desorption ionization (MALDI) methods, however, face a particular challenge when dealing with integral membrane proteins. A MALDI method specifically optimized for membrane protein analysis is presented here, with detailed information on the sample preparation and deposition, as well as guidelines for domain determination by limited proteolysis. MALDI-time of flight mass spectrometry can be used to do a proper inventory of initiation sites, to tailor a protein to a stable, well-folded form, and to evaluate selenomethionine replacement. These approaches are illustrated with a few examples drawn from the structural biology of ion channels.

Expression, purification, crystallization and preliminary crystallographic study of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1.

The voltage-gated proton channel Hv1 is essential to proton permeation and contains a voltage-sensor domain without a pore domain. It contains three predicted domains: an N-terminal acid and proline-rich domain, a transmembrane voltage-sensor domain and a C-terminal domain that is responsible for the dimeric architecture of Hv1. Here, the C-terminal domain of the human voltage-gated proton channel Hv1 (C-Hv1) was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals have a tetragonal form and diffraction data were collected to 2.5 A resolution in-house. The crystal belongs to space group P4(1)2(1)2, with unit-cell parameters a = b = 37.76, c = 137.52 A. Structural determination of C-Hv1 is in progress.