Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles

Nisin is an example of type-A lantibiotics that contain cyclic lanthionine rings and unusual dehydrated amino acids. Among the numerous pore-forming antimicrobial peptides, type-A lantibiotics form an unique family of post-translationally modified peptides. Via the recognition of cell wall precursor lipid II, nisin has the capacity to form pores against Gram-positive bacteria with an extremely high activity in the nanomolar (nM) range. Here we report a high-resolution NMR spectroscopy study of nisin/lipid II interactions in SDS micelles as a model membrane system in order to elucidate the mechanism of molecular recognition at residue level. The binding to lipid II was studied through (15)N-(1)H HSQC titration, backbone amide proton temperature coefficient analysis, and heteronuclear (15)N[(1)H]-NOE relaxation dynamics experiments. Upon the addition of lipid II, significant changes were monitored in the N-terminal part of nisin. An extremely low amide proton temperature coefficient (Delta delta/Delta T) was found for the amide proton of Ala3 (> -0.1 ppb/K) in the complex form. This suggests tight hydrogen bonding and/or isolation from the bulk solvent for this residue. Large chemical shift perturbations were also observed in the first two rings. In contrast, the C-terminal part of nisin was almost unaffected. This part of the molecule remains flexible and solvent-exposed. On the basis of our results, a multistep pore-forming mechanism is proposed. The N-terminal part of nisin first binds to lipid II, and a subsequent structural rearrangement takes place. The C-terminal part of nisin is possibly responsible for the activation of the pore formation. In light of the emerging antibiotic resistance problems, an understanding of the specific recognition mechanism of nisin with lipid II at the residue specific level may therefore aid in the development of novel antibiotics.     

Strain-specific ureolytic microbial calcium carbonate precipitation

During a study of ureolytic microbial calcium carbonate (CaCO(3)) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large CaCO(3) crystal aggregates precipitated within bacterial colonies grown on agar. Based on these differences, 12 isolates were selected for further study. We hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differences in the functional attributes of the isolates selected. Sequencing of 16S rRNA genes showed that all of the isolates were phylogenetically closely related to the Bacillus sphaericus group. Urease gene diversity among the isolates was examined by using a novel application of PCR-denaturing gradient gel electrophoresis (DGGE). This approach revealed significant differences between the isolates. Moreover, for several isolates, multiple bands appeared on the DGGE gels, suggesting the apparent presence of different urease genes in these isolates. The substrate affinities (K(m)) and maximum hydrolysis rates (V(max)) of crude enzyme extracts differed considerably for the different strains. For certain isolates, the urease activity increased up to 10-fold in the presence of 30 mM calcium, and apparently this contributed to the characteristic crystal formation by these isolates. We show that strain-specific calcification occurred during ureolytic microbial carbonate precipitation. The specificity was mainly due to differences in urease expression and the response to calcium.     

Optimizing expression and purification from cell culture medium of trispecific recombinant antibody derivatives

Antibody fragments offer the possibility to build multifunctional manifolds tailored to meet a large variety of needs. We optimized the production of a manifold consisting of one (bibody) or two (tribody) single-chain variable fragments coupled to the C-terminus of Fab chains. Different strong mammalian promoters were compared and the influence of expression media on production and recovery was investigated. Since the physical and chemical nature of these molecules largely depends on the nature of the antibody building blocks incorporated, a generally applicable process for the purification of recombinant antibody derivatives from serum containing mammalian cell culture medium was designed. To this end we compared protein L, hydroxyapatite, immobilized metal affinity chromatography, cation-exchange chromatography and hydrophobic charge induction chromatography.     

Minor effect of depletion of resident macrophages from peritoneal cavity on resistance of common carp Cyprinus carpio to blood flagellates

Carp Cyprinus carpio macrophages were depleted by intraperitoneal (i.p.) injection of clodronate-liposomes for the in vivo study of the effect of macrophage depletion on the resistance of carp to infection with blood flagellate parasites. Clodronate released inside the cell induces apoptosis of (murine) macrophages. Following i.p. injection of carp with liposomes alone, but not with Trypanoplasma borreli, neutrophilic granulocytes rapidly migrated from the head kidney to the peritoneal cavity. The majority of liposomes in the peritoneal cavity were not taken up by newly arrived neutrophilic granulocytes, however, but by resident macrophages. After 2 i.p. injections of clodronate-liposomes, the percentage of macrophages present in the peritoneal cavity was significantly reduced, as evaluated by flow cytometry. Macrophage-depleted carp that were infected i.p. with T. borreli suffered from high mortality. However, these fish did not show lethal parasitaemia but did show clear bacteraemia. Macrophage-depleted carp that were infected i.p. with Trypanosoma carassii showed a minor increase in parasitaemia. In addition, macrophage-depleted carp, immune to T. borreli as a result of having survived a prior infection, remained immune to i.p. reinfection with T. borreli. Succesful depletion of peritoneal macrophages seemed to have a minor effect on the resistance of carp against blood flagellates. However, carp macrophages are essential as a first line of defence against (bacterial) infection.     

Herpes Simplex Virus Type 2 ICP47 Inhibits Human TAP but Not Mouse TAP

Herpes simplex virus serotype 1 (HSV-1) expresses an immediate-early protein, ICP47, that effectively blocks the major histocompatibility complex class I antigen presentation pathway. HSV-1 ICP47 (ICP47-1) binds with high affinity to the human transporter associated with antigen presentation (TAP) and blocks the binding of antigenic peptides. HSV type 2 (HSV-2) ICP47 (ICP47-2) has only 42% amino acid sequence identity with ICP47-1. Here, we compared the levels of inhibition of human and murine TAP, expressed in insect cell microsomes, by ICP47-1 and ICP47-2. Both proteins inhibited human TAP at similar concentrations, and the K_D for ICP47-2 binding to human TAP was 4.8 × 10⁻⁸ M, virtually identical to that measured for ICP47-1 (5.2 × 10⁻⁸ M). There was some inhibition of murine TAP by both ICP47-2 and ICP47-1, but this inhibition was incomplete and only at ICP47 concentrations 50 to 100 times that required to inhibit human TAP. Lack of inhibition of murine TAP by ICP47-1 and ICP47-2 could be explained by an inability of both proteins to bind to murine TAP.Previously, we showed that herpes simplex virus serotype 1 (HSV-1) ICP47 (ICP47-1) caused major histocompatibility complex (MHC) class I proteins to be retained in the endoplasmic reticulum (ER) of cells and that antigen presentation to CD8⁺ T cells was inhibited after ICP47-1 was expressed in human fibroblasts (9). ICP47-1 blocked peptide transport across the ER membrane by TAP (2, 6), so that, without peptides, class I proteins were retained in the ER. By contrast, ICP47 did not detectably inhibit MHC class I antigen presentation in mouse cells (9) and inhibited murine TAP poorly (2, 6). ICP47-1 inhibited peptide binding to TAP without affecting the binding of ATP (1, 7) and bound with high affinity, and in a stable fashion, to human TAP (7). Peptides could competitively inhibit ICP47 binding to TAP, consistent with the hypothesis that ICP47-1 binds to a site which includes the peptide binding domain of TAP (7). Others have suggested that the present data do not exclude a distortion in TAP caused by the binding of ICP47 at a site distant from the peptide binding site (3). This seems improbable given our observations that ICP47 inhibits peptide binding and that peptides competitively inhibit ICP47 binding. In order for peptides to inhibit ICP47 binding and vice versa, one would have to invoke allosteric inhibition by both ICP47 and peptides, a highly unlikely prospect.The predicted amino acid sequence of HSV type 2 ICP47 (ICP47-2) was recently described (3), and it was of some interest that ICP47-1 and ICP47-2 share only 42% amino acid identity (see Fig. ​Fig.1A).1A). Most of the homology is near the N termini and in the central regions of the molecules. A peptide including residues 2 to 35 of ICP47-1 blocked human TAP in permeabilized cells (3). This observation was somewhat surprising given that this peptide did not include residues 33 to 51, a sequence that is most homologous between ICP47-1 and ICP47-2. Presumably, this conserved domain, and even the C-terminal third of the protein, is important in virus-infected cells for stability or for functions that are not apparent in this in vitro assay involving detergent-permeabilized cells.Open in a separate windowFIG. 1Comparison of ICP47-1 and ICP47-2 protein sequences and preparation of purified proteins. (A) The predicted amino acid sequences of ICP47-1 derived from HSV-1 strain 17 (6a) and of ICP47-2 derived from HSV-2 strain HG52 (3) are shown. The boldface, underlined letters denote identical amino acids, and the italicized letters denote conserved residues. (B) ICP47-1 and ICP47-2 were produced in Escherichia coli by expressing the proteins as GST fusion proteins by fusing the ICP47 coding sequences to GST sequences in plasmid pGEX-2T as described previously (7). Lysates from bacteria were incubated with glutathione-Sepharose and washed several times, and then ICP47-1 or ICP47-2 was eluted by incubation with thrombin, which cleaves between the GST and ICP47 sequences (7). The thrombin was inactivated with phenylmethylsulfonyl fluoride, and the ICP47 preparations were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by Bradford protein analysis. The positions of GST-ICP47, GST, and ICP47 protein, as well as those of molecular weight markers 104, 80, 48, 34, 24, and 18 KDa in size, are indicated.Given the differences between the primary structures of ICP47-1 and ICP47-2, we were interested in whether ICP47-2 might inhibit the murine TAP. If this were the case, it would make possible animal studies of the effects of ICP47. Here, we have produced a recombinant form of ICP47-2 and compared the effects of ICP47-2 and ICP47-1 on human and murine TAP proteins expressed in insect cell microsomes. Like ICP47-1, ICP47-2 efficiently blocked human TAP but even at high concentrations did not effectively block murine TAP. Moreover, there was little or no significant binding of either protein to insect microsomes containing mouse TAP.The HSV-2 ICP47 gene was subcloned from plasmid pBB17, which contains a KpnI-HindIII 8,477-bp fragment derived from the genome of HSV-2 strain HG52 inserted into pUC19, by using PCR to amplify ICP47-2 coding sequences. One PCR primer hybridized with the 5′ end of the ICP47-2 coding sequences and extended 5′ to generate a new BglII site just upstream of the initiation codon. The second PCR primer hybridized with 3′ sequences of the ICP47-2 gene, then diverged to produce an EcoRI site just downstream of the translation termination codon. After PCR, the DNA fragment was digested with EcoRI and inserted into the HincII (blunt) and EcoRI sites of pUC19, producing plasmid pUC47-2, which was subjected to DNA sequencing. The ICP47-2 coding sequences were excised from pUC47-2 with BglII and EcoRI and inserted into the BamHI and EcoRI sites of pGEX-2T to generate a fusion protein with glutathione S-transferase (GST). The ICP47-GST fusion protein was expressed in bacteria and purified by using glutathione-Sepharose, and then the GST sequences were removed with thrombin as described previously for ICP47-1 (7). A comparison between the predicted amino acid sequences of ICP47-2 and ICP47-1 is shown in Fig. ​Fig.1,1, with a comparative gel (Fig. ​(Fig.1B)1B) showing the purified preparations of ICP47-1 and ICP47-2 from bacteria. Microsomes purified from Sf9 insect cells infected with baculoviruses expressing human TAP1 and TAP2 have been described previously (7, 8), as were microsomes from Drosophila cells expressing murine TAP1 and TAP2 (1). We previously estimated that approximately 2% of the protein associated with the insect microsomes was human TAP (7), and the microsomes containing mouse TAP possessed similar TAP activity (see below). Peptide translocation by these microsomes was measured by using a library of ¹²⁵I-labelled peptides (5) that are glycosylated after transport into the ER. Radioactive peptides able to bind to concanavalin A were quantified as an indirect measure of peptide transport (6). Over a range of membranes from 2.5 to 20 μl, with protein concentrations of 10 to 12 mg/ml for human TAP microsomes and 5.0 to 7.0 mg/ml for mouse TAP microsomes, there was a linear increase in peptide transport (Fig. ​(Fig.2).2). Thus, peptides and ATP were not limiting. Peptide transport was specific because the transport observed with control membranes not containing TAP amounted to less than 1% of that observed when microsomes contained TAP. The levels of peptide transport associated with microsomes containing human or mouse TAP were also compared and standardized. Thus, in subsequent assays, 7.5 to 10 μl of microsomes exhibiting similar amounts of TAP activity were used. Open in a separate windowFIG. 2Peptide transport by insect microsomes containing human or murine TAP. Microsomes were derived from insect Sf9 cells coinfected with BacTAP1 and BacTAP2 (Human TAP) (7) or from Sf9 cells infected with a control baculovirus, BacgH (Human control). Alternatively, microsomes were derived from Drosophila cells induced to express mouse TAP (Murine TAP) (1) or from Drosophila cells which were not induced to express mouse TAP (Murine control). Various concentrations of each microsome preparation were incubated with ¹²⁵I-labelled peptides and 5 mM ATP in a volume of 150 μl for 10 min at 23°C. The microsomes were washed, pelleted, and disrupted in detergent as described previously (7). Peptides able to bind to concanavalin A-Sepharose were eluted with alpha-methylmannoside and quantified (7).ICP47-2 inhibited peptide transport by human TAP, and the inhibition was similar to that of ICP47-1; the 50% inhibitory concentration (IC₅₀) for ICP47-2 was 0.24 μM and for ICP47-1 was 0.27 μM (Fig. ​(Fig.3A).3A). In other experiments the IC₅₀ values for ICP47-1 and ICP47-2 varied from 0.15 to 0.35 μM, and there were no experiments in which there was a significant difference in the abilities of the two proteins to inhibit human TAP. Moreover, the binding properties of ICP47-2 to human TAP were similar to those of ICP47-1. Binding experiments were performed as described previously for ICP47-1 (7) by using membranes containing human TAP and ¹²⁵I-labelled ICP47-2. Specific binding of ICP47-2 was calculated by subtracting the binding to control microsomes derived from insect cells infected with a baculovirus expressing HSV gH (7). The binding of ICP47-2 was saturable, so that at a protein concentration of 1 μM approximately 16 ng of protein bound to human TAP (Fig. ​(Fig.4A).4A). In previous experiments with a similar preparation of insect microsomes containing human TAP, the binding of ICP47-1 also saturated at 15 to 16 ng (7). The ICP47-2 binding data were analyzed in a standard Scatchard plot, and the K_D was calculated to be 4.8 × 10⁻⁸ M (Fig. ​(Fig.4B),4B), compared with 5.2 × 10⁻⁸ M for ICP47-1 (7). These values are greater than those of high-affinity peptides that bind to human TAP with affinities reaching 4 × 10⁻⁷ M, though the vast majority of peptides bind to TAP with much lower affinities (8). Open in a separate windowFIG. 3Inhibition of human and murine TAP-mediated peptide transport by ICP47-1 and ICP47-2. TAP assays were performed as described in the legend for Fig. ​Fig.22 by using insect microsomes containing human TAP (10 μl of membranes containing 12 mg of membrane protein per ml) (A) or murine TAP (7.5 μl of membranes containing 4.8 mg of membrane protein per ml but with equivalent levels of TAP activity compared with microsomes containing human TAP) (B) and various concentrations of ICP47-1 and ICP47-2. The results shown are combined from two separate experiments, each involving human and murine TAP.Open in a separate windowFIG. 4Binding of ICP47-2 to human TAP. (A) Microsomes (15 μl of membranes with a 7.5-mg/ml concentration of membrane protein) derived from Sf9 cells expressing TAP1 and TAP2 or expressing HSV-1 gH (control membranes not containing TAP) were incubated with various amounts of ¹²⁵I-labelled ICP47-2 for 60 min at 4°C as described previously (7). Binding to control membranes was subtracted from binding to microsomes containing TAP at each point. (B) Scatchard analysis of the data in panel A. The K_D for ICP47-2 binding to TAP was calculated to be 4.8 × 10⁻⁸ M.To determine whether ICP47-2 could inhibit the murine TAP, microsomes from insect cells expressing mouse TAP were incubated with various concentrations of ICP47-1 and ICP47-2 and TAP assays were performed. Inhibition of the mouse TAP was observed with both ICP47-1 and ICP47-2, but relatively high concentrations of both proteins were required (Fig. ​(Fig.3B).3B). The IC₅₀ values for ICP47-1 and ICP47-2 in this experiment were 10.8 and 16.2 μM, respectively. However, we were unable to reduce TAP activity beyond approximately 40% with ICP47-1 or ICP47-2 concentrations reaching 30 μM. This was 100 times the concentration required to inhibit human TAP by 50%. We attempted to measure the specific binding of radiolabelled ICP47-1 and ICP47-2 to microsomes containing mouse TAP in experiments similar to those shown in Fig. ​Fig.4.4. However, there was little specific binding of ICP47-1 and ICP47-2, and it was difficult to measure binding at lower protein concentrations. We therefore measured binding at a single, higher protein concentration (2.75 μM), one sufficient to inhibit 10 to 20% of the mouse TAP activity and all of the human TAP activity. In this experiment, specific binding to microsomes containing murine TAP was determined by subtracting the binding to microsomes from insect cells that were not induced to express murine TAP (1). The binding of ICP47-1 and ICP47-2 to human TAP was easily measured (Fig. ​(Fig.5),5), although under these conditions it is important to note that ICP47-1 and ICP47-2 were present at concentrations beyond those required to saturate the TAP (Fig. ​(Fig.4A).4A). By contrast, it was found that there was little or no significant binding of ICP47-1 or ICP47-2 to microsomes containing murine TAP when background binding to control membranes was subtracted. In the experiment shown, specific ICP47-2 binding was greater than zero, but in other experiments this binding was less than zero, and thus we concluded that there was no detectable binding overall. In every experiment, it was clear that the level of binding of ICP47-1 and ICP47-2 to murine TAP was at least 25-fold lower than to human TAP. However, the human TAP present in these microsomes was limiting in these experiments, and thus it is very likely that the 25-fold difference between the levels of binding to human and mouse TAP is an underestimate. More likely this difference is 50- to 100-fold. On the basis of the inhibitory concentrations required to block murine TAP and the binding studies described above, estimates of the binding affinities of ICP47-1 and ICP47-2 for murine TAP may fall in the range of 5 × 10⁻⁶ M. Therefore, ICP47-1 and ICP47-2 bind poorly to the murine TAP, and this largely accounts for their inability to block mouse TAP peptide transport. Open in a separate windowFIG. 5Binding of ICP47-1 and ICP47-2 to microsomes containing murine TAP. Microsomes containing human TAP or control membranes without human TAP (100 μg of membrane protein per 150-μl assay) or microsomes containing mouse TAP or control membranes without mouse TAP (50 μg of membrane protein with the same TAP activity as with the human microsomes) were incubated with ¹²⁵I-labelled ICP47-1 or ICP47-2 at 2.75 μM for 60 min at 4°C. The microsomes were washed twice, pelleted, and disrupted with detergents as described previously (7). Radioactivity associated with the microsomes was quantified by gamma counting. “ICP47 bound” refers to specific binding, calculated by subtracting the binding to control membranes (without TAP) from that observed with microsomes containing human or murine TAP.In summary, ICP47-2 and ICP47-1 could block human TAP and bound to TAP with similar high affinities. It was interesting that these two proteins, whose primary structures are only about 40% identical, inhibit human TAP with indistinguishable profiles and bind to human TAP with virtually identical affinities. Moreover, both proteins blocked murine TAP poorly and only at high protein concentrations and could not bind to murine TAP. These results, at face value, would suggest that mice will not be an appropriate model in which to test the effects of ICP47 on HSV replication or as a selective inhibitor of CD8⁺ T-cell responses in other systems. However, we recently found that an HSV-1 ICP47 mutant showed dramatically reduced neurovirulence in mice, without altering the course of disease in the cornea (4). Therefore, ICP47 may attain sufficient concentrations in certain cells in the nervous systems of mice to inhibit TAP. This may be related to the fact that TAP and class I proteins are expressed at low levels in the nervous system. Alternatively, ICP47 may have other functions in the nervous system.     

Evaluating options in LCA: The emergence of conflicting paradigms for impact assessment and evaluation

LCA aims to help direct decisions in an environmentally sustainable direction. It indicates the environmental effects of choices and evaluates these against this background. Approaches to evaluation in LCA differ substantially, related to the way of modelling environmental effects and to the way these effects are combined into an overall judgement on alternative options. Several approaches are now operational, which are linked to different paradigms in decision making. It is shown that the choice of paradigm is quite decisive on the outcome of the analysis. Also within similar paradigms, different methods now operational may lead to different outcomes. These latter differences may be alleviated more easily than those related to paradigmatic choices, as they are partly a matter of refinement, and they partly result from legitimate differences in subjective priorities. The more basic paradigmatic differences can hardly be bridged. The practical relevancy of the subject is proven by applying different operational methods to one case, showing widely differing outcomes. The paradigm behind evaluating environmental effects is either values based, directly or through policy decisions, or economics based, as individual preferences measured in the monetary terms of willingness-to-pay. Accordingly, the different methods are “policy-oriented” or “monetary”. It may be doubted if the differences between these can be overcome in standardisation.     

Immucillins ImmA and ImmH Are Effective and Non-toxic in the Treatment of Experimental Visceral Leishmaniasis

Background

Immucillins ImmA (IA), ImmH (IH) and SerMe-ImmH (SMIH) are synthetic deazapurine nucleoside analogues that inhibit Leishmania (L.) infantum chagasi and Leishmania (L.) amazonensis multiplication in vitro without macrophage toxicity. Immucillins are compared to the Glucantime standard drug in the chemotherapy of Leishmania (L.) infantum chagasi infection in mice and hamsters. These agents are tested for toxicity and immune system response.

Methodology/Principal Findings

BALB/c mice were infected with 10⁷ amastigotes, treated with IA, IH, SMIH or Glucantime (2.5mg/kg/day) and monitored for clinical variables, parasite load, antibody levels and splenocyte IFN-γ, TNF-α, and IL-10 expression. Cytokines and CD4+, CD8+ and CD19+ lymphocyte frequencies were assessed in uninfected controls and in response to immucillins. Urea, creatinine, GOT and GPT levels were monitored in sera. Anti-Leishmania-specific IgG1 antibodies (anti-NH36) increased in untreated animals. IgG2a response, high levels of IFN-γ, TNF-α and lower levels of IL-10 were detected in mice treated with the immucillins and Glucantime. Immucillins permitted normal weight gain, prevented hepato-splenomegaly and cleared the parasite infection (85–89%) without renal and hepatic toxicity. Immucillins promoted 35% lower secretion of IFN-γ in uninfected controls than in infected mice. IA and IH increased the CD4+ T and CD19+ B cell frequencies. SMIH increased only the proportion of CD-19 B cells. IA and IH also cured infected hamsters with lower toxicity than Glucantime.

Conclusions/Significance

Immucillins IA, IH and SMIH were effective in treating leishmaniasis in mice. In hamsters, IA and IH were also effective. The highest therapeutic efficacy was obtained with IA, possibly due to its induction of a TH1 immune response. Low immucillin doses were required and showed no toxicity. Our results disclose the potential use of IA and IH in the therapy of visceral leishmaniasis.     

Dried Blood Spots - Preparing and Processing for Use in Immunoassays and in Molecular Techniques

The idea of collecting blood on a paper card and subsequently using the dried blood spots (DBS) for diagnostic purposes originated a century ago. Since then, DBS testing for decades has remained predominantly focused on the diagnosis of infectious diseases especially in resource-limited settings or the systematic screening of newborns for inherited metabolic disorders and only recently have a variety of new and innovative DBS applications begun to emerge. For many years, pre-analytical variables were only inappropriately considered in the field of DBS testing and even today, with the exception of newborn screening, the entire pre-analytical phase, which comprises the preparation and processing of DBS for their final analysis has not been standardized. Given this background, a comprehensive step-by-step protocol, which covers al the essential phases, is proposed, i.e., collection of blood; preparation of blood spots; drying of blood spots; storage and transportation of DBS; elution of DBS, and finally analyses of DBS eluates. The effectiveness of this protocol was first evaluated with 1,762 coupled serum/DBS pairs for detecting markers of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus infections on an automated analytical platform. In a second step, the protocol was utilized during a pilot study, which was conducted on active drug users in the German cities of Berlin and Essen.