Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel

The AmtB channel passively allows the transport of NH₄⁺ across the membranes of bacteria via a “gas” NH₃ intermediate and is related by homology (sequentially, structurally, and functionally) to many forms of Rh protein (both erythroid and nonerythroid) found in animals and humans. New structural information on this channel has inspired computational studies aimed at clarifying various aspects of NH₄⁺ recruitment and binding in the periplasm, as well as its deprotonation. However, precise mechanisms for these events are still unknown, and, so far, explanations for subsequent NH₃ translocation and reprotonation at the cytoplasmic end of the channel have not been rigorously addressed. We employ molecular dynamics simulations and free energy methods on a full AmtB trimer system in membrane and bathed in electrolyte. Combining the potential of mean force for NH₄⁺/NH₃ translocation with data from thermodynamic integration calculations allows us to find the apparent pK_a of NH₄⁺ as a function of the transport axis. Our calculations reveal the specific sites at which its deprotonation (at the periplasmic end) and reprotonation (at the cytoplasmic end) occurs. Contrary to most hypotheses, which ascribe a proton-accepting role to various periplasmic or luminal residues of the channel, our results suggest that the most plausible proton donor/acceptor at either of these sites is water. Free-energetic analysis not only verifies crystallographically determined binding sites for NH₄⁺ and NH₃ along the transport axis, but also reveals a previously undetermined binding site for NH₄⁺ at the cytoplasmic end of the channel. Analysis of dynamics and the free energies of all possible loading states for NH₃ inside the channel also reveal that hydrophobic pressure and the free-energetic profile provided by the pore lumen drives this species toward the cytoplasm for protonation just before reaching the newly discovered site.     

In vitro interaction between the ammonium transport protein AmtB and partially uridylylated forms of the P(II) protein GlnZ

The ammonium transport family Amt/Rh comprises ubiquitous integral membrane proteins that facilitate ammonium movement across biological membranes. Besides their role in transport, Amt proteins also play a role in sensing the levels of ammonium in the environment, a process that depends on complex formation with cytosolic proteins of the P(II) family. Trimeric P(II) proteins from a variety of organisms undergo a cycle of reversible posttranslational modification according to the prevailing nitrogen supply. In proteobacteria, P(II) proteins are subjected to reversible uridylylation of each monomer. In this study we used the purified proteins from Azospirillum brasilense to analyze the effect of P(II) uridylylation on the protein's ability to engage complex formation with AmtB in vitro. Our results show that partially uridylylated P(II) trimers can interact with AmtB in vitro, the implication of this finding in the regulation of nitrogen metabolism is discussed. We also report an improved expression and purification protocol for the A. brasilense AmtB protein that might be applicable to AmtB proteins from other organisms.     

Proton-coupled protein transport through the anthrax toxin channel

Anthrax toxin consists of three proteins (approx. 90kDa each): lethal factor (LF); oedema factor (OF); and protective antigen (PA). The former two are enzymes that act when they reach the cytosol of a targeted cell. To enter the cytosol, however, which they do after being endocytosed into an acidic vesicle compartment, they require the third component, PA. PA (or rather its proteolytically generated fragment PA63) forms at low pH a heptameric beta-barrel channel, (PA63)7, through which LF and OF are transported--a phenomenon we have demonstrated in planar phospholipid bilayers. It might appear that (PA63)7 simply forms a large hole through which LF and OF diffuse. However, LF and OF are folded proteins, much too large to fit through the approximately 15A diameter (PA63)7 beta-barrel. This paper discusses how the (PA63)7 channel both participates in the unfolding of LF and OF and functions in their translocation as a proton-protein symporter.     

Computational studies of proton transport through the M2 channel

The M2 ion channel is an essential component of the influenza A virus. This low-pH gated channel has a high selectivity for protons. Evidence from various experimental data has indicated that the essential structure responsible for the channel is a parallel homo-tetrameric alpha-helix bundle having a left-handed twist with each helix tilted with respect to the membrane normal. A backbone structure has been determined by solid state nuclear magnetic resonance (NMR). Though detailed structures for the side chains are not available yet, evidence has indicated that His37 and Trp41 in the alpha-helix are implicated in the local molecular structure responsible for the selectivity and channel gate. More definitive conformations for the two residues were recently suggested based on the known backbone structure and recently obtained NMR data. While two competitive proton-conductance mechanisms have been proposed, the actual proton-conductance mechanism remains an unsolved problem. Computer simulations of an excess proton in the channel and computational studies of the His37/Trp41 conformations have provided insights into these structural and mechanism issues.     

Human erythrocyte ammonium transport is mediated by functional interaction of ammonium (RhAG) and anion (AE1) transporters

The ammonia/ammonium (NH₃/NH ₄ ⁺ ) influx into red blood cells (RBCs) is mediated by surface glycoprotein RhAG that forms a structural complex with anion exchanger 1 (AE1, band 3). Owing to the activity of this complex, RBCs exposed to the isosmotic ammonium buffer swell and finally lyse. Isoosmotic NH ₄ ⁺ -containing media alters the pH gradient in RBCs (intracellular alkalosis in response to NH₃/NH ₄ ⁺ influx) and triggers the AE1 activity resulting in redundant chloride and water influx and finally in cell swelling. Here we demonstrate that the ammonia/ammonium transport in human RBCs depends on the pH (pH optimum 7.4 ± 0.1), temperature (Q₁₀ 2.6 ± 0.3), HCO ₃ ^? concentration (EC₅₀ 4.7 ± 0.3 mM), and AE1 function. The data confirm functional interactions between AE1 and RhAG. The initial velocity of cell swelling increased almost 50-fold in the isosmotic ammonium buffer containing 25 mM HCO ₃ ^? (37°C) in comparison to the reaction in the same buffer without HCO ₃ ^? . This indicates that the reaction is facilitated mostly by the carrier proteins, not just owing to the simple diffusion of NH₃ across the erythrocyte membrane. We demonstrate that pH_i reaches its maximum value much faster than the volume increase does. These data suggest that there is no direct correlation between pH_i changes and the influx of NH₃/NH ₄ ⁺ . Taken together, our data show that the RhAG and AE1 complex activity enables erythrocytes to be ammonia/ammonium storage sites in order to maintain the physiological blood ammonia/ammonium equilibrium.     

DNA-protein cross-links as a possible reason for genomic damage during its protonation]

The change in survival of bacteriophages with DNA of different GC-contents after their incubation in media of different acidities with subsequent neutralization was studied. It was shown that the higher the GC-content, the more sensitive is the phage to the action of H(+)-ions. Evidence is presented that the acidic inactivation of virions is not connected with the helix-coil transition of the intraphage DNA due to its protonation. The extractability of DNA from phages subjected to different concentrations of H(+)-ions with subsequent neutralization of the medium to pH 8 was determined. The changes in: transfection ability, UV-spectra, the quantity of the residual proteins, and the contents of glutamic and lysine amino acid residues in these proteins were investigated. The effect of glutamic acid on the parameters of DNA melting curves was followed for different pH values. Proceeding from the data obtained, we concluded that acidification of the medium from neutral tp pH congruent to 4 leads to formation of non-covalent DNA-protein cross-links due to interaction of the GC base pairs of DNA with glutamic and aspartic amino acid residues, whereas acidification of the medium to pH less than 4 with subsequent neutralization to pH 8 results in the formation of covalent DNA-protein cross-links of Schiff base type. The influence of non-covalent DNA-protein cross-links on the properties of DNA and their regulatory role in genome functioning are discussed.     

A kinetic analysis of protein transport through the anthrax toxin channel

Anthrax toxin is composed of three proteins: a translocase heptameric channel, (PA(63))(7), formed from protective antigen (PA), which allows the other two proteins, lethal factor (LF) and edema factor (EF), to translocate across a host cell's endosomal membrane, disrupting cellular homeostasis. (PA(63))(7) incorporated into planar phospholipid bilayer membranes forms a channel capable of transporting LF and EF. Protein translocation through the channel can be driven by voltage on a timescale of seconds. A characteristic of the translocation of LF(N), the N-terminal 263 residues of LF, is its S-shaped kinetics. Because all of the translocation experiments reported in the literature have been performed with more than one LF(N) molecule bound to most of the channels, it is not clear whether the S-shaped kinetics are an intrinsic characteristic of translocation kinetics or are merely a consequence of the translocation in tandem of two or three LF(N)s. In this paper, we show both in macroscopic and single-channel experiments that even with only one LF(N) bound to the channel, the translocation kinetics are S shaped. As expected, the translocation rate is slower with more than one LF(N) bound. We also present a simple electrodiffusion model of translocation in which LF(N) is represented as a charged rod that moves subject to both Brownian motion and an applied electric field. The cumulative distribution of first-passage times of the rod past the end of the channel displays S-shaped kinetics with a voltage dependence in agreement with experimental data.     

Characteristics and regulation of ammonium (methylammonium) transport in Rhizobium meliloti

Abstract Rhizobium meliloti can synthesize an ammonium carrier as demonstrated by concentrative methylammonium uptake ( K _m= 2 μ M), which is competitively inhibited by ammonium ( K _i= 1.2 μ M). The carrier is under nitrogen control: its synthesis is repressed by ammonium, glutamine and asparagine. The asparagine effect may be of importance for the transfer of ammonia from the bacterium to the plant in the nodule.     

Developmental regulation of methylammonium (ammonium) transport activity in the cyanobacterium Anabaena doliolum

Abstract Whiel heterocystous vegetative filaments of A. doliolum exhibited biphasic pattern of methylammonium (ammonium) uptake, its populations of akinetes deficient in chlorophylla, phycocyanin, oxygenic photosynthesis and aerobic nitrogenase activity showed monophasic uptake pattern with no evidence for second phase activity. Such akinetes with monophasic uptake pattern of methylammonium became biphasic by developing second phase activity at a stage during their germination at which oxygenic photosynthesis also developed. It is suggested that first phase activity of the methylammonium uptake process corresponds to plasma membrane regulated uptake activity leading to one methylammonium pool and that second phase activity of the metylammonium uptake process corresponds to the thylakoid membrane regulated uptake activity leading to the other methylammonium pool.     

Temperature dependence of single channel currents and the peptide libration mechanism for ion transport through the gramicidin A transmembrane channel

Summary A study of the temperature dependence of gramicidin A conductance of K⁺ in diphytanoyllecithin/n-decane membranes shows the plot of In (single channel conductance) as a function of reciprocal temperature to be nonlinear for the most probable set of conductance, states. These results are considered in terms of a series of barriers, of the dynamics of channel conformation,vis-a-vis the peptide libration mechanism, and of the effect of lipid viscosity on side chain motions again as affecting the energetics of peptide libration.     

The composition and bioavailability of phosphorus transport through the Changjiang (Yangtze) River during the 1998 flood

Water and suspended sediment (SS) samples were collected from the Changjiang River at the Datong Hydrological Station (DHS), five times from May 1997 through January 1999 in order to evaluate transport, composition and bioavailability of phosphorus (P) during a 1998 flood. Transport of most of the phosphorus compositions was substantially higher during the 1998 flood than at other sampling dates. Phosphorus associated with suspended sediment (TPP) accounted for more than 85% of total phosphorus (TP) transport during periods of preflood and flood. The high transport of TPP during the flood was due to unusually high concentrations of TPP and sediment discharge. The potentially bioavailable phosphorus in SS (PBAP) accounted for about 10% of TPP. PBAP with dissolved inorganic phosphorus (DIP) consisted of 15–89% of TP. For all the sampling dates, the concentrations of potential bioavailable phosphorus (BAP) ranged from 0.035–0.08 mg L^–1, significantly higher than the limiting concentration for eutrophication. Therefore, the increasing temporal trends of TP concentration and high bioavailability of TP appear to support more frequent algal blooms in receiving East China Sea coastal waters in recent years. Hence, the underestimate of TPP transport by large rivers may also underestimate the biogeochemical cycling of other associated nutrients, such as nitrogen and carbon.     

Evidence for channel mediated transport of boric acid in squash (Cucurbita pepo)

Boron (B) is taken up by plant roots as undissociated boric acid which is a non-electrolyte of similar size to urea and other non-electrolytes. In animal systems, non-electrolytes are transported across biological membranes through aquaporins or through non-aquaporin channels. In artificial lipids boric acid is known to diffuse directly through the lipid bilayer at a rate that is determined by lipid composition. A possible role for channel proteins in in-vitro B uptake is suggested by recent work in which B uptake into isolated membrane vesicles was inhibited by channel blockers and by demonstration that the expression of the plant channel protein PIP1 in Xenopus oocytes increases boric acid uptake by 30%. This study examines whether B transport is a channel-mediated process in intact plants. In the presence of the channel inhibitors HgCl₂, phloretin, and DIDS, B uptake by squash plants was reduced by 40–90% by HgCl₂ (as HgCl₂ varied from 50 M to 1 mM), 44% by phloretin (250 M) and 58% by DIDS (250 M). The effect of Hg ions on B uptake was reversed by 2-mercaptoethanol. The addition of other non-electrolytes in size ranges similar to boric acid inhibited B uptake to various degrees. Addition of urea resulted in 54% decrease in B uptake, while, acetamide, formamide, thiourea and glycerol inhibited uptake by 50, 35, 53 and 44%, respectively. The effect of HgCl₂ on B uptake was greater at high B concentrations than at low B concentrations. These data and information from in-vivo studies suggest two possible mechanisms of B uptake: passive diffusion through lipid bilayers and channel-mediated transport.     

Diffusion through channel derivatives of the Escherichia coli FhuA transport protein.

FhuA is a multifunctional protein in the outer membrane of Escherichia coli that actively transports [Fe3+]ferrichrome, the antibiotics albomycin and rifamycin CGP 4832, and mediates sensitivity of cells to the unrelated phages T5, T1, phi80 and UC-1, and to colicin M and microcin J25. The energy source of active transport is the proton motive force of the cytoplasmic membrane that is required for all FhuA functions except for infection by phage T5. The FhuA crystal structure reveals 22 antiparallel transmembrane beta-strands that form a beta-barrel which is closed by a globular N-terminal domain. FhuA still displays active transport and sensitivity to all ligands except microcin J25 when the globular domain (residues 5-160) is excised and supports weakly unspecific diffusion of substrates across the outer membrane. Here it is shown that isolated FhuADelta5-160 supported diffusion of ions through artificial planar lipid bilayer membranes but did not form stable channels. The double mutant FhuADelta5-160 Delta322-336 lacking in addition to the globular domain most of the large surface loop 4 which partially constricts the channel entrance, displayed an increased single-channel conductance but formed no stable channels. It transported in vivo[Fe3+]ferrichrome with 45% of the rate of wild-type FhuA and did not increase sensitivity of cells to antibiotics. In contrast, a second FhuA double mutant derivative which in addition to the globular domain contained a deletion of residues 335-355 comprising one-third of surface loop 4 and half of the transmembrane beta-strand 8 formed stable channels in lipid bilayers with a large single-channel conductance of 2.5 nS in 1 m KCl. Cells that synthesized FhuADelta5-160 Delta335-355 showed an increased sensitivity to antibiotics and supported diffusion of maltodextrins, SDS and ferrichrome across the outer membrane. FhuADelta5-160 Delta335-355 showed no FhuA specific functions such as active transport of [Fe3+]ferrichrome or sensitivity to the other FhuA ligands. It is concluded that FhuADelta5-160 Delta335-355 assumes a conformation that is incompatible with any of the FhuA functions.     

Mechanism of sugar transport through the sugar-specific LamB channel ofEscherichia coli outer membrane

Summary Lipid bilayer experiments were performed with the sugar-specific LamB (maltoporin) channel ofEscherichia coli outer membrane. Single-channel analysis of the conductance steps caused by LamB showed that there was a linear relationship between the salt concentration in the aqueous phase and the channel conductance, indicating only small or no binding between the ions and the channel interior. The total or the partial blockage of the ion movement through the LamB channel was not dependent on the ion concentration in the aqueous phase. Both results allowed the investigation of the sugar binding in more detail, and the stability constants of the binding of a large variety of sugars to the binding site inside the channel were calculated from titration experiments of the membrane conductance with the sugars. The channel was highly cation selective, both in the presence and absence of sugars, which may be explained by the existence of carbonyl groups inside the channel. These carbonyl groups may also be involved in the sugar binding via hydrogen bonds. The kinetics of the sugar transport through the LamB channel were estimated relative to maltose by assuming a simple one-site, two-barrier model from the relative rates of permeation taken from M. Luckey and H. Nikaido (Proc. Natl. Acad. Sci. USA 77:165–171 (1980a)) and the stability constants for the sugar binding given in this study.     

Mechanism of ion transport through the anion-selective channel of the Pseudomonas aeruginosa outer membrane

Protein P trimers isolated and purified from Pseudomonas aeruginosa outer membrane were reconstituted in planar lipid bilayer membranes from diphytanoyl phosphatidylcholine. The protein trimers formed highly anion-specific channels with an average single channel conductance of 160 pS in 0.1 M Cl solution. A variety of different nonvalent anions were found to be permeable through the channel, which suggests a channel diameter between 0.5 and 0.7 nm. The selectivity for the halides followed the Eisenman sequence AVI (without At-). The ion transport through the protein P channel could be explained reasonably well by a one-site, two-barrier model. The stability constant of the binding of Cl- to the site was 20 M-1 at neutral pH. The binding of anions to the site was pH dependent, which suggested that several charges are involved in the closely spaced selectivity filter. Permeability ratios for different anions as calculated from bi-ionic potentials showed agreement with corresponding ratios of single channel conductances. The protein P channels were not voltage-gated and had lifetimes of the order of several minutes. The current-voltage curves were linear for membrane potentials up to 150 mV, which suggested that Nernst-Planck-type barriers rather than Eyring barriers were involved in the movement of anions through the protein P channel.     

Bromelain purification through unconventional aqueous two-phase system (PEG/ammonium sulphate)

This paper focuses on the feasibility of unconventional aqueous two-phase systems for bromelain purification from pineapple processing waste. The main difference in comparison with conventional systems is the integration of the liquid–liquid extraction technique with fractional precipitation, which can decrease the protein content with no loss of biological activity by removing of unwanted molecules. The analysis of the results was based on the response surface methodology and revealed that the use of the desirability optimisation methodology (DOM) was necessary to achieve higher purification factor values and greater bromelain recovery. The use of DOM yielded an 11.80-fold purification factor and 66.38 % biological activity recovery using poly(ethylene glycol) (PEG) with a molar mass of 4,000, 10.86 % PEG concentration (m/m) and 36.21 % saturation of ammonium sulphate.     

Characteristics of the methylammonium/ammonium transport systems of the nitrogen-fixing cyanobacterium Anabaena 7120 (ATCC 27893)

NH4(+)-transport in Anabaena 7120 was studied using the NH4+ analogue, 14CH3NH3+. At pH 7, two energy-dependent NH4(+)-transport systems were detected in both N2- and NO3(-)-grown cells, but none in NH4(+)-grown cells. Both transport systems showed a low and a high affinity mode of operation depending on the substrate concentration. One of the transport systems showed Km values of 8 microM (Vmax = 1 nmole min-1mg-1protein) and 80 microM (Vmax = 7 nmole min-1mg-1protein), and was insensitive to L-methionine-DL-sulphoximine, a glutamate analogue and irreversible inhibitor of glutamine synthetase. The other transport system showed Km values of 2.5 microM (Vmax = 0.1 nmole min-1mg-1protein) and 70 microM (Vmax = 0.7 nmole min-1mg-1protein), and was sensitive to L-methionine-DL-sulphoximine. Intracellular accumulation of free 14CH3NH3+ showed a biphasic pattern in response to variation in external 14CH3NH3+ concentrations. A maximum intracellular concentration of 2.5 mM and 7.5 mM was reached in the external 14CH3NH3+ concentration range of 1-50 microM and 1-500 microM, respectively. At pH 9, an energy-independent diffusion of 14CH3NH2 leading to a higher intracellular accumulation and assimilation rate, than that at pH 7, was observed.