Presence of distinct virtual backbone torsion angles in dipeptide conformers.

Zwitterionic dipeptides have recently been shown to exist in water mainly as nine conformational forms with specific combinations of backbone Psi, omega and Phi torsions, which allows conformer-specific molecular recognition of peptide ligands by proteins. Here, we show that pairs of virtual backbone torsions can also define these nine conformational forms, and that comparing these virtual torsions in dipeptides with those of backbone-modified pseudopeptides offers an improved procedure for evaluating peptidomimetics for therapeutic applications.

Conformational limitations of glycylsarcosine as a prototypic substrate for peptide transporters.

Peptide transporters are present in all species to absorb the small peptides that occur ubiquitously as products of proteolysis. The broad substrate specificities of these systems allow them to be exploited therapeutically for delivery of peptidomimetic drugs in microbes and man. To this end, glycylsarcosine is currently used as a standard substrate for assaying peptidomimetic transport by peptide transporters. However, in this study we find it is unsuitable as a general substrate, based on assays of its transport by model bacterial peptide transporters and computer-based conformational analysis of its structure. Of the two generic transporters for di- and tripeptides, exemplified by Dpp and Tpp in Escherichia coli, only Dpp can transport glycylsarcosine. The explanation for this finding came from molecular modelling, which indicated that glycylsarcosine can adopt only a restricted range of conformers compared with typical dipeptides, and that of the conformers with a trans peptide bond, the majority have the specific psi and phi backbone torsion angles needed for molecular recognition and transport by Dpp but none possessed psi and phi torsions required for recognition by Tpp; moreover, 38% of its conformers have cis peptide bonds that are not substrates for any peptide transporter. Thus, using glycylsarcosine as substrate in competition assays with compounds that typically form conformers recognised by both types of peptide transporter will underestimate their transport. These findings have implications for assays of oral availability of peptidomimetic drugs such as beta-lactams, ACE inhibitors and anti-viral compounds, for which glycylsarcosine is routinely used.

Predominant torsional forms adopted by oligopeptide conformers in solution: parameters for molecular recognition.

In this paper, we describe the predominant conformational forms adopted by tripeptides and higher oligopeptides in aqueous solution. About 50 tripeptides and almost 20 higher oligopeptides (4-6 residues) were subjected to conformational analysis using SYBYL Random Search. As with dipeptides (Grail BM, Payne JW. J. Peptide Sci. 2000; 6: 186-199), both tripeptides and higher oligopeptides were found to occupy relatively few combinations of psi-phi space that were distinct from those associated with predominant protein secondary structures (e.g. helices and beta-sheets). Again, the preferred psi (psi) values for the first residue (i - 1) were in sectors encompassed by the ranges from +150 degrees to +/-180 degrees, +60 degrees to +90 degrees and -60 degrees to -90 degrees, which were combined with preferred phi (phi) values for the second residue (i) in sectors with ranges from -150 degrees to +/-180 degrees, -60 degrees to -90 degrees and +30 degrees to +60 degrees. It was notable that tripeptides and, to a greater extent, higher oligopeptides adopted an initial psi (psi) (Tor2) from +150 degrees to +/-180 degrees. For tripeptides, their N-C distances (distance between N-terminal nitrogen and C-terminal carbon atoms) distribute about 6.5 A to give shorter, 'folded' conformers that are similar in length to dipeptides, and longer, 'extended' conformers that are distinct. Furthermore, for higher oligopeptides, their N-C distances did not increment in relation to their increasing number of residues and short, 'folded' conformers were still present. These findings have a bearing upon the recognition of these molecules as substrates for widely distributed peptidases and peptide transporters.

Cloning, sequencing, and characterization of a gene cluster involved in EDTA degradation from the bacterium BNC1.

EDTA is a chelating agent, widely used in many industries. Because of its ability to mobilize heavy metals and radionuclides, it can be an environmental pollutant. The EDTA monooxygenases that initiate EDTA degradation have been purified and characterized in bacterial strains BNC1 and DSM 9103. However, the genes encoding the enzymes have not been reported. The EDTA monooxygenase gene was cloned by probing a genomic library of strain BNC1 with a probe generated from the N-terminal amino acid sequence of the monooxygenase. Sequencing of the cloned DNA fragment revealed a gene cluster containing eight genes. Two of the genes, emoA and emoB, were expressed in Escherichia coli, and the gene products, EmoA and EmoB, were purified and characterized. Both experimental data and sequence analysis showed that EmoA is a reduced flavin mononucleotide-utilizing monooxygenase and that EmoB is an NADH:flavin mononucleotide oxidoreductase. The two-enzyme system oxidized EDTA to ethylenediaminediacetate (EDDA) and nitrilotriacetate (NTA) to iminodiacetate (IDA) with the production of glyoxylate. The emoA and emoB genes were cotranscribed when BNC1 cells were grown on EDTA. Other genes in the cluster encoded a hypothetical transport system, a putative regulatory protein, and IDA oxidase that oxidizes IDA and EDDA. We concluded that this gene cluster is responsible for the initial steps of EDTA and NTA degradation.

Evaluation of the conformational propensities of peptide isosteres as a basis for selecting bioactive pseudopeptides.

Our aim was to compare the repertoires of conformers formed by the model zwitterionic peptides AA and AAA in aqueous solution with the conformational profiles of a range of their peptide isosteres, so as to facilitate selection of isosteres for synthesis and testing as biologically stable surrogates of bioactive di- and tripeptides. Comparisons were based upon the results of conformational analysis using a random search approach implemented within the SYBYL molecular modelling package, using zwitterionic molecules, simulated aqueous solvation using a dielectric constant of 80 and allowing all torsions to vary. For each compound, individual conformers were grouped on the basis of specific combinations of psi, phi and omega torsions and, using their energies, the aggregated percentage for each group was calculated using a Boltzmann distribution and displayed using a 3D pseudo Ramachandran plot relating percentage conformer to psi and phi torsions. Retroamide, N-methylamide and thioamide isosteres showed the best match to natural peptides and to the molecular recognition parameters defined for substrates of peptide transporters. The results should aid rational design of therapeutic agents in various areas, e.g. oral delivery of drugs by peptide transporters and of peptidase inhibitors. This approach may usefully be applied to various biochemical and pharmaceutical topics.

Predominant torsional forms adopted by dipeptide conformers in solution: parameters for molecular recognition.

The present paper describes the predominant conformational forms adopted by dipeptides in aqueous solution. More than 50 dipeptides were subjected to conformational analysis using SYBYL Random Search. The resultant collections of conformers for individual dipeptides, for small groups with related side chain residues and for large groups of about 50 dipeptides were visualized graphically and analysed using a novel three-dimensional pseudo-Ramachandran plot. The distribution of conformers, weighted according to the percentage of each in the total conformer pool, was found to be restricted to nine main combinations of backbone psi (psi) and phi (phi) torsion angles. The preferred psi values were in sectors A7 (+150 degrees to +/-180 degrees), A10 (+60 degrees to +90 degrees) and A4 (-60 degrees to -90 degrees), and these were combined with preferred phi values in sectors B12 (-150 degrees to +/-180 degrees), B9 (-60 degrees to -90 degrees) and B2 (+30 degrees to +60 degrees). These combinations of psi and phi values are distinct from those found in common secondary structures of proteins. These results show that although dipeptides can each adopt many conformations in solution, each possesses a profile of common conformers that is quantifiable. A similarly weighted distribution of dipeptide conformers according to distance between amino-terminal nitrogen and carboxyl-terminal carbon shows how the preferred combinations of backbone torsional angles result in particular N-C geometries for the conformers. This approach gives insight into the important conformational parameters of dipeptides that provide the basis for their molecular recognition as substrates by widely distributed peptide transporters. It offers a basis for the rational design of peptide-based bioactive compounds able to exploit these transporters for targeting and delivery.

Molecular recognition templates of peptides: driving force for molecular evolution of peptide transporters.

Small peptides derived from protein hydrolysis occur ubiquitously. To utilize these structurally diverse compounds, organisms possess generic peptide transporters for di- (Dpp), tri- (Tpp), and oligopeptides (Opp). Using conformational analysis, we describe the predominant conformers of di-, tri-, and oligopeptides in water; dipeptides occur as nine main groups, defined by specific combinations of torsional angles. The molecular recognition templates (MRTs) of substrates for Dpp and Tpp comprise distinct groups of dipeptide conformers plus folded tripeptide conformers with matching spatial distribution of recognition features; for Opp, the MRT involves specific oligopeptide conformers with extended backbones. For any peptide, the proportion of its conformers in a particular MRT correlates with its relative binding and transport by each transporter. Thus, peptide transporters have evolved complementary specificities to optimize utilization of the universal peptide pool. The general applicability of MRTs should facilitate rational design and targeting of peptide-based prodrugs.

Structural basis for recognition of dipeptides by peptide transporters.

Our objective in this work was to identify the structural basis for the molecular recognition of peptides by peptide transporters. Various assays for dipeptide transport by the dipeptide and tripeptide permeases of Escherichia coli were performed, together with measurements of thermodynamic parameters of substrate binding to the dipeptide binding protein using isothermal titration calorimetry. Computer-based conformational analysis of the test dipeptides was performed to define the repertoire of conformers that each dipeptide adopts in solution. Strict correlations were identified between the complement of particular conformers adopted by a peptide and its bioactivity as a substrate for each transporter. Details of the structural and electronic parameters that define the molecular recognition templates (MRTs) of the dipeptide substrates of these transporters are presented; similar MRTs are likely to apply with dipeptidases. These MRTs provide the essential information for the rational design of peptide-based drugs tailored for exploitation of peptide transporters in microorganisms and man.

Substrate specificity of the periplasmic dipeptide-binding protein from Escherichia coli: experimental basis for the design of peptide prodrugs.

Pure dipeptide-binding protein (DppA) from Escherichia coli was studied in a filter binding assay to determine its binding specificity. A substrate:DppA stoichiometry of 1:1 was found with both [14C]AlaAla and Ala[14C]Phe. Surprisingly, substrate binding did not vary over the pH range pH 3-9.5. Different dipeptides yielded liganded protein with various pI values, implying that DppA can undergo subtly different conformational changes to accommodate different substrates. Using [125I]Tyr-peptides as substrates in competition assays, the relative binding affinities for a range of dipeptides were found to parallel their overall transport rates into E. coli through the dipeptide permease (Dpp), showing that DppA alone controls the specificity of Dpp. With a series of substituted glycyl peptides, binding affinity was progressively enhanced by alkylation (with methyl to butyl) of the N-terminal alpha-amino group. Thus, results from this approach provide an essential experimental basis, which complements the information from the crystal structure of DppA, for the design of peptidomimetic antibacterials targeted for transport through Dpp.

Purification and characterization of EDTA monooxygenase from the EDTA-degrading bacterium BNC1.

The synthetic chelating agent EDTA can mobilize radionuclides and heavy metals in the environment. Biodegradation of EDTA should reduce this mobilization. Although several bacteria have been reported to mineralize EDTA, little is known about the biochemistry of EDTA degradation. Understanding the biochemistry will facilitate the removal of EDTA from the environment. EDTA-degrading activities were detected in cell extracts of bacterium BNC1 when flavin mononucleotide (FMN), NADH, and O2 were present. The degradative enzyme system was separated into two different enzymes, EDTA monooxygenase and an FMN reductase. EDTA monooxygenase oxidized EDTA to glyoxylate and ethylenediaminetriacetate (ED3A), with the coconsumption of FMNH2 and O2. The FMN reductase provided EDTA monooxygenase with FMNH2 by reducing FMN with NADH. The FMN reductase was successfully substituted in the assay mixture by other FMN reductases. EDTA monooxygenase was purified to greater than 95% homogeneity and had a single polypeptide with a molecular weight of 45,000. The enzyme oxidized both EDTA complexed with various metal ions and uncomplexed EDTA. The optimal conditions for activity were pH 7.8 and 35 degreesC. Kms were 34.1 microM for uncomplexed EDTA and 8.5 microM for MgEDTA2-; this difference in Km indicates that the enzyme has greater affinity for MgEDTA2-. The enzyme also catalyzed the release of glyoxylate from nitrilotriacetate and diethylenetriaminepentaacetate. EDTA monooxygenase belongs to a small group of FMNH2-utilizing monooxygenases that attack carbon-nitrogen, carbon-sulfur, and carbon-carbon double bonds.

Substrate binding mutants of the higher plant ADP-glucose pyrophosphorylase.

To explore the structure-function relationships of the heterotetrameric higher plant ADP-glucose pyrophosphorylase, composed of a pair of large and small subunits, the small subunit cDNA was subjected to chemical mutagenesis and then co-expressed with the wild-type large subunit cDNA. Mutants were selected for their inability to complement a defective bacterial ADP-glucose pyrophosphorylase gene and, in turn, to accumulate glycogen as viewed by iodine staining of the cells. Based on these initial analyses, we subsequently identified four distinct classes of mutations which were glycogen-deficient but exhibited enzyme activity levels comparable to the normal recombinant enzyme under saturating reaction conditions. Three classes, each a product of single amino acid substitution, showed altered kinetic constants for substrates. Substitution of Asp252 to Asn conferred the enzyme lower affinity for glucose-1-phosphate, replacement of Asp121 to Asn resulted in an enzyme less responsive to both glucose-1-phosphate and ATP, while the Ala106 to Thr substituted enzyme contains altered sensitivity primarily to ATP. The fourth class, a Pro43 to Ser substitution, resulted in an enzyme with decreased sensitivity (8-fold) to the activator 3-PGA. Overall, the results of this study suggests that the two subunit types do not have identical roles in enzyme function and that the small subunit plays a more dominant role in catalysis than the large subunit.

Choice processing in emotionally difficult decisions.

Choice conflicts between one's important values may cause negative emotion. This article extends the standard effort-accuracy approach to explaining task influences on decision processing by arguing that coping goals will interact with effort minimization and accuracy maximization goals for negatively emotion-laden decision tasks. These coping goals may involve both a desire to process in a thorough, accurate manner and a desire to avoid particularly distressing aspects of processing. On the basis of this extended framework, the authors hypothesized and found in 3 experiments that decision processing under increasing negative emotion both becomes more extensive and proceeds more by focusing on one attribute at a time. In particular, increased negative emotion leads to more attribute-based processing at the beginning of the decision process. The results are inconsistent with views that negative emotion acts only as an incentive or only as a source of decision complexity.

Autosomal dominant vitreoretinochoroidopathy. Report of the third family.

A family composed of 13 affected members in five generations (10 patients from four generations examined) had vitreal and ophthalmoscopic findings characteristic of autosomal dominant vitreoretinochoroidopathy, as described in two previous kindreds. Visual acuity was 20/25 or better in all but one patient. All affected individuals had vitreous liquefaction with or without peripheral vitreal condensations. Peripheral pigmentary changes and choroidal atrophy were characteristic. Six patients developed cataracts in their early 40s that required extraction. One patient had glaucoma, one developed a retinal detachment, and one had a spontaneous vitreous hemorrhage. Autosomal dominant vitreoretinochoroidopathy is a well-defined condition featuring presenile cataracts, vitreal degeneration, characteristic ophthalmoscopic findings, and good visual prognosis.

Expression of periplasmic binding proteins for peptide transport is subject to negative regulation by phosphate limitation in Escherichia coli.

It is well recognised that phosphate limitation in Escherichia coli causes enhanced synthesis of a variety of proteins involved in maximising the uptake and utilisation of the available phosphate. In contrast to this situation, we report here that these same conditions repress synthesis of the periplasmic binding proteins for both the oligopeptide (Opp) and dipeptide permeases (Dpp), and of certain other periplasmic proteins. Regulation in the former case is mediated by the Pho regulon; genes controlled by this mechanism lack efficient -35 promoter regions, and instead, an activator protein, PhoB, binds to a specific 'Pho box' sequence, ten bases upstream from a -10 promoter, thereby facilitating binding of RNA polymerase and leading to enhanced transcription. In the latter case, putative Pho boxes can be identified in the promoter regions of opp and dpp (and of other binding proteins), but in these genes they overlap the RNA polymerase binding sites of good promoters. We speculate that this different Pho box location may allow PhoB to act as a repressor of transcription of these genes. The promoter region for the sigma factor, sigma 32, (RpoH) also contains a putative Pho box, implying that it may be involved in the enhanced synthesis and secretion of proteins required under phosphate limitation.

The sequestration of [3H]spiperone by lymphocytes in schizophrenics and their first-degree relatives: a limited vulnerability marker?

The sequestration of [3H]spiperone by lymphocytes was studied in preserved cells obtained from 22 schizophrenic subjects and 40 of their relatives, and the results were compared with those obtained from 25 healthy control subjects. Mean displaceable sequestration values, obtained from measurements made at a single radioligand concentration (1nM) which optimised the relative contribution of "high affinity" sequestration, were found to be similar for all groups of subjects. Furthermore, displaceable spiperone sequestration was abnormally high in only a small proportion of the schizophrenics (13.6%) and their relatives (5%). There was no evidence that either exposure to neuroleptic medication or duration of illness had an effect on sequestration values. The results suggest that, at least until the required experimental conditions are better established, [3H]spiperone sequestration by lymphocytes does not offer a useful vulnerability marker for schizophrenia.

Peptide substrates rapidly modulate expression of dipeptide and oligopeptide permeases in Candida albicans.

Previous studies showed that peptide transport activity in Candida albicans was completely repressed by NH4+, and that growth on amino acids as sole nitrogen source stimulated transport to a basal level. Here we show that addition of peptide mixtures to culture media gives a further 5-fold increase in transport of dipeptides and oligopeptides; the effect is specific for peptide transport, amino acid uptake being unaffected. Presence of peptides but not amino acids overrides NH4+ repression of peptide transport. Step-up activation of transport activity, caused by addition of peptides to incubation media, and step-down inhibition that accompanies removal of peptides, occurs rapidly (within 30 min at 28 degrees C). Step-up is independent of de novo protein synthesis. This substrate-induced regulation is compatible with a rapid, reversible activation of plasma membrane-bound peptide permease(s), or a mechanism of endocytosis involving a cycle of insertion and retrieval of preformed permease components. These results are considered in relation to the expression of peptide permeases in vivo, and the development of synthetic anticandidal peptide carrier prodrugs designed to exploit these systems.

Evaluation of the dipeptide and oligopeptide permeases of Candida albicans as uptake routes for synthetic anticandidal agents.

In order to obtain information essential for the design of synthetic anticandidal drugs that can exploit peptide permeases to gain access to intracellular targets, the substrate specificities of the dipeptide permease (Dpp) and oligopeptide permease (Opp) of Candida albicans have been studied. The permeases show strict stereospecificity, a preference for large, hydrophobic and N-terminal Ala residues, and marked discrimination against basic and acidic side chain residues. Comparison of results from several transport assays indicated that measuring loss of peptide substrate from the medium using fluorescence labelling procedures gave reliable transport rates and kinetic parameters, whereas in contrast, measuring accumulation of radioactivity from labelled substrates gave erroneous results arising from substrate metabolism and exodus. Intact accumulation of peptidase-resistant substrate against a concentration gradient was demonstrated. From amongst a variety of protein reagents tested, selective inhibition of dipeptide transport and presumed labelling of essential carboxyl group(s) in Dpp proteins was demonstrated using Woodward's reagent K.

Analysis of the peptide carrier in the scutellum of barley embryos by photoaffinity labelling.

The preparation of a phenylalanine analogue containing an azido group and its incorporation into dipeptides is described. Peptides modified in this way are taken up into barley (Hordeum vulgare L.) scutella via the previously characterized peptide-transport system. Photoactivation of modified peptides in the presence of isolated scutella resulted in irreversible inhibition of peptide uptake in a concentration-dependent manner. Transport of other solutes which share a common mechanism of energy coupling, but which are transported via distinct carriers, was not inhibited after photo-derivatization of scutella with the modified peptides. Derivatization of isolated scutellar tissue with a (14)C-labelled peptide analogue, resulted in incorporation of label into two proteins of Mr = 54000 and 41000. Scutellar tissue from early-germinating seeds, which do not show active peptide uptake, did not incorporate label into these polypeptides. It is concluded that these proteins are components of the barley peptide-transport system.