The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion

The Amt/Mep ammonium channels are trimers in which each monomer contains a long, narrow, hydrophobic pore. Whether the substrate conducted by these pores is NH(3) or NH(4)(+) remains controversial. Substitution of leucine for the highly conserved tryptophan 148 residue at the external opening to Escherichia coli AmtB pores allowed us to address this issue. A strain carrying AmtB(W148L) accumulates much larger amounts of both [(14)C]methylammonium and [(14)C]methylglutamine in a washed cell assay than a strain carrying wild-type AmtB. Accumulation of methylammonium occurs within seconds and appears to reflect channel conductance, whereas accumulation of methylglutamine, which depends on the ATP-dependent activity of glutamine synthetase, increases for many minutes. Concentration of methylammonium was most easily studied in strains that lack glutamine synthetase. It is eliminated by the protonophore carbonyl cyanide m-chlorophenyl hydrazone and is approximately 10-fold higher in the strain carrying AmtB(W148L) than wild-type AmtB. The results indicate that AmtB allows accumulation of CH(3)NH(3)(+) ion in response to the electrical potential across the membrane and that the rate of flux through AmtB(W148L) is approximately 10 times faster than through wild-type AmtB. We infer that both mutant and wild-type proteins also carry NH(4)(+). Contrary to our previous views, we assess that E. coli AmtB does not differ from plant Amt proteins in this regard; both carry ions. We address the role of W148 in decreasing the activity and increasing the selectivity of AmtB and the implications of our findings with respect to the function of Rh proteins, the only known homologues of Amt/Mep proteins.     

Direct observation of electrogenic NH4+ transport in ammonium transport (Amt) proteins

Ammonium transport (Amt) proteins form a ubiquitous family of integral membrane proteins that specifically shuttle ammonium across membranes. In prokaryotes, archaea, and plants, Amts are used as environmental NH₄⁺ scavengers for uptake and assimilation of nitrogen. In the eukaryotic homologs, the Rhesus proteins, NH₄⁺/NH₃ transport is used instead in acid–base and pH homeostasis in kidney or NH₄⁺/NH₃ (and eventually CO₂) detoxification in erythrocytes. Crystal structures and variant proteins are available, but the inherent challenges associated with the unambiguous identification of substrate and monitoring of transport events severely inhibit further progress in the field. Here we report a reliable in vitro assay that allows us to quantify the electrogenic capacity of Amt proteins. Using solid-supported membrane (SSM)-based electrophysiology, we have investigated the three Amt orthologs from the euryarchaeon Archaeoglobus fulgidus. Af-Amt1 and Af-Amt3 are electrogenic and transport the ammonium and methylammonium cation with high specificity. Transport is pH-dependent, with a steep decline at pH values of ∼5.0. Despite significant sequence homologies, functional differences between the three proteins became apparent. SSM electrophysiology provides a long-sought-after functional assay for the ubiquitous ammonium transporters.Ammonium transport (Amt) proteins are a class of trimeric, integral membrane proteins found throughout all domains of life. Despite moderate primary sequence homologies, distinct family members from bacteria, archaea, and eukarya (including humans) share conserved structural features and a high number of conserved amino acid residues that are considered functionally relevant (1–4). Although the involvement of all Amt proteins in transporting NH₄⁺/NH₃ across biological membranes is undisputed, their functional context is diverse. Prokaryotes and plants use Amt proteins to scavenge NH₄⁺/NH₃—a preferred nitrogen source for cell growth—from their environment, whereas mammals use Amt orthologs, the Rhesus proteins, for detoxification and ion homeostasis in erythrocytes and in the kidney and liver tissues (1, 5, 6).Three decades ago, Kleiner and coworkers suggested that Amt proteins are secondary active and electrogenic transporters for ammonium (7–9). Various groups have subsequently confirmed this finding by two-electrode voltage-clamp experiments with protein produced recombinantly from RNA injected into Xenopus laevis oocytes. Here, plant Amt and Rhesus proteins were the main object of study, but some mechanistic details remained unclear, in particular the distinction between electrogenic NH₄⁺ uniport (10–13), NH₃/H⁺ symport (11, 12), or electroneutral NH₄⁺/H⁺ antiport (14, 15). In contrast, bacterial Amt proteins were described as passive channels for the uncharged gas ammonia (NH₃) (16). The first crystal structure for an Amt family member, AmtB from Escherichia coli (17), was interpreted to support this hypothesis, and an ongoing controversy concerning the transported species has persisted in the field ever since. Several points have been raised to challenge the possibility of gas channeling, the most critical of which seems to be that at physiological pH the protonation equilibrium of NH₃—with a pK_a of 9.4—would be >99% on the side of charged NH₄⁺. This point implies that the import of neutral ammonia gas must be preceded by extracellular deprotonation and followed immediately by intracellular protonation. In summary, the import of NH₃ would thus result in a net NH₄⁺/H⁺ antiport. Such a mechanism would be electroneutral, but it would be secondary active in the presence of a proton motive force, resulting in a vectorial pumping of ammonium out of the cell—which is, of course, physiologically unreasonable. A second point is that biological membranes are themselves highly permeable for uncharged ammonia, with a permeability coefficient, P_d = 10⁻³ cm·s⁻¹, similar to that of water (18), such that a dedicated transport protein would hardly be required. Westerhoff and coworkers have argued that active Amt transport thus is imperative and that cells must be able to quickly block Amt transport upon intracellular accumulation of ammonium to avoid uncoupling of the proton gradient through back-diffusion of NH₃ (19). In prokaryotes and some plants, this blocking is the task of regulatory GlnK proteins belonging to the signal transducing P_II family that bind to corresponding ammonium transporters when their regulatory ligand 2-oxoglutarate, the primary metabolic acceptor for NH₄⁺ during nitrogen assimilation, is depleted (20).The high expectations to understand the mechanism of Amt transport from 3D structures have not been met to date. The available structures of E. coli AmtB (17, 21) and its complex with GlnK (22, 23) of A. fulgidus Amt-1 (24), Nitrosomonas europaea Rh50 (25, 26), and human RhCG (27) all show the same, inward-facing state of the protein. Such apparent structural rigidity would match the picture of a fast channel, whereas active transport is generally considered to involve conformational changes that expose a binding site for the cargo molecule(s) alternatingly to either side of the membrane (28). In addition, the difficulties to detect NH₄⁺/NH₃ and to assay Amt transport led to a lack of functional studies carried out in vitro on well-defined systems. An uptake assay with AmtB reconstituted in proteoliposomes was described to provide evidence for passive gas channeling (17), but the methodology was later contested (2). Assays based on the detection of radioactive methylammonium (MA) uptake were only carried out in whole cells of E. coli, and studies with voltage-clamp electrophysiology using Amt-1 reconstituted in planar lipid bilayers did not yield conclusive results (our work). A series of potentially important variants have been produced (29–39), but the lack of an adequate functional assay has precluded definite conclusions.The debate concerning the transport mechanism of Amt proteins has not been settled to date, necessitating a reliable functional in vitro assay. The finding that electrogenic transport was observed in X. laevis oocytes, but not in the far smaller membrane patch of a planar lipid bilayer setup, suggested that the transport rate of Amt proteins was possibly too low to lead to a detectable current response, unless a larger number of protein units were incorporated into the bilayer. We have therefore focused on a controlled method of in vitro electrophysiology that allows the simultaneous activation of >10⁸ protein units, the solid-supported membrane (SSM) electrophysiology (40). With this approach, pioneered by Fendler and coworkers, we were able to detect robust ion currents from isolated and reconstituted Amt proteins.     

Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB

The conduction mechanism of Escherichia coli AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic "gate" formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH(4)(+) deprotonation takes place at S1 before NH(3) conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport.     

The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location.

The dif locus (deletion-induced filamentation) of Escherichia coli is a resolvase site, located in the terminus region of the chromosome, that reduces chromosome multimers to monomers. In strains in which this site has been deleted, a fraction of the cells is filamentous, has abnormal nucleoid structure, and exhibits elevated levels of the SOS repair system. We have demonstrated that a 33-bp sequence, which is sufficient for RecA-independent recombination and which shows similarity to the cer site of pColE1, suppresses the Dif phenotype when inserted in the terminus region. Flanking sequences were not required, since suppression occurred in strains in which dif as well as 12 kb or 173 kb of DNA had been deleted. However, location was important, and insertions at a site 118 kb away from the normal site did not suppress the Dif phenotype. These sites were otherwise still functional, and they exhibited wild-type levels of RecA-independent recombination with dif-containing plasmids and recombined with other chromosomal dif sites to cause deletions and inversions. It is proposed that the functions expressed by a dif site depend on chromosome location and structure, and analysis of these functions provides a way to examine the structure of the terminus region.     

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

The matrix 2 (M2) protein from influenza A virus is a proton channel that uses His37 as a selectivity filter. Here we report high-resolution (1.10 Å) cryogenic crystallographic structures of the transmembrane domain of M2 at low and high pH. These structures reveal that waters within the pore form hydrogen-bonded networks or “water wires” spanning 17 Å from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium via second-shell interactions involving bridging water molecules. In addition, room temperature crystallographic structures indicate that water becomes increasingly fluid with increasing temperature and decreasing pH, despite the higher electrostatic field. Complementary molecular dynamics simulations reveal a collective switch of hydrogen bond orientations that can contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle.Proton transport and conduction is essential to life. Proteins conduct protons over long distances through membranes to facilitate proton-coupled electron transfer and the formation and utilization of proton gradients. The M2 proton channel from the influenza A virus (1) is not only a medically important protein but also a simple, well-defined system for studying proton transport through confined spaces (2–4). This channel is the target of the anti-flu drug amantadine. M2 is activated at low pH by protonation of His37, which also participates in proton conduction by shuttling protons into the interior of the virus (5–7). His37 lies near the center of the bilayer, where it is connected to the viral exterior by a water-filled pore through which protons must pass to gain access to the viral interior (8–13).Visualizing the flow of protons within protein channels such as M2 is one of the long-standing challenges in molecular biophysics. Based on computational studies (9, 14–19) it has been suggested that protons reach His37 through “water wires” via the Grotthuss mechanism, but there is little high-resolution information concerning the path by which protons are conducted. A previously solved 1.65-Å crystal structure (9) showed six ordered waters immediately above the His37 tetrad, but ordered waters spanning the entire aqueous pore of M2 have not been observed until now. Previous MD simulations suggested a pore with mobile waters (12, 15), whereas the results of NMR and IR experiments are more consistent with an environment that is more similar to bulk water at low pH (13, 19, 20). However, it is difficult to deconvolute the changes in the water structure and dynamics when the protonation of His37 is raised from those induced indirectly via the conformation of the protein’s main chain.The M2 channel is known to have at least two conformational states that are populated to differing extents at low versus high pH (1, 10, 12). One, seen primarily at high pH, has been characterized extensively by solution NMR (21, 22), solid-state NMR (SSNMR) (10, 12), and X-ray crystallography (9). A second form is observed in dynamic equilibrium at lower pH (21–23), as evidenced by a broadening of magnetic resonances that thus far has made it impractical to determine a high-resolution structure of the protein in this state by SSNMR or solution NMR. X-ray crystallographic studies, however, have provided structures of both states (8, 9), which differ primarily in the conformation of the C terminus where protons exit the channel. Here we have obtained crystals that diffract to high resolution (1.10 Å) at both low and high pH, allowing visualization of water wires leading to His37 as a function of pH. The conformations of the backbone at the two pH values are essentially identical, permitting us to isolate changes in the organization of the water without any confounding factors.     

Phase separation in the outer membrane of Escherichia coli

Gram-negative bacteria are surrounded by a protective outer membrane (OM) with phospholipids in its inner leaflet and lipopolysaccharides (LPS) in its outer leaflet. The OM is also populated with many β-barrel outer-membrane proteins (OMPs), some of which have been shown to cluster into supramolecular assemblies. However, it remains unknown how abundant OMPs are organized across the entire bacterial surface and how this relates to the lipids in the membrane. Here, we reveal how the OM is organized from molecular to cellular length scales, using atomic force microscopy to visualize the OM of live bacteria, including engineered Escherichia coli strains and complemented by specific labeling of abundant OMPs. We find that a predominant OMP in the E. coli OM, the porin OmpF, forms a near-static network across the surface, which is interspersed with barren patches of LPS that grow and merge with other patches during cell elongation. Embedded within the porin network is OmpA, which forms noncovalent interactions to the underlying cell wall. When the OM is destabilized by mislocalization of phospholipids to the outer leaflet, a new phase appears, correlating with bacterial sensitivity to harsh environments. We conclude that the OM is a mosaic of phase-separated LPS-rich and OMP-rich regions, the maintenance of which is essential to the integrity of the membrane and hence to the lifestyle of a gram-negative bacterium.

Diderm bacteria, such as Escherichia coli, are surrounded by an outer membrane (OM) that protects cells against the immune systems of plants and animals, contributes to the mechanical stability of the cell, and excludes many classes of antibiotics, thereby contributing to antimicrobial resistance (1, 2). The OM is comprised of an asymmetric bilayer of phospholipids in the inner leaflet, lipopolysaccharides (LPS) in the outer leaflet, and many outer-membrane proteins (OMPs). OMPs are hugely diverse β-barrel proteins that can be present at hundreds to hundreds of thousands of copies per cell (3). They have been shown to be relatively static (4), probably due to promiscuous protein–protein interactions and binding of LPS that exists in a slow-moving, liquid-crystalline state (5, 6). Using fluorescent labels, some OMPs have been shown to cluster into supramolecular islands of ∼0.3- to 0.5-μm sizes (4, 7–9). However, it remains unknown how abundant OMPs are organized across the entire bacterial surface and how this relates to the lipids in the membrane.To address this fundamental question, we have imaged the entire surface of live and metabolically active bacteria at nanometer resolution using atomic force microscopy (AFM). Applying such large-scale, high-resolution imaging on engineered E. coli strains and complementing it by specific labeling of abundant OMPs, we identify large-scale and near-static protein-rich networks interspersed with nanoscale domains that are enriched in LPS. Key components of the protein-rich networks are abundant trimeric porins such as OmpF, in addition to (the monomeric) OmpA, which forms noncovalent interactions to the underlying cell wall (10). By contrast, no significant protein content is detected in the LPS-rich domains, which are also found to grow and merge with other patches during cell elongation. When the LPS–phospholipid asymmetry of the OM is perturbed by mislocalization of phospholipids to the outer leaflet (11), we find deformation of the membrane rather than expansion of LPS patches, indicating the appearance of a new, phospholipid-enriched phase at the bacterial surface.     

The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli

Ammonium is one of the most important nitrogen sources for bacteria, fungi, and plants, but it is toxic to animals. The ammonium transport proteins (methylamine permeases/ammonium transporters/rhesus) are present in all domains of life; however, functional studies with members of this family have yielded controversial results with respect to the chemical identity (NH(4)(+) or NH(3)) of the transported species. We have solved the structure of wild-type AmtB from Escherichia coli in two crystal forms at 1.8- and 2.1-A resolution, respectively. Substrate transport occurs through a narrow mainly hydrophobic pore located at the center of each monomer of the trimeric AmtB. At the periplasmic entry, a binding site for NH(4)(+) is observed. Two phenylalanine side chains (F107 and F215) block access into the pore from the periplasmic side. Further into the pore, the side chains of two highly conserved histidine residues (H168 and H318) bridged by a H-bond lie adjacent, with their edges pointing into the cavity. These histidine residues may facilitate the deprotonation of an ammonium ion entering the pore. Adiabatic free energy calculations support the hypothesis that an electrostatic barrier between H168 and H318 hinders the permeation of cations but not that of the uncharged NH(3.) The structural data and energetic considerations strongly indicate that the methylamine permeases/ammonium transporters/rhesus proteins are ammonia gas channels. Interestingly, at the cytoplasmic exit of the pore, two different conformational states are observed that might be related to the inactivation mechanism by its regulatory partner.     

The fusion-related hydrophobic domain of Sendai F protein can be moved through the cytoplasmic membrane of Escherichia coli.

Recent work on a prokaryotic membrane protein, gene III protein (pIII) of coliphage f1, showed that polypeptide segments of sufficient hydrophobicity functioned to stop transfer of the polypeptide across the cell membrane: strings of 16 or more hydrophobic amino acids sufficed. A fusion-related hydrophobic domain (FRHD) of Sendai F protein, a sequence of 26 consecutive uncharged residues, has been implicated in the fusion of the viral membrane envelope and the target-cell membrane through a hydrophobic interaction. As it is located on the exterior of the viral membrane, this sequence must be transferred across the host-cell membrane during synthesis. We have inserted either the FRHD or the F protein membrane anchor (the COOH-terminal region of the F protein) into an internal site of a secreted pIII, which lacks its natural membrane anchor. These two hydrophobic sequences behave in the bacteria just as they do in their natural eukaryotic cell host. The F protein membrane anchor functions to stop transfer, conferring a membrane-spanning topology to the F-pIII hybrid protein; however, the FRHD is moved through the cytoplasmic membrane and derivatives carrying this sequence are secreted to the periplasm. We discuss how the FRHD is compatible with passage through the membrane and yet is still able to mediate membrane fusion through a presumed hydrophobic interaction.     

The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains

The recent characterization of the prokaryotic Cys₂His₂ zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified ≈300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys₂His₂ zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros_56–142C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys₂His₂ coordination, in Ros homologues can either exploit a CysAspHis₂ coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.     

Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel

Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating.Ion conduction through the pore domain of cation channels is regulated by two gates: an inner gate at the bundle crossing of the pore-lining transmembrane helices and an outer gate located at the selectivity filter (Fig. 1 B and C). These two gates are functionally coupled as demonstrated by C-type inactivation, in which channel opening triggers loss of conduction at the selectivity filter (1–4). A structural model for C-type inactivation has been developed for KcsA, with selectivity filter collapse occurring upon channel opening (4–10). In the reverse pathway, inactivation of the selectivity filter has been linked to changes at the inner gate (5–14). However, flux-dependent inactivation occurs in Na⁺ and Ca²⁺ channels as well and would likely require a structurally different mechanism to explain coupling between the selectivity filter and inner gate (7, 13–18).Open in a separate windowFig. 1.Crystal structures of the nonselective cation channel NaK and the potassium-selective NaK2K mutant show structural changes restricted to the area of the selectivity filter. Alignment of the WT NaK (gray; PDB 3E8H) and NaK2K (light blue; PDB 3OUF) selectivity filters shows a KcsA-like four-ion-binding-site selectivity filter is created by the NaK2K mutations (D66Y and N68D) (A), but no structural changes occur outside the vicinity of the selectivity filter (B). (C) Full-length NaK (green; PDB 2AHZ) represents a closed conformation. Alignment of this structure with NaK (gray) highlights the changes in the M2 hinge (arrow), hydrophobic cluster (residues F24, F28, and F94 shown as sticks), and constriction point (arrow; residue Q103 shown as sticks) upon channel opening. Two (A) or three monomers (B and C) from the tetramer are shown for clarity.This study provides experimental evidence of structural and dynamic coupling between the inner gate and selectivity filter in the NaK channel, a nonselective cation channel from Bacillus cereus (19). These results were entirely unexpected given the available high-resolution crystal structures (20, 21). The NaK channel has the same basic pore architecture as K⁺ channels (Fig. 1 B and C) and has become a second model system for investigating ion selectivity and gating due to its distinct selectivity filter sequence (₆₃TVGDGN₆₈) and structure (19–23). Most strikingly, there are only two ion binding sites in the selectivity filter of the nonselective NaK channel (Fig. 1A) (21, 24). However, mutation of two residues in the selectivity filter sequence converts the NaK selectivity filter to the canonical KcsA sequence (₆₃TVGYGD₆₈; Fig. 1 A and B), leading to K⁺ selectivity and a KcsA-like selectivity filter structure with four ion binding sites (21, 23). This K⁺-selective mutant of NaK is called NaK2K. Outside of the immediate vicinity of the two mutations in the selectivity filter, high-resolution crystal structures of NaK and NaK2K are essentially identical (Fig. 1B) with an all-atom rmsd of only 0.24 Å.NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating because there is no evidence for any collapse or structural change in the selectivity filter. The NaK selectivity filter structure is identical in Na⁺ or K⁺ (22) and even in low-ion conditions (25), consistent with its nonselective behavior. Even the selective NaK2K filter appears structurally stable in all available crystal structures (25). Here we use NMR spectroscopy to study bicelle-solubilized NaK. Surprisingly, we find significant differences in the NMR spectra of NaK and NaK2K that extend throughout the protein and are not localized to the selectivity filter region. This, combined with NMR dynamics studies of NaK, suggests a dynamic pathway for transmembrane coupling between the inner gate and selectivity filter of NaK.     

普罗帕酮对Kv1.4ΔN钾通道的作用及细胞外钾离子和pH浓度变化时的影响

目的:探讨抗心律失常药物普罗帕酮对Kv1.4△N钾通道的作用,以及细胞外钾离子和pH浓度变化时对该作用的影响,并探讨该作用可能的机制.方法:将Kv1.4ΔN的mRNA注射入非洲爪蟾卵母细胞并使用双电极钳制法观察普罗帕酮对Kv1.4ΔN电生理特性的影响,以及细胞外钾离子和pH变化时的电生理特性改变.结果:pH7 4状态下,普罗帕酮对Kv1.4ΔN通道的峰电流有抑制作用,这种阻滞作用具有电压依赖性、浓度依赖性以及频率依赖性,并且随电位的升高而作用加强,符合单指数和线性关系.普罗帕酮加速电流的失活过程.在不同的钾离子浓度下,这种阻滞作用具有pH依赖性,细胞外高钾pH7 4时,不同浓度普罗帕酮灌流显示IC50为121 μmol/L;细胞外酸性环境下(pH6 0)IC50提高到463 μmol/L,碱性化的环境(pH8 0)降至58 μmol/L.结论:普罗帕酮是Kv1.4ΔN的阻滞剂,可能与作用于细胞内的某些位点有关.     

结核分枝杆菌phoS2基因在大肠埃希菌中的高效表达及其产物抗原性分析

目的在大肠埃希菌中高效表达结核杆菌phoS2,通过免疫印迹反应初步鉴定重组蛋白的抗原性和特异性。方法采用DNA重组技术构建结核分枝杆菌phoS2抗原表达载体,用双酶切和PCR等方法鉴定转化子,重组质粒转化大肠埃希菌,诱导表达phoS2;用SDS-PAGE初步鉴定其表达量;将表达产物进行纯化;重组蛋白用Western blot分析其抗原性和特异性。结果phoS2基因在大肠埃希菌中得到高效表达,表达量占全菌蛋白的40％以上;重组蛋白与结核病患者血清标本呈强阳性反应,与健康人血清标本呈阴性反应。结论重组phoS2蛋白在大肠埃希菌中主要以包涵体形式表达,有很好的抗原特异性和免疫原性,对结核病诊断有潜在的应用价值。     

Opening and closing of the periplasmic gate in lactose permease

X-ray crystal structures of lactose permease (LacY) reveal pseudosymmetrically arranged N- and C-terminal six-transmembrane helix bundles surrounding a deep internal cavity open on the cytoplasmic side and completely closed on the periplasmic side. The residues essential for sugar recognition and H(+) translocation are located at the apex of the cavity and are inaccessible from the outside. On the periplasmic side, helices I/II and VII from the N- and C- six helix bundles, respectively, participate in sealing the cavity from the outside. Three paired double-Cys mutants-Ile-40 --> Cys/Asn-245 --> Cys, Thr-45 --> Cys/Asn-245 --> Cys, and Ile-32 --> Cys/Asn-245 --> Cys-located in the interface between helices I/II and VII on the periplasmic side of LacY were constructed. After cross-linking with homobifunctional reagents less than approximately 15 A in length, all three mutants lose the ability to catalyze lactose transport. Strikingly, however, full or partial activity is observed when cross-linking is mediated by flexible reagents greater than approximately 15 A in length. The results provide direct support for the argument that transport via LacY involves opening and closing of a large periplasmic cavity.     

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus

The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2⁺ and 3⁺ with a pK_a near 6. A 1.65 Å resolution X-ray structure of the transmembrane protein (residues 25–46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models.     

The restriction–modification genes of Escherichia coli K-12 may not be selfish: They do not resist loss and are readily replaced by alleles conferring different specificities

Type II restriction and modification (R-M) genes have been described as selfish because they have been shown to impose selection for the maintenance of the plasmid that encodes them. In our experiments, the type I R-M system EcoKI does not behave in the same way. The genes specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector. If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss of the relevant chromosomal genes by mutation or recombination should lead to cell death because the cell would become deficient in modification enzyme and the bacterial chromosome would be vulnerable to the restriction endonuclease. Our data contradict this prediction; they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant alleles and by alleles encoding a type I R-M system of different specificity. The acquisition of allelic genes conferring a new sequence specificity, but not the loss of the resident genes, is dependent on the product of an unlinked gene, one predicted [Prakash-Cheng, A., Chung, S. S. & Ryu, J. (1993) Mol. Gen. Genet. 241, 491–496] to be relevant to control of expression of the genes that encode EcoKI. Our evidence suggests that not all R-M systems are evolving as “selfish” units; rather, the diversity and distribution of the family of type I enzymes we have investigated require an alternative selective pressure.     

A mutation in the first intracellular loop of CACNA1A prevents P/Q channel modulation by SNARE proteins and lowers exocytosis

Familial hemiplegic migraine (FHM)-causing mutations in the gene encoding the P/Q Ca²⁺ channel α_1A subunit (CACNA1A) locate to the pore and voltage sensor regions and normally involve gain-of-channel function. We now report on a mutation identified in the first intracellular loop of CACNA1A (α_1A(A454T)) that does not cause FHM but is associated with the absence of sensorimotor symptoms in a migraine with aura pedigree. α_1A(A454T) channels showed weakened regulation of voltage-dependent steady-state inactivation by Ca_Vβ subunits. More interestingy, A454T mutation suppressed P/Q channel modulation by syntaxin 1A or SNAP-25 and decreased exocytosis. Our findings reveal the importance of I-II loop structural integrity in the functional interaction between P/Q channel and proteins of the vesicle-docking/fusion machinery, and that genetic variation in CACNA1A may be not only a cause but also a modifier of migraine phenotype.     

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli

The thiamin- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from E. coli catalyzes the oxidative decarboxylation of the central metabolite pyruvate to CO₂ and acetate. Concomitant reduction of the enzyme-bound flavin triggers membrane binding of the C terminus and shuttling of 2 electrons to ubiquinone 8, a membrane-bound mobile carrier of the electron transport chain. Binding to the membrane in vivo or limited proteolysis in vitro stimulate the catalytic proficiency by 2 orders of magnitude. The molecular mechanisms by which membrane binding and activation are governed have remained enigmatic. Here, we present the X-ray crystal structures of the full-length enzyme and a proteolytically activated truncation variant lacking the last 23 C-terminal residues inferred as important in membrane binding. In conjunction with spectroscopic results, the structural data pinpoint a conformational rearrangement upon activation that exposes the autoinhibitory C terminus, thereby freeing the active site. In the activated enzyme, Phe-465 swings into the active site and wires both cofactors for efficient electron transfer. The isolated C terminus, which has no intrinsic helix propensity, folds into a helical structure in the presence of micelles.     

提取程度及电泳上样量对布氏菌外膜蛋白电泳图谱恒定性的影响

由于难以从布氏菌的外膜蛋白中将干扰因素多糖成分去除到恒定水平的最低限度,迄今未能获得可用于分类的恒定的外膜蛋白电泳图谱。我们最大限度地提取出外膜蛋白及牢固附于其上的多糖成分;在电泳过程中又以超载的手段促使该二成分的相互作用达到综合平衡状态。由此可以消除不等程度多糖的干扰而产生的外膜蛋白电泳谱带的不恒定。为揭示了不同种布氏菌微孔蛋白热解聚前后电泳谱带变化规律及其所表现出的种的特异性奠定了基础。     

Interacting cytoplasmic loops of subunits a and c of Escherichia coli F1F0 ATP synthase gate H+ transport to the cytoplasm

H⁺-transporting F₁F₀ ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F₀ and F₁. H⁺ transport at the subunit a–c interface in transmembranous F₀ drives rotation of a cylindrical c₁₀ oligomer within the membrane, which is coupled to rotation of subunit γ within the α₃β₃ sector of F₁ to mechanically drive ATP synthesis. F₁F₀ functions in a reversible manner, with ATP hydrolysis driving H⁺ transport. ATP-driven H⁺ transport in a select group of cysteine mutants in subunits a and c is inhibited after chelation of Ag⁺ and/or Cd⁺² with the substituted sulfhydryl groups. The H⁺ transport pathway mapped via these Ag⁺(Cd⁺²)-sensitive Cys extends from the transmembrane helices (TMHs) of subunits a and c into cytoplasmic loops connecting the TMHs, suggesting these loop regions could be involved in gating H⁺ release to the cytoplasm. Here, using select loop-region Cys from the single cytoplasmic loop of subunit c and multiple cytoplasmic loops of subunit a, we show that Cd⁺² directly inhibits passive H⁺ transport mediated by F₀ reconstituted in liposomes. Further, in extensions of previous studies, we show that the regions mediating passive H⁺ transport can be cross-linked to each other. We conclude that the loop-regions in subunits a and c that are implicated in H⁺ transport likely interact in a single structural domain, which then functions in gating H⁺ release to the cytoplasm.The F₁F₀-ATP synthase of oxidative phosphorylation uses the energy of a transmembrane electrochemical gradient of H⁺ or Na⁺ to mechanically drive the synthesis of ATP via two coupled rotary motors in the F₁ and F₀ sectors of the enzyme (1). H⁺ transport through the transmembrane F₀ sector is coupled to ATP synthesis or hydrolysis in the F₁ sector at the surface of the membrane. Homologous ATP synthases are found in mitochondria, chloroplasts, and many bacteria. In Escherichia coli and other eubacteria, F₁ consists of five subunits in an α₃β₃γδε stoichiometry. F₀ is composed of three subunits in a likely ratio of a₁b₂c₁₀ in E. coli and Bacillus PS3 (2, 3) or a₁b₂c₁₁ in the Na⁺ translocating Ilyobacter tartaricus ATP synthase (1, 4) and may contain as many as 15 c subunits in other bacterial species (5). Subunit c spans the membrane as a hairpin of two α-helices, with the first transmembrane helix (TMH) on the inside and the second TMH on the outside of the c ring (1, 4). The binding of Na⁺ or H⁺ occurs at an essential, membrane-embedded Glu or Asp on cTMH2. High-resolution X-ray structures of both Na⁺- and H⁺-binding c-rings have revealed the details and variations in the cation binding sites (4–8). In the H⁺-translocating E. coli enzyme, Asp-61 at the center of cTMH2 is thought to undergo protonation and deprotonation, as each subunit of the c ring moves past the stationary subunit a. In the functioning enzyme, the rotation of the c ring is thought to be driven by H⁺ transport at the subunit a/c interface. Subunit γ physically binds to the cytoplasmic surface of the c-ring, which results in the coupling of c-ring rotation with rotation of subunit γ within the α₃β₃ hexamer of F₁ to mechanically drive ATP synthesis (1).E. coli subunit a folds in the membrane with five TMHs and is thought to provide aqueous access channels to the H⁺-binding cAsp-61 residue (9, 10). Interaction of the conserved Arg-210 residue in aTMH4 with cTMH2 is thought to be critical during the deprotonation–protonation cycle of cAsp-61 (1, 11, 12). At this time, very limited biophysical or crystallographic information is available on the 3D arrangement of the TMHs in subunit a. TMHs 2–5 of subunit a pack in a four-helix bundle, which was initially defined by cross-linking (13), but now, such a bundle, packing at the periphery of the c-ring, has been viewed directly by high-resolution cryoelectron microscopy in the I. tartaricus enzyme (14). Previously published cross-linking experiments support the identification of aTMH4 and aTMH5 packing at the periphery of the c-ring and the identification of aTHM2 and aTMH3 as the other components of the four-helix bundle seen in these images (13, 15, 16). More recently, published cross-linking experiments identify the N-terminal α-helices of two b subunits, one of which packs at one surface of aTMH2 with close enough proximity to the c-ring to permit cross-linking (17). The other subunit b N-terminal helix packs on the opposite peripheral surface of aTMH2 in a position where it can also be cross-linked to aTMH3 (17). The last helix density shown in Hakulinen and colleagues (14) packs at the periphery of the c-ring next to aTMH5 and is very likely to be aTMH1.The aqueous accessibility of Cys residues introduced into the five TMHs of subunit a has been probed on the basis of their reactivity with and inhibitory effects of Ag⁺ and other thiolate-reactive agents (18–20). Two regions of aqueous access were found with distinctly different properties. One region in TMH4, extending from Asn-214 and Arg-210 at the center of the membrane to the cytoplasmic surface, contains Cys substitutions that are sensitive to inhibition by both N-ethylmaleimide (NEM) and Ag⁺ (18–20; Fig. 1). These NEM- and Ag⁺-sensitive residues in TMH4 pack at or near the peripheral face and cytoplasmic side of the modeled four-helix bundle (11, 13). A second set of Ag⁺-sensitive substitutions in subunit a mapped to the opposite face and periplasmic side of aTMH4 (18, 19), and Ag⁺-sensitive substitutions were also found in TMHs 2, 3, and 5, where they extend from the center of the membrane to the periplasmic surface (19, 20). The Ag⁺-sensitive substitutions on the periplasmic side of TMHs 2–5 cluster at the interior of the four-helix bundle predicted by cross-linking and could interact to form a continuous aqueous pathway extending from the periplasmic surface to the central region of the lipid bilayer (11, 13, 19, 20). We have proposed that the movement of H⁺ from the periplasmic half-channel and binding to the single ionized Asp61 in the c-ring is mediated by a swiveling of TMHs at the a–c subunit interface (16, 21–24). This gating is thought to be coupled with ionization of a protonated cAsp61 in the adjacent subunit of the c-ring and with release of the H⁺ into the cytoplasmic half-channel at the subunit a–c interface. The route of aqueous access to the cytoplasmic side of the c subunit packing at the a–c interface has also been mapped by the chemical probing of Cys substitutions and, more recently, by molecular dynamics simulations (22, 25, 26).Open in a separate windowFig. 1.The predicted topology of subunit a in the E. coli inner membrane. The location of the most Ag⁺-sensitive Cys substitutions are highlighted in red (>85% inhibition) or orange (66–85% inhibition). The five proposed TMHs are shown in boxes, each with a span of 21 amino acids, which is the minimum length required to span the hydrophobic core of a lipid bilayer. The α-helical segments shown in loops 1–2 and 3–4 are consistent with the predictions of TALOS, based on backbone chemical shifts seen by NMR (29). Others have also predicted extensive α-helical regions in these loops (12, 30), but the possible positions remain largely speculative. aArg210 is highlighted in green. Figure is modified from those shown previously (21, 23, 24, 27).We have also reported Ag⁺-sensitive Cys substitutions in two cytoplasmic loops of subunit a (27) and, more recently, in the cytoplasmic loop of subunit c (28). The mechanism by which Ag⁺ inhibited F₁F₀-mediated H⁺ transport was uncertain. Several of these substitutions were also sensitive to inhibition by Cd⁺², and these substitutions provided a means of testing whether Cd⁺² directly inhibits passive H⁺ transport through F₀ (28). In the case of two subunit c loop substitutions, Cd⁺² was shown to directly inhibit passive F₀-mediated transport activity. In this study, we have extended the survey to Cd⁺²-sensitive Cys substitutions in cytoplasmic loops of subunit a. We report four loop substitutions in which Cd⁺² inhibits passive F₀-mediated H⁺ transport. Further, in two cases, we show cross-linking between pairs of Cys substitutions, which lie in subunits a and c, respectively, and which individually mediate passive H⁺ transport activity. These results suggest that the a and c loops, which gate H⁺ release to the cytoplasm, fold into a single domain at the surface of F₀.     

The thermodynamic H+/ATP ratios of the H+-ATPsynthases from chloroplasts and Escherichia coli

The H(+)/ATP ratio is an important parameter for the energy balance of all cells and for the coupling mechanism between proton transport and ATP synthesis. A straightforward interpretation of rotational catalysis predicts that the H(+)/ATP coincides with the ratio of the c-subunits to beta-subunits, implying that, for the chloroplast and Escherichia coli ATPsynthases, numbers of 4.7 and 3.3 are expected. Here, the energetics described by the chemiosmotic theory was used to determine the H(+)/ATP ratio for the two enzymes. The isolated complexes were reconstituted into liposomes, and parallel measurements were performed under identical conditions. The internal phase of the liposomes was equilibrated with the acidic medium during reconstitution, allowing to measure the internal pH with a glass electrode. An acid-base transition was carried out and the initial rates of ATP synthesis or ATP hydrolysis were measured with luciferin/luciferase as a function of DeltapH at constant Q = [ATP]/([ADP][P(i)]). From the shift of the equilibrium DeltapH as a function of Q the standard Gibbs free energy for phosphorylation, DeltaG(p)(0)'; and the H(+)/ATP ratio were determined. It resulted DeltaG(p)(0)' = 38 +/- 3 kJ.mol(-1) and H(+)/ATP = 4.0 +/- 0.2 for the chloroplast and H(+)/ATP = 4.0 +/- 0.3 for the E. coli enzyme, indicating that the thermodynamic H(+)/ATP ratio is the same for both enzymes and that it is different from the subunit stoichiometric ratio.