Isolation of Hippocampal Synaptosomes on Percoll Gradients: Cholinergic Markers and Ligand Binding Sites

The S1 Percoll procedure, devised empirically for cortical tissue, provides highly purified, functionally viable synaptosomes on a four-step Percoll gradient. Here, for the first time, the procedure has been applied to rat hippocampus, and the gradient fractions have been analysed with respect to cholinergic markers and the synaptosomal index, lactate dehydrogenase. The presynaptic cholinergic markers choline acetyltransferase and [3H]choline uptake were most enriched in fraction 4. In contrast, acetylcholinesterase activity was broadly distributed across the gradient, consistent with the separation of synaptic plasma membranes (in fractions 1 and 2) from synaptosomes (in fractions 3 and 4). This is supported by the recovery of muscarinic binding sites labelled with [3H]quinuclidinylbenzilate in fractions 1 and 2. (-)-[3H]-Nicotine binding sites, however, were most enriched in fraction 4, consistent with their predominantly presynaptic localisation in the CNS. These results demonstrate the applicability of the S1 Percoll method to discrete brain regions for the recovery of homogeneous and viable synaptosome fractions. The separation of presynaptic terminals from post-synaptic membranes is a further advantage of this technique.     

Protease Cleavage Sites in HIV-1 gp120 Recognized by Antigen Processing Enzymes Are Conserved and Located at Receptor Binding Sites

The identification of vaccine immunogens able to elicit broadly neutralizing antibodies (bNAbs) is a major goal in HIV vaccine research. Although it has been possible to produce recombinant envelope glycoproteins able to adsorb bNAbs from HIV-positive sera, immunization with these proteins has failed to elicit antibody responses effective against clinical isolates of HIV-1. Thus, the epitopes recognized by bNAbs are present on recombinant proteins, but they are not immunogenic. These results led us to consider the possibility that changes in the pattern of antigen processing might alter the immune response to the envelope glycoprotein to better elicit protective immunity. In these studies, we have defined protease cleavage sites on HIV gp120 recognized by three major human proteases (cathepsins L, S, and D) important for antigen processing and presentation. Remarkably, six of the eight sites identified in gp120 were highly conserved and clustered in regions of the molecule associated with receptor binding and/or the binding of neutralizing antibodies. These results suggested that HIV may have evolved to take advantage of major histocompatibility complex (MHC) class II antigen processing enzymes in order to evade or direct the antiviral immune response.A major goal of HIV vaccine development is the development of immunogens that elicit protective antiviral antibody and cellular immune responses. However, after more than 25 years of research, vaccine immunogens able to elicit protective immunity in humans have yet to be described (11, 31). Although it has been possible to produce recombinant envelope proteins (gp120 and gp140) with many of the features of native virus proteins (e.g., complex glycosylation and the ability to bind CD4, chemokine receptors, and neutralizing antibodies), these antigens have not been able to elicit broadly neutralizing antibodies (bNAbs) or protective immune responses when used as immunogens (11, 32, 43, 50, 56, 74, 79). The fact that recombinant proteins can adsorb virus bNAbs from HIV-1-positive sera (59, 91) indicates that many recombinant envelope proteins are correctly folded but that the epitopes recognized by bNAbs are simply not immunogenic. Over the last decade, several different approaches have been employed to create immunogens able to elicit broadly neutralizing antibodies. These strategies have included efforts to duplicate and/or stabilize the oligomeric structure of HIV envelope proteins (5, 26, 87), the creation of minimal antigenic structures lacking epitopes that conceal important neutralizing sites (27, 46, 70, 89), and prime/boost strategies combining protein immunization with DNA immunization or infection with recombinant viruses in order to stimulate the endogenous synthesis and presentation of HIV immunogens (15, 29, 30, 83). However, none of these approaches has resulted in a clinically significant improvement in antiviral immunity or HIV vaccine efficacy. Efforts to elicit protective cellular immune responses (e.g., cytotoxic lymphocytes) by use of recombinant virus vaccines have likewise been disappointing (10, 61). In fact, such vaccines may have promoted HIV infection rather than inhibiting it (22, 23).In the present study, we describe the first steps in a new approach to reengineering the immunogenicity of HIV envelope proteins in order to improve the potency and specificity of humoral and cellular immune responses. The approach is based on defining the determinants of antigen processing and presentation of HIV envelope glycoproteins. Both humoral and cellular immune responses depend on proteolytic degradation of protein antigens prior to antigen presentation, mediated by professional antigen-presenting cells (APCs) such as macrophages, dendritic cells, and B cells (97). Normally, proteins of intracellular origin are processed by the proteasome, a 14- to 17-subunit protein complex located in the cytosol. Proteins of extracellular origin are processed in lysosomes or late endosomes of APCs. The resulting peptide epitopes are then loaded into major histocompatibility complex (MHC) class I or class II molecules and presented on the surfaces of APCs to CD8 or CD4 T cells. Within the endosomes and lysosomes of APCs, there are cathepsins, acid thiol reductase, and aspartyl endopeptidase. The enzymes perform two activities: degrading endocytosed protein antigens to liberate peptides for MHC class II binding (99) and removing the invariant chain chaperone (6, 94). Although all cathepsins can liberate epitopes from a diverse range of antigens (16), only cathepsins S and L have nonredundant roles in antigen processing in vivo (reviewed by Hsing and Rudensky [45]). Cathepsin L is expressed in thymic cortical epithelial cells but not in B cells or dendritic cells, while cathepsin S is found in all three types of APCs. Unlike cathepsins L and S, which are cysteine proteases and active at neutral pH, cathepsin D is an aspartic protease, is active at acidic pH, and participates in proteolysis and antigen presentation in connection with MHC class I and class II antigen presentation pathways established for CD4 and CD8 T cells. In considering the use of envelope proteins as potential vaccines, the route of immunization, formulation (e.g., adjuvants), protein folding, disulfide bonding, and glycosylation pattern all determine which peptides are available for MHC-restricted presentation.Previous studies provided evidence that gp120 was sensitive to digestion by cathepsins B, D, and L, but the specific cleavage sites were not defined (18). In the present study, we (i) describe the locations of eight protease cleavage sites on HIV-1 gp120 recognized by cathepsins L, S, and D, involved in antigen processing; (ii) determine the extent to which they are conserved; and (iii) evaluate the effect of cathepsin cleavage on the binding of gp120 to CD4-IgG and neutralizing antibodies. The results obtained provide new insights into the basis of envelope immunogenicity that may prove to be useful in the development of HIV vaccine antigens.     

Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases

Nt-acetylation is among the most common protein modifications in eukaryotes. Although thought for a long time to protect proteins from degradation, the role of Nt-acetylation is still debated. It is catalyzed by enzymes called N-terminal acetyltransferases (NATs). In eukaryotes, several NATs, composed of at least one catalytic domain, target different substrates based on their N-terminal sequences. In order to better understand the substrate specificity of human NATs, we investigated in silico the enzyme-substrate interactions in four catalytic subunits of human NATs (Naa10p, Naa20p, Naa30p and Naa50p). To date hNaa50p is the only human subunit for which X-ray structures are available. We used the structure of the ternary hNaa50p/AcCoA/MLG complex and a structural model of hNaa10p as a starting point for multiple molecular dynamics simulations of hNaa50p/AcCoA/substrate (substrate = MLG, EEE, MKG), hNaa10p/AcCoA/substrate (substrate = MLG, EEE). Nine alanine point-mutants of the hNaa50p/AcCoA/MLG complex were also simulated. Homology models of hNaa20p and hNaa30p were built and compared to hNaa50p and hNaa10p. The simulations of hNaa50p/AcCoA/MLG reproduce the interactions revealed by the X-ray data. We observed strong hydrogen bonds between MLG and tyrosines 31, 138 and 139. Yet the tyrosines interacting with the substrate’s backbone suggest that their role in specificity is limited. This is confirmed by the simulations of hNaa50p/AcCoA/EEE and hNaa10p/AcCoA/MLG, where these hydrogen bonds are still observed. Moreover these tyrosines are all conserved in hNaa20p and hNaa30p. Other amino acids tune the specificity of the S1’ sites that is different for hNaa10p (acidic), hNaa20p (hydrophobic/basic), hNaa30p (basic) and hNaa50p (hydrophobic). We also observe dynamic correlation between the ligand binding site and helix that tightens under substrate binding. Finally, by comparing the four structures we propose maps of the peptide-enzyme interactions that should help rationalizing substrate-specificity and lay the ground for inhibitor design.     

In Situ Hydration of Enzymes in Non-Polar Organic Media Can Increase the Catalytic Rate

The nature of the buffer species used in the drying process is important when lyophilized enzyme preparations are suspended in organic media. The activity of subtilisin Carlsberg in a transesterification reaction was found to vary depending on the nature of the buffer used. It was postulated that the large excess of salt present in the dried powder could be affecting enzymatic activity by alterations to the microscopic structure of the powder. To establish if this were true, microscopic changes were eliminated by covalently immobilising the enzyme onto a macroporous polymer support so that the counter-ions could be exchanged by washing with dilute salt solutions. It was found that in the immobilised samples no significant effects of salt ions were noted. This was the case even when salt ions were in considerable excess of that needed to balance protein charges. Hence the activity variations noted in freeze-dried powders are probably due to changes to the microscopic structure, rather than to molecular scale interactions. Similarly the previously observed activating effect of crown ether solutions on freeze-dried powders is not repeated on an immobilised preparation suggesting that this too may be due to a microscopic effect on the powder.     

Tachykinins Induce Secretion of Prolactin from Perifused Rat Anterior Pituitary Cells by Interactions with Two Different Binding Sites

Abstract

Substance P and the two other mammalian tachykinins, neurokinin A and B, are accepted to have direct regulating effects at the anterior pituitary level. We have examined the effects of substance P (SP) and neurokinin B (NKB), alone and in combination, on prolactin release from cultured anterior pituitary cells grown on collagen-coated micro beads and placed in a perfusion system. Prolactin (Prl) secretion was observed within 25 s after exposure to either secretagogue and reached a maximum within 60-80 s. Furthermore, the prolactin response induced by SP and NKB was dose-dependent. Prl secretion remained constant for up to 4 h when SP or NKB were perifused and then fell gradually towards basal levels. Simultaneous addition of submaximal concentrations of SP and NKB resulted in an additive response compared with the responses of either secretagogue alone. Continuous (8 h) perifusion with SP did not prevent a normal prolactin response by NKB or TRH. These results indicate that the tachykinins, substance P and neurokinin B, release Prl from perifused female rat anterior pituitary cells by interaction with two different receptors, possibly the NK1 and NK3 tachykinin receptor subtypes.     

Changes in the Catalytic Properties of Pyrococcus furiosus Thermostable Amylase by Mutagenesis of the Substrate Binding Sites

Pyrococcus furiosus thermostable amylase (TA) is a cyclodextrin (CD)-degrading enzyme with a high preference for CDs over maltooligosaccharides. In this study, we investigated the roles of four residues (His414, Gly415, Met439, and Asp440) in the function of P. furiosus TA by using site-directed mutagenesis and kinetic analysis. A variant form of P. furiosus TA containing two mutations (H414N and G415E) exhibited strongly enhanced α-(1,4)-transglycosylation activity, resulting in the production of a series of maltooligosaccharides that were longer than the initial substrates. In contrast, the variant enzymes with single mutations (H414N or G415E) showed a substrate preference similar to that of the wild-type enzyme. Other mutations (M439W and D440H) reversed the substrate preference of P. furiosus TA from CDs to maltooligosaccharides. Relative substrate preferences for maltoheptaose over β-CD, calculated by comparing k_cat/K_m ratios, of 1, 8, and 26 for wild-type P. furiosus TA, P. furiosus TA with D440H, and P. furiosus TA with M439W and D440H, respectively, were found. Our results suggest that His414, Gly415, Met439, and Asp440 play important roles in substrate recognition and transglycosylation. Therefore, this study provides information useful in engineering glycoside hydrolase family 13 enzymes.     

Opiate Binding Sites in Bovine Adrenal Medulla

Abstract

Previous studies using a variety of opiate ligands have suggested the existence of several subclasses of opiate receptors in crude membrane fractions of rat brain, and a similar diversity in bovine adrenal medulla. To examine the receptor profile of bovine adrenal medulla in detail we have studied the binding of classical ligands for mu (μ), delta (δ) and kappa (k) opiate receptors. [³H]naloxone ([³H]NAL), [³H] morphine ([³H]MOR), [³H]D-Ala²-D-Leu⁵-enkephalin ([³H]DAL) and [³H]ethyl-ketocyclazocine ([³H]EKCZ) were used as tracers; unlabeled competitors were NAL, MOR, DAL and ketocyclazocine (KCZ). In adrenal medulla [³H]NAL was specifically bound with a hierarchy of displacement NAL > MOR > KCZ ? DAL. No specific binding of [³H]DAL or [³H]EKCZ was found; for [³H]MOR very low levels of binding were seen, with no displacement by NAL or DAL, inconsistent displacement by KCZ and substantial displacement by MOR with an ED₅₀ of 1.5 nM. In parallel studies rat brain membranes bound each labeled ligand with affinity and specificity consistent with previously published reports. Identical results were obtained in membranes from both tissues prepared with a preincubation step including 100 mM Na⁺, suggesting that the results were not influenced by occupation of binding sites by endogenous ligands. We interpret these data as supporting the existence of opiate receptors of the μ subtype in bovine adrenal medulla. We find, however, no evidence of δ or k sites in this tissue.     

The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales

Phylogenetic analyses of DNA sequence data can provide estimates of evolutionary rates and timescales. Nearly all phylogenetic methods rely on accurate models of nucleotide substitution. A key feature of molecular evolution is the heterogeneity of substitution rates among sites, which is often modelled using a discrete gamma distribution. A widely used derivative of this is the gamma-invariable mixture model, which assumes that a proportion of sites in the sequence are completely resistant to change, while substitution rates at the remaining sites are gamma-distributed. For data sampled at the intraspecific level, however, biological assumptions involved in the invariable-sites model are commonly violated. We examined the use of these models in analyses of five intraspecific data sets. We show that using 6–10 rate categories for the discrete gamma distribution of rates among sites is sufficient to provide a good approximation of the marginal likelihood. Increasing the number of gamma rate categories did not have a substantial effect on estimates of the substitution rate or coalescence time, unless rates varied strongly among sites in a non-gamma-distributed manner. The assumption of a proportion of invariable sites provided a better approximation of the asymptotic marginal likelihood when the number of gamma categories was small, but had minimal impact on estimates of rates and coalescence times. However, the estimated proportion of invariable sites was highly susceptible to changes in the number of gamma rate categories. The concurrent use of gamma and invariable-site models for intraspecific data is not biologically meaningful and has been challenged on statistical grounds; here we have found that the assumption of a proportion of invariable sites has no obvious impact on Bayesian estimates of rates and timescales from intraspecific data.     

A BCR-ABL Mutant Lacking Direct Binding Sites for the GRB2, CBL and CRKL Adapter Proteins Fails to Induce Leukemia in Mice

The BCR-ABL tyrosine kinase is the defining feature of chronic myeloid leukemia (CML) and its kinase activity is required for induction of this disease. Current thinking holds that BCR-ABL forms a multi-protein complex that incorporates several substrates and adaptor proteins and is stabilized by multiple direct and indirect interactions. Signaling output from this highly redundant network leads to cellular transformation. Proteins known to be associated with BCR-ABL in this complex include: GRB2, c-CBL, p62^DOK, and CRKL. These proteins in turn, link BCR-ABL to various signaling pathways indicated in cellular transformation. In this study we show that a triple mutant of BCR-ABL with mutations of the direct binding sites for GRB2, CBL, p62^DOK and CRKL, is defective for transformation of primary hematopoietic cells in vitro and in a murine CML model, while it retains the capacity to induce IL-3 independence in 32D cells. Compared to BCR-ABL, the triple mutant''s ability to activate the MAP kinase and PI3-kinase pathways is severely compromised, while STAT5 phosphorylation is maintained, suggesting that the former are crucial for the transformation of primary cells, but dispensable for transformation of factor dependent cell lines. Our data suggest that inhibition of BCR-ABL-induced leukemia by disrupting protein interactions could be possible, but would require blocking of multiple sites.     

Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants

Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.     

Sequence Conservation in the Prediction of Catalytic Sites

Predicting catalytic sites of a given enzyme is an important open problem of Bioinformatics. Recently, many machine learning-based methods have been developed which have the advantage that they can account for many sequential or structural features. We found that although many kinds of features are incorporated, protein sequence conservation is the main part of information they used and should play an important role in the future. So we tested several conservation features in their ability to predict catalytic sites by using the Support Vector Machine classifier. Our results suggest that position specific scoring matrix performs better than other features and incorporating conservation information of sequentially adjacent sites is more effective than that of structurally adjacent ones. Moreover, although conservation information is effective in predicting catalytic sites, it is a difficult problem to optimize the combination of conservation features and other ones.     

Binding of Aminoalkylindoles to Noncannabinoid Binding Sites in NG108-15 Cells

1. Aminoalkylindoles, typified by WIN 55212-2, bind to G protein-coupled cannabinoid receptors in brain. Although cannabinoids inhibit adenylyl cyclase in NG108-15 neuroblastoma × glioma hybrid cells, cannabinoid receptor binding in these cells has not been described previously. This study compares pharamcological characteristics of [³H]WIN 55212-2 binding sites in rat cerebellar membranes and in NG108-15 membranes.2. Although the K _D of specifid [³H]WIN 55212-2 binding was similar in brain and NG108-15 membranes, the B _max was 10 times lower in NG108-15 than in cerebellar membranes. In both brain and NG108-15 membranes, aminoalkylindole analogues were relatively potent in displacing [³H]WIN 55212-2 binding.However, IC₅₀ values for more traditional cannabinoids were significantly higher in NG108-15 membranes than in brain, e.g., the K _i values for CP55,940 were1.2nM in brain and >5000nM in NG108-15 membranes. Moreover, sodium and GTP--S decreased [³H]WIN 55212-2 binding in brain but not in NG108-15membranes.3. These data suggest that WIN 55212-2 does not label traditional cannabinoid receptors in NG108-15 cells and that these novel aminoalkylindolebinding sites are not coupled to G proteins.     

Brainstem 5-Hydroxytrytamine1A Binding Sites are not Down-Regulated by Agonists which Induce Tolerance in the Rat: Myoclonus and other Serotonergic Behaviors

Abstract

To study the regulation of 5-HT_1A receptors in the brainstem, the region most relevant to the serotonin syndrome and to serotonin-responsive human myoclonic disorders, we chronically treated rats with various 5-HT_1A agonists and labeled 5-HT_1A sites with [³H]8-OH-DPAT. Daily injection for 30 consecutive days of 10 mg/kg ip 8-OH-DPAT (pre- and post-synaptic 5-HT_1A agonist) significantly decreased 8-OH-DPAT-evoked flat body posture, forelimb myoclonus, and hypothermia compared to chronic vehicle injection. There was no cross tolerance to 8-OH-DPAT in rats chronically injected with ipsapirone or buspirone (presynaptic 5-HT_1A agonists). However, none of the 5HT_1A agonists significantly altered B_max of brainstem 5-HT_1A binding sites. Chronic injection with other drugs such as 1-propranolol, (±) pindolol and spiperone (5-HT_1A and 5-HT₂ antagonists), methysergide (5-HT₁ and 5-HT₂ antagonist), and agonists and antagonists at various other 5-HT receptors also had no effect on binding parameters. These data demonstrate lack of cross-tolerance between pre- and post-synaptically acting 5-HT_1A agonists and absence of down-regulation of presynaptic 5-HT_1A sites at doses which induced tolerance of 5-HT_1A-mediated behaviors of the serotonin syndrome. They suggest changes in the post-synaptic cell rather than the receptor recognition site as the mechanism of tolerance.     

Identification of Strychnine Binding Sites in the Rat Retina

Abstract: [³H]Strychnine specifically binds to membrane fractions isolated from rat retinae. The binding is saturable, with an apparent dissociation constant, K _D, of 14.3 × 10⁻⁹ M and 205 fmol bound/mg protein. Specific binding is time-dependent and proportional to protein concentration. Glycine and taurine are equally potent inhibitors of [³H]strychnine binding ( K _i= 4 × 10⁻⁵ M); no other amino acids endogenously present in the retina inhibited [³H]strychnine binding.     

The Sites and Consequences of Melatonin Binding in Mammals

SYNOPSIS. Melatonin, a hormone of the pineal gland, exerts multipleeffects upon the brain-pituitary axis of vertebrates. Amongmammals, the best documented physiological roles of melatonininvolve the photoperiodic induction of reproductive and otherseasonal adjustments. Daylength regulates the effects of gonadalsteroids upon gonadotropin secretion and sexual behavior aswell as the frequency of a neural generator of GnRH pulses.In hamsters, these effects are paralleled by changes in GnRH,AVP and beta-endorphin immunoreactivity, and in opiate receptordensity in the medial amygdala. Autoradiographic studies indicatea high concentration of 2[¹²⁵I]-iodomelatonin binding sitesin the suprachiasmatic nuclei of some photoperiodic mammalsbut not in others. In contrast, such binding sites have beenfound in the pars tuberalis of all seasonally breeding mammalsstudied to date.     

Heterogeneity of Estrogen Binding Sites in Mouse Mammary Cancer

Abstract

The recent demonstration in our laboratory of at least two specific estrogen binding sites in the rat uterus prompted us to investigate similar heterogeneity of binding sites in a trans-plantable ovarian dependent mouse mammary tumor (MXT-3590). Saturation analysis of cytoplasmic (protamine sulfate or hydroxylapatite exchange assay) or crude nuclear fractions (protamine sulfate precipitated nuclear exchange assay) revealed two binding components: type I which conforms to the classically described estrogen receptor and type II which has a lower affinity for estradiol but a greater capacity than type I sites. Exposure of cytosol to charcoal partially removes bound ³H-estradiol from type II sites but not from type I sites. Type II sites are specific for estrogens and do not translocate from the cytoplasmic to the nuclear compartment. Although Type II sites undergo dissociation on prelabeled sucrose density gradients, they are readily demonstrable by postlabeling sucrose density gradient fractions and hydroxylapatite adsorption. Since the presence of type II sites interferes with the measurement of the estrogen receptor (type I) which may also undergo dissociation on sucrose gradients, we recommended that the technique of postlabeling be used for the sucrose gradient analysis of type I and II sites. In addition, saturation assays should be performed over a wide range of ³H-es-tradiol concentrations (0.1–120 nM) for proper evaluation of both sites. These considerations may contribute to more accurate predictions about the response of breast cancers to endocrine therapies.