Tr-Noe and MD studies of Leishmania gp63 SRYD-containing sequences bound to anti-SRYD monoclonal antibody

Summary The I²⁵⁰ ASRYDQL²⁵⁷ synthetic octapeptide of theLeishmania major surface glycoprotein gp63, which efficiently inhibits parasite attachment to the macrophage receptors and mimics antigenically and functionally the RGDS sequence of fibronectin, was studied by 2D TR-NOESY in the presence of an anti-SRYD monoclonal antibody (mAbSRYD) that recognizes both SRYD-containing peptides and the cognate protein on intact parasites. Molecular modeling was performed using distance constraints obtained from TR-NOEs. The bound structure was compared with that of the free peptide in DMSO solution and with the crystal structure of the RYD fragment of the OPG2 Fab, an antireceptor antibody that mimics an RGD cell adhesion site.     

Crystal structure of the complex between the F(ab)' fragment of the cross-neutralizing anti-HIV-1 antibody 2F5 and the F(ab) fragment of its anti-idiotypic antibody 3H6

The monoclonal antibody 2F5 neutralizes a broad range of human immunodeficiency virus-1 isolates via a conserved epitope on the viral glycoprotein gp41. The conformation of the principal epitope is a type I β-turn centered on gp41 residues ⁶⁶⁴DKW⁶⁶⁶; in addition, binding studies indicate that residues N- and C-terminal to this core as well as structurally more distant parts of gp41 also contribute to the interaction. Ab2/3H6 is an anti-idiotypic antibody that inhibits the interaction between 2F5 and gp41 and as such, Ab2/3H6 may, in principle, possess a paratope that mimics the gp41 epitope. To establish the potential of Ab2/3H6 to serve as a guide for the design of vaccine components against human immunodeficiency virus, we investigated the crystal structure of the heterodimeric complex of Ab2/3H6 F_ab and 2F5 F_ab′. Ab2/3H6 F_ab binds to 2F5 F_ab′ via a helix-like protrusion formed by residues ^58(H)RYSPSLNTRL^67(H) of the 2F5 F_ab′ variable domain and proximal to but not overlapping with the gp41 ⁶⁶⁴DKW⁶⁶⁶ epitope-binding pocket. This defines Ab2/3H6 as an anti-idiotypic antibody of the Ab2γ class, i.e., an antigen-inhibitable idiotype that does not carry the internal image of the linear primary gp41 ⁶⁶²ELDKWAS⁶⁶⁸ epitope.     

Structural Mimicry of Receptor Interaction by Antagonistic Interleukin-6 (IL-6) Antibodies

Interleukin 6 plays a key role in mediating inflammatory reactions in autoimmune diseases and cancer, where it is also involved in metastasis and tissue invasion. Neutralizing antibodies against IL-6 and its receptor have been approved for therapeutic intervention or are in advanced stages of clinical development. Here we describe the crystal structures of the complexes of IL-6 with two Fabs derived from conventional camelid antibodies that antagonize the interaction between the cytokine and its receptor. The x-ray structures of these complexes provide insights into the mechanism of neutralization by the two antibodies and explain the very high potency of one of the antibodies. It effectively competes for binding to the cytokine with IL-6 receptor (IL-6R) by using side chains of two CDR residues filling the site I cavities of IL-6, thus mimicking the interactions of Phe²²⁹ and Phe²⁷⁹ of IL-6R. In the first antibody, a HCDR3 tryptophan binds similarly to hot spot residue Phe²⁷⁹. Mutation of this HCDR3 Trp residue into any other residue except Tyr or Phe significantly weakens binding of the antibody to IL-6, as was also observed for IL-6R mutants of Phe²⁷⁹. In the second antibody, the side chain of HCDR3 valine ties into site I like IL-6R Phe²⁷⁹, whereas a LCDR1 tyrosine side chain occupies a second cavity within site I and mimics the interactions of IL-6R Phe²²⁹.     

The Contribution of Crab Burrow Excavation to Carbon Availability in Surficial Salt-marsh Sediments

Geomorphology, vegetation and tidal fluxes are usually identified as the factors introducing variation in the flushing of particulate organic matter (POM) from tidal marshes to adjacent waters. Such variables may, however, be insufficient to explain export characteristics in marshes inhabited by ecosystem engineers that can alter the quantity and quality of POM on the marsh surface that is subject to tidal flushing. In this study we evaluated the balance between transfer of buried sedimentary organic carbon (C) to the marsh surface due to crab excavation (measured from the mounds of sediment excavated from burrows) and outputs of C from the surface due to sediment deposition within crab burrows (estimated from sediment deposited within PVC burrow mimics), in a Southwestern Atlantic salt marsh supporting dense (approximately 70 ind m⁻²) populations of the crab Chasmagnathus granulatus. C excavation by crabs was much greater than deposition of C within crab burrow mimics. Per area unit estimates of the balance between these two processes indicated that crabs excavated 5.98 g m⁻² d⁻¹ and 4.80 mg m⁻² d⁻¹ of total and readily (10 d) labile C, respectively. However, sediments excavated by crabs showed a significantly lower content of both total and readily-labile C than sediment collected in burrow mimics. This indicates that ecosystem engineering by burrowing crabs causes a net decrease in the concentration of C in the superficial sediment layers and, thus, an overall decrease in the amount of C that can be washed out of the marsh by tidal action. Incorporating the in situ activities of ecosystem engineers in models of marsh export should enhance understanding of the function of marshes in estuarine ecosystems.     

Fluorescent fusion proteins derived from the tenth human fibronectin domain

Hybrid molecules of a new type bearing a red fluorescent protein mCherry and one of the alternative scaffold proteins, the 10th human fibronectin type III domain (¹⁰Fn3), which can be used for the construction of antibody mimics with various binding specificity, were obtained. Different variants of the gene encoding the hybrid fluorescent protein were constructed and their expression in Escherichia coli cells was studied. The mCherry N-terminal position and the modification of its N-terminal amino acid sequence proposed were shown to promote the efficient bacterial expression of the hybrid protein in the soluble form. On the basis of the proposed construct a hybrid fluorescent protein ChIBF containing an α_Vβ₃-integrin binding variant of ¹⁰Fn3 was obtained, and its use for the visualization of α_Vβ₃-integrin at the surface of MDCK epithelial cells was demonstrated by confocal microscopy.     

Effects of affinity-purified antibodies on the Ca2+ pumping ATPase of erythrocyte membranes

Antibodies raised in rabbits against the purified erythrocyte membrane Ca²⁺ pumping ATPase were affinity-purified using an ATPase-Sepharose column. Addition of a few molecules of the purified antibody per molecule of ATPase was sufficient to inhibit the ATPase activity. Extensively washed ghosts or preincubated pure ATPase sometimes develop an appreciable Mg²⁺-ATPase activity. In such cases, the antibodies inhibited the Mg²⁺-ATPase as well as the Ca²⁺-ATPase. This is consistent with the hypothesis that a portion of the Mg²⁺-ATPase activity of ghosts is derived from the Ca²⁺-ATPase. When nitrophenylphosphatase activity was observed, both Mg²⁺ - and Ca²⁺-stimulated activities were observed. Only the Ca²⁺ activity was inhibited by the antibodies, confirming that this activity is due to the Ca²⁺ pump, and suggesting that the Mg²⁺-nitrophenylphosphatase is due to a separate enzyme. Amounts of antibody comparable to those which inhibited the Ca²⁺-ATPases had no effect on the Na⁺-K⁺-ATPase; 4-fold higher amounts of antibody significantly stimulated the Na⁺-K⁺-ATPase, but this effect of the antibody was not specific: Immunoglobulins from the nonimmune serum also significantly stimulated the Na⁺-K⁺-ATPase.In resealed erythrocyte membranes, antibodies incorporated into the ghosts inactivated the Ca²⁺-ATPase, while antibodies added to the outside had no significant effect.     

Nitroxide Sod-Mimics: Modes of Action

Low molecular weight superoxide dismutase mimics have been shown to afford protection from oxidative damage. Such SOD-mimics can readily permeate cell membrane achieving sufficiently high levels both inside and outside the cell to effectively detoxify intracellular O^?₂. Preliminary findings also indicated that metal-based and metal-free SOD-mimics can protect hypoxic cells from H₂O₂-induced damage. The present study explored the possibility that SOD-mimics such as desferrioxamine-Mn(III) chelate [DF-Mn] or cyclic nitroxide stable free radicals could protect from O^?₂-independent damage. Killing of monolayered V79 Chinese hamster cells was induced by H₂O₂ or by t-butyl hydroperoxide (t-BHP) and assayed clonogenically. Neither catalase nor native SOD protected the cells from t-BHP. In contrast. both DF-Mn and cyclic nitroxides protected suggesting cytotoxic processes independent of O^?₂ or of O^?₂ -derived active species. The inhibition of the damage by both metal-free and metal-based SOD mimics is attributable to either SOD-mimic reacting with reduced transition metal to block the Fenton reaction and/or intercepting and detoxifying intracellular organic free radicals.     

SOD mimics: From the tool box of the chemists to cellular studies

Superoxide dismutases (SODs) are metalloproteins that protect cells against oxidative stress by controlling the concentration of superoxide (O₂⁻) through catalysis of its dismutation. The activity of superoxide dismutases can be mimicked by low-molecular-weight complexes having potential therapeutic applications. This review presents recent strategies for designing efficient SOD mimics, from molecular metal complexes to nanomaterials. Studies of these systems in cells reveal that some SOD mimics, designed to react directly with superoxide, may also indirectly enhance the cellular antioxidant arsenal. Finally, a good understanding of the bioactivity requires information on the cell-penetration, speciation, and subcellular location of the SOD mimics: we will describe recent studies and new techniques that open opportunities for characterizing SOD mimics in biological environments.     

Structural basis of p21H-ras molecular switch inhibition by a neutralizing antibody

The ras oncogene product p21 functions as a molecular switch in the early section of the signal transduction pathway that is involved in cell growth and differentiation. When the protein is in its GTP-complexed form it is active in signal transduction, whereas it is inactive in its GDP-complexed form. The transforming activity of p21^ras is neutralized by the mouse monoclonal antibody Y13-259, possibly by preventing GDP-GTP exchange. A molecular model of the variable fragment of Y13-259 has been derived using a knowledge-based prediction approach and computer-assisted modeling techniques. An analysis of this model while complexed with p21^ras/(GDP) indicated that the two molecular switch regions are constrained by complex formation. Antibody binding inhibits GDP-GTP exchange through a mechanism of steric hindrance. Having identified necessary bound sites for inhibition, and explored their electrostatic properties, it should be possible to proceed with the design of antibody mimics as therapeutic agents in cancer control.     

Altered expression and editing of miRNA-100 regulates iTreg differentiation

RNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4⁺ T cell differentiation. CD4⁺ T cells are an integral component of the adaptive immune system. Naïve CD4⁺ T cells, on encountering an antigen, get differentiated either into inflammatory subtypes like Th1, Th2 or Th17, or into immunosuppressive subtype Treg, depending on the cytokine milieu. We found C-to-U editing at fifth position of mature miR-100, specifically in Treg. The C-to-U editing of miR-100 is functionally associated with at least one biologically relevant target change, from MTOR to SMAD2. Treg cell polarization by TGFβ1 was reduced by both edited and unedited miR-100 mimics, but percentage of Treg in PBMCs was only reduced by edited miR-100 mimics, suggesting a model in which de-repression of MTOR due to loss of unedited mir-100, promotes tolerogenic signaling, while gain of edited miR-100 represses SMAD2, thereby limiting the Treg. Such delicately counterbalanced systems are a hallmark of immune plasticity and we propose that miR-100 editing is a novel mechanism toward this end.     

Structural complexity and juvenile fish predation on meiobenthos: an experimental approach

The impact of juvenile spot (Leiostomus xanthurus Lacépède) predation/disturbance on meiofauna and the effectiveness of simulated worm tubes as refuges from predators were assessed in a series of laboratory experiments with intact natural estuarine sediments and three densities of worm tube mimics (0, 1.6, and 6.3 tubes/0.01 m²). There was no statistically significant predation on any meiofaunal taxa in the habitat containing no tube mimics. However, mortality was significant for three of six taxa in the “low complexity” habitat (1.6 tubes/0.01 m²) and three of six taxa in the “high complexity” habitat (6.3 tubes/0.01 m²) when fish were present. The evidence for predation in more complex habitats suggests structure promotes mortality for certain meiofaunal taxa. Such effects could result from

• 1.(1) the interaction of predators and/or prey with the refuge element such that certain prey became more vulnerable
• 2.(2) the ability of certain predators to forage more efficiently amidst structure.

     

The “erythromycin-resistance” methylated sequence of Staphylococcus aureus ribosomal RNA

We have determined the sequence of an oligonucleotide from the large ribosomal subunit RNA of Staphylococcus aureus whose methylation renders the organism resistant to erythromycin and other antibiotics (the “MLS” phenotype). Analysis of RNase A digests of [³H]methyl-, ³²P-labeled RNA yielded the sequence GG · m₂⁶A · AAGACp, where m₂⁶A is an N⁶-dimethylated adenosine residue that in sensitive cells is unmethylated. Comparison with homologous sequences recently reported for Saccharomyces cerevesiae mitochondria indicates that an A to G mutation in this latter system mimics dimethylation in St. aureus with regard to functional consequences.     

Adolescence as a vulnerable period to alter rodent behavior

Induction of HIF-1α by oxygen limitation promotes increased phosphorylation and catalytic depression of mitochondrial pyruvate dehydrogenase (PDH) and an enhanced glycolytic poise in cells. Cobalt chloride and desferrioxamine are widely used as mimics for hypoxia because they increase the levels of HIF-1α. We evaluated the ability of these agents to elicit selected physiological responses to hypoxia as a means to metabolically precondition mammalian cells, but without the detrimental effects of hypoxia. We show that, while CoCl₂ does increase HIF-1α in a dose-dependent manner, it unexpectedly and strikingly decreases PDH phosphorylation at E1α sites 1, 2, and 3 (Ser²⁹³, Ser³⁰⁰, and Ser²³², respectively) in HepG2 cells. This same effect is also observed for site 1 in mouse NIH/3T3 fibroblasts and J774 macrophages. CoCl₂ unexpectedly decreases the mRNA expression for PDH kinase-2 in HepG2 cells, which likely explains the dephosphorylation of PDH observed. And nor does desferrioxamine promote the expected increase in PDH phosphorylation. Dimethyloxaloylglycine (a prolyl hydroxylase inhibitor) performs better in this regard, but failed to promote the stronger effects seen with hypoxia. Consequently, CoCl₂ and desferrioxamine are unreliable mimics of hypoxia for physiological events downstream of HIF-1α stabilization. Our study demonstrates that mimetic chemicals must be chosen with caution and evaluated thoroughly if bona fide cellular outcomes are to be promoted with fidelity.     

Regulation of the in vitro secondary antibody response: I. Suppression by relatively high,but physiological levels of calcium ion

Secondary antibody responses generated in vitro with spleen cells from mice primed and boosted with SRBC or TNP-KLH antigen were found to be influenced by the amount of Ca²⁺ in the culture medium. Relatively low levels of Ca²⁺ (0.1 mM) were optimally supportive for the generation of PFC in vitro, with higher, more physiological levels of Ca²⁺ (1.0–1.7 mM) suppressing the generation of PFC by as much as 100%. Suppression by high levels of Ca²⁺ was most pronounced when the amount of antigen used to elicit the in vitro antibody response was high, whereas responses generated by lesser amounts of antigen were minimally affected by Ca²⁺ level. Ca²⁺-mediated suppression was localized to an intermediate phase (24–48 hr) of the response. Mitogenic and polyclonal antibody responses were not affected by high levels of Ca²⁺. The effect of Ca²⁺ concentration on the secondary, IgG-producing antibody response may be significant in terms of understanding the various control mechanisms interacting in regulation of IgG synthesis.     

Factors in the Fermentation-Inhibition Test for Measurement of Growth-Inhibiting Antibody to Mycoplasma pneumoniae

Factors in the fermentation-inhibition test for the measurement of growth-inhibiting antibody in serum to Mycoplasma pneumoniae were studied. The fermentation-inhibiting antibody titer, as read on the day when the color of the control cup without serum had just changed to yellow, was constant among inoculum dilutions of 10^–2 to 10^–5 (10⁶ to 10³ CFU/ml) of a M. pneumoniae broth culture. The use of 10^–3 to 10^–5 dilutions (10⁵ to 10³ CFU/ml) was adequate for inoculation, inasmuch as one day delay in reading did not result in a significant decrease in the test. Heat inactivation of the serum gave no significant effect on the titer. The test was simple and reliable. The growth-inhibiting antibody was shown to be detectable in the test, when the growth of M. pneumoniae was suppressed at least to 1/100 of the growth of the control without serum. The growth-inhibiting antibody titer rose later than the complement-fixing antibody titer in some cases after M. pneumoniae infection. It is suggested that, when an erythromycin-sensitive strain of M. pneumoniae is used, the titer transiently rises and does not show a real growth-inhibiting antibody titer in sera from patients under erythromycin administration.     

Methionine Aminopeptidase II: A Molecular Chaperone for Sarcoplasmic Reticulum Calcium ATPase

The monoclonal antibody to the β-subunit of H⁺/K⁺-ATPase (mAbHKβ) cross-reacts with a protein that acts as a molecular chaperone for the structural maturation of sarcoplasmic reticulum (SR) Ca²⁺-ATPase. We partially purified a mAbHKβ-reactive 65-kDa protein from Xenopus ovary. After in-gel digestion and peptide sequencing, the 65-kDa protein was identified as methionine aminopeptidase II (MetAP2). The effects of MetAP2 on SR Ca²⁺-ATPase expression were examined by injecting the cRNA for MetAP2 into Xenopus oocytes. Immunoprecipitation and pulse-chase experiments showed that MetAP2 was transiently associated with the nascent SR Ca²⁺-ATPase. Synthesis of functional SR Ca²⁺-ATPase was facilitated by MetAP2 and prevented by injecting an antibody specific for MetAP2. These results suggest that MetAP2 acts as a molecular chaperone for SR Ca²⁺-ATPase synthesis.     

Inhibition of a conjugation-like gene transfer process in Bacillus thuringiensis subsp. israelensis by the anti-s-layer protein antibody

Extraction of the S-layer protein by treatment with 6 m urea revealed a high-molecularweight protein in the extracts obtained from Bacillus thuringiensis subsp. israelensis (B.t.i) strain 4Q2. This protein band was found to be absent in partially cured (4Q2-72) and completely cured (c4Q2-72) strains. The antibody toward this S-layer protein was prepared and used to locate its antigenic protein on B.t.i cells by using indirect immunofluorescence. Immunodiffusion reactions and Western blot analysis confirmed the specificity of the anti-S-layer protein antibody. It was found that the antibody against 4Q2 S-layer protein, inhibited plasmid transfer via a conjugationlike process between, B.t.i. strains 4Q2-16 and c4Q2-72. That is, the frequency of transfer of plasmid pBC16 was reduced from 9.7×10^-6 in the absence of the antibody to less than 1.0×10^-8 in the presence of the antibody. The antibody was also found to reduce the frequency of pBC16 plasmid transfer via a conjugation-like process between B.t.i. strains A084-16-194 and c4Q2-72 from 2.2×10^-5 in the absence of the antibody to 1.2×10^-6 in the presence of the antibody.     

Regulation of natural killer cell activity by anti-I-region monoclonal antibodies

The effects of a monoclonal antibody directed against immune response gene products on mouse NK activity were examined. In vivo administration of an anti-I-A^k antibody to C3H/He (H-2^k) mice modulated their peritoneal cell (PC) and spleen cell (SC) natural killer (NK) activity against YAC-1 lymphoma target cells in vitro. No such effect was observed when BALB/c (H-2^d) mice were treated with this antibody. Administration of anti-I-A^k antibody to mice before and after infection with Toxoplasma or treatment with poly(I:C) leads to suppression of NK activity in comparison to NK activity of mice infected with Toxoplasma or injected with poly(I:C) alone. A similar treatment regimen with M5/114 antibody which reacts with I-A^b, I-A^d, I-E^d, and I-E^k molecules resulted in decreased NK activity in B10.D2 (H-2^d) but not in B10.BR (H-2^k) mice. Serum and cell culture supernatant interferon (IFN) concentrations were not altered as a result of anti-I-A^k treatment. Removal of adherent cells did not restore NK activity of anti-I-A^k-treated Toxoplasma-infected mice to levels obtained with mice infected with Toxoplasma. In contrast, depletion of Ly 2.1⁺ cells from nylon-wool nonadherent SC of mice treated with anti-I-A^k antibody, before and after infection with Toxoplasma, resulted in restoration of NK activity to the same level as that observed in Toxoptasma-infected mice.     

miR-34a在幼鼠海马神经元细胞增殖和凋亡中的作用

目的:探讨miR-34a在幼鼠海马神经元细胞增殖凋亡中的作用。方法:分离幼鼠海马神经元细胞,转染miR-34a抑制剂(miR-34a inhibitor)、抑制剂对照(inhibitor control)、miR-34a模拟物(miR-34a mimics)、模拟物对照(mimics control),RT-PCR检测细胞中miR-34a表达水平。MTT检测转染后细胞增殖情况。流式细胞仪检测细胞凋亡情况。Western blot检测细胞中Cleaved-caspase-3、Bcl-2、Bax的表达水平。结果:转染miR-34a inhibitor可以抑制miR-34a的表达,miR-34a mimics可以促进miR-34a的表达。miR-34a mimics对细胞增殖抑制率明显高于mimics control组(P0.05),miR-34a inhibitor组抑制率明显低于inhibitor control组(P0.05)。miR-34a inhibitor组神经元细胞凋亡率明显低于inhibitor control组(P0.05),miR-34a mimics组神经元细胞凋亡率明显高于mimics control组(P0.01),inhibitor control组和mimics control组神经元细胞凋亡率差异不显著(P0.05)。miR-34a inhibitor组Cleaved-caspase-3、Bax蛋白表达量低于inhibitor control组,差异显著(P0.05);miR-34a inhibitor组Bcl-2蛋白表达量高于inhibitor control组,差异显著(P0.05);miR-34a mimics组Cleaved-caspase-3、Bax蛋白表达量高于mimics control,差异显著(P0.05);miR-34a mimics组Bcl-2蛋白表达量低于mimics control,差异显著(P0.05)。结论:miR-34a抑制海马神经元细胞增殖,促进细胞凋亡,其作用机制可能与调控Cleaved-caspase-3、Bcl-2、Bax表达有关。     

Synthesis of aminoacylated N6,N6-dimethyladenosine solid support for efficient access to hydrolysis-resistant 3′-charged tRNA mimics

RNA-amino acid and RNA-peptide conjugates that mimic charged tRNA 3′-ends are valuable substrates for structural and functional investigations of ribosomal complexes. To obtain such conjugates, most synthetic approaches that are found in the literature make use of puromycin. This well available aminonucleoside antibiotic contains a dimethylamino group at the nucleobase and a methylated tyrosine that is connected via an amide linkage to the ribose moiety. To increase structural diversity, we present the synthesis of a N⁶,N⁶-dimethylated 3′-azido-3′-deoxyadenosine precursor that can be coupled to any amino acid. Further derivatization results in the solid support that is eligible for the preparation of stable 3′-aminoacyl- or 3′-peptidyl-tRNA termini with an amide instead of the natural ester linkage. The present work expands our previously established route that delivered a broad range of peptidyl-tRNA mimics to the corresponding counterparts with N⁶,N⁶-dimethylation pattern of the terminal adenosine (A76). This aspect is of significance to modulate the binding preferences of the mimics for ribosomal A- versus P-site.