Is there a relationship between DNA sequences encoding peptide ligands and their receptors?

Computational design of fully overlapping coding schemes for protein pairs and triplets

Gene pairs that overlap in their coding regions are rare except in viruses. They may occur transiently in gene creation and are of biotechnological interest. We have examined the possibility to encode an arbitrary pair of protein domains as a dual gene, with the shorter coding sequence completely embedded in the longer one. For 500 × 500 domain pairs (X, Y), we computationally designed homologous pairs (X', Y') coded this way, using an algorithm that provably maximizes the sequence similarity between (X', Y') and (X, Y). Three schemes were considered, with X' and Y' coded on the same or complementary strands. For 16% of the pairs, an overlapping coding exists where the level of homology of X', Y' to the natural proteins represents an E-value of 10-10 or better. Thus, for an arbitrary domain pair, it is surprisingly easy to design homologous sequences that can be encoded as a fully-overlapping gene pair. The algorithm is general and was used to design 200 triple genes, with three proteins encoded by the same DNA segment. The ease of design suggests overlapping genes may have occurred frequently in evolution and could be readily used to compress or constrain artificial genomes.

Peptide self-aggregation and peptide complementarity as bases for the evolution of peptide receptors: a review

This paper reviews the three major theories of peptide receptor evolution: (1) Dwyer's theory that peptide receptors evolved from self-aggregating peptides; (2) Root-Bernstein's theory that peptide receptors evolved from functionally and structurally complementary peptides; and (3) Blalock's theory that receptors evolved from hydropathically complementary sequences encoded in the antisense strand of the DNA encoding each peptide. The evidence to date suggests that the co-yevolution of peptides and their receptors is strongly constrained by one or more of these physicochemically based mechanisms, which argues against a random or frozen accident' model. The data also suggest that structure and function are integrally related from the earliest steps of receptor-ligand evolution so that peptide functionality is non-random and highly conserved in its origin. The result is a molecular paleontology' that reveals the evolutionary constraints that shaped the interaction of structure and function.

Structural study of binding of flagellin by Toll-like receptor 5

In order to predict the binding regions within the complex formed by Toll-like receptor 5 (TLR-5) and flagellin, a complementary hydropathy between the two proteins was sought. A region common to the flagellins of Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa, and Listeria monocytogenes was shown to be hydropathically complementary to the 552-to-561 fragment of TLR-5, whose sequence is EILDISRNQL. The hydrophobicity profile of this region is shared with flagellins of 377 bacterial species out of a total of 723 publicly available sequences. A conformational analysis of the predicted binding site of TLR-5, whose structure is still unknown, was carried out with a methodology already applied to similar problems. To sample the conformations available to the peptide chain, a plot of the number of conformations per unit energy interval (density of states) versus energy was built. Following a theoretical argument, conformations belonging to maxima in this plot were selected. The most stable structure obtained in this search, an alpha-helical conformation, was shown to form the electrostatic interactions Glu552-Gln89, Asp555-Arg92, and Arg558-Glu93 with the predicted binding site of the flagellin of S. enterica serovar Typhimurium, formed by the 88-to-97 chain fragment (LQRVRELAVQ), which is likewise alpha helical.

Molecular complementarity III. peptide complementarity as a basis for peptide receptor evolution: a bioinformatic case study of insulin, glucagon and gastrin

Dwyer has suggested that peptide receptors evolved from self-aggregating peptides so that peptide receptors should incorporate regions of high homology with the peptide ligand. If one considers self-aggregation to be a particular manifestation of molecular complementarity in general, then it is possible to extend Dwyer's hypothesis to a broader set of peptides: complementary peptides that bind to each other. In the latter case, one would expect to find homologous copies of the complementary peptide in the receptor. Thirteen peptides, 10 of which are not known to self-aggregate (amylin, ACTH, LHRH, angiotensin II, atrial natriuretic peptide, somatostatin, oxytocin, neurotensin, vasopressin, and substance P), and three that are known to self-aggregate (insulin, glucagon, and gastrin), were chosen. In addition to being self-aggregating, insulin and glucagon are also known to bind to each other, making them a mutually complementary pair. All possible combinations of the 13 peptides and the extracellular regions of their receptors were investigated using bioinformatic tools (a total of 325 combinations). Multiple, statistically significant homologies were found for insulin in the insulin receptor; insulin in the glucagon receptor; glucagon in the glucagon receptor; glucagon in the insulin receptor; and gastrin in gastrin binding protein and its receptor. Most of these homologies are in regions or sequences known to contribute to receptor binding of the respective hormone. These results suggest that the Dwyer hypothesis for receptor evolution may be generalizable beyond self-aggregating to complementary peptides. The evolution of receptors may have been driven by small molecule complementarity augmented by modular evolutionary processes that left a "molecular paleontology" that is still evident in the genome today. This "paleontology" may allow identification of peptide receptor sites.

Inhibition of HIV-1 infection by an intramolecular antisense peptide to T20 in gp160

Antisense amino acids are amino acids which can be translated from the corresponding anti-codons of a sense amino acid. Antisense peptides encoded by the noncoding DNA strand have a tendency to interact with each other. We have demonstrated that antisense peptide sequences are present intramolecularly, and these may contribute to the folding and maintenance of the tertiary structure of a protein. T20 is a synthetic peptide with an amino acid sequence in the gp41 of HIV-1 and has been demonstrated to be a potent inhibitor of HIV-1 infection. We searched for intramolecular peptide sequences which are antisense to portions of T20. A synthetic peptide (TA-1L) consisting of amino acids 84 to 97 of gp160, which contains an antisense peptide sequence (TA-1) to T20, was shown to inhibit HIV-1(IIIB) infection of MT-4 cells. Interaction of these antisense peptides could be involved in sustaining HIV-1 infectivity. The TA-1L site, which exists in the C1 domain of gp160, is highly homologous among strains of HIV-1, especially at TA-1 and in the amino acids flanking the C terminus. Although the TA-1 sites of 18 out of 30 HIV-1 strains were antisense to the T20 region, those of the remaining 12 strains, including HIV-1(MN), were not. However, TA-1L inhibited infection by HIV-1(MN), which has no antisense peptide in T20 corresponding to TA-1, although the inhibitory effect was weaker. TA-1L may thus also interfere with the gp160 interaction with CD4, which has an antisense sequence to TA-1.

Antisense peptide interactions studied by electrospray ionization mass spectrometry

Non-covalent interactions between met- and leu-enkephalins and their antisense peptides were studied by electrospray ionization mass spectrometry. Mixtures of sense and antisense peptides gave both the corresponding homodimers and heterodimers. The relative abundance ratios of the heterodimer to that of the homodimer of the sense peptide and the relative stability constants of the heterodimers were compared with the corresponding values from mixtures of the sense peptides and a control peptide. The results show that there is a preferential interaction between the sense and antisense peptides compared with that between the sense and control peptides.

Specific amino acid content and codon usage account for the existence of overlapping ORFS

Here we present a novel hypothesis for the origin of overlapping open reading frames (O-ORFs) observed in the 'non-coding frames' of several genes of yeast chromosome II. By computer analysis it was found that the specific amino acid content and base distribution pattern at certain genomic locations and the presence of O-ORFs were related. This observation prompt us to conclude that these O-ORFs are mere statistical curiosities without any biological function, which is in contrast to the hypotheses proposed by other authors.

Augmentation of aortic ring contractions by angiotensin II antisense peptide

Previous biochemical experiments have revealed two antisense peptide antagonists to human angiotensin II (Ang II), one encoded in the cDNA in the antiparallel reading, the other in the parallel reading. Neither peptide's ability to produce physiological antagonism has been demonstrated previously. Both peptides were tested for their ability to antagonize Ang II-induced contractions on rabbit aorta smooth muscle. Neither peptide had any direct contractile activity. The antiparallel Ang II peptide had physiological antagonism to Ang II contractions at a lower sensitivity than reported in biochemical studies, and its antagonist activity was partially blocked by Ang II antiserum, suggesting that it is not an antipeptide but an Ang II homologue. The parallel Ang II antipeptide also required high concentrations for physiological inhibition. Its contractile inhibition was not affected by Ang II antiserum and diminished the Ang II contraction at high micromolar concentrations, findings consistent with physicochemical data showing that it is an Ang II complement. The concentration of either peptide required to produce an antagonistic physiological effect was too high to predict any pharmacological usefulness. The parallel antipeptide, however, significantly increased the force of muscle contractions at high nanomolar concentrations, thus displaying a unique dual augmentation/antagonist activity. This antipeptide seems to have highly sequence-specific activity because other similar parallel antipeptides had no activity. The parallel antipeptide augmentation mimics the shift in the Ang II dose-response curve produced in hypertension studies of the slow pressor effect of Ang II and may be useful in deducing the currently unknown cause of the slow pressor effect. It may also have some uses in migraine studies.

Molecular characterization of a dual endothelin-1/Angiotensin II receptor

BACKGROUND

The molecular recognition theory (MRT) provides a conceptual framework that could explain the evolution of intermolecular and intramolecular interaction of peptides and proteins. As such, it predicts that binding sites of peptide hormones, and its receptor binding sites were originally encoded by and evolved from complementary strands of genomic DNA.

MATERIALS AND METHODS

On the basis of principles underlying the MRT, we screened a rat brain complementary DNA library using an AngII followed by an endothelin-1 (ET-1) antisense oligonucleotide probe, expecting to isolate potential cognate receptors.

RESULTS

An identical cDNA clone was isolated independently from both the AngII and ET-1 oligonucleotide screenings. Structural analysis revealed a receptor polypeptide containing a single predicted transmembrane region with distinct ET-1 and AngII putative binding domains. Functional analysis demonstrated ET-1- and AngII-specific binding as well as ET-1- and AngII-induced coupling to a Ca2+ mobilizing transduction system. Amino acid substitutions within the predicted ET-1 binding domain obliterate ET-1 binding while preserving AngII binding, thus defining the structural determinants of ET-1 binding within the dual ET-1/AngII receptor, as well as corroborating the dual nature of the receptor.

CONCLUSIONS

Elucidation of the dual ET-1/AngII receptor provides further molecular genetic evidence in support of the molecular recognition theory and identifies for the first time a molecular link between the ET-1 and AngII hormonal systems that could underlie observed similar physiological responses elicited by ET-1 and AngII in different organ systems. The prominent expression of the ET-1/AngII receptor mRNA in brain and heart tissues suggests an important role in cardiovascular function in normal and pathophysiological states.

Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid

The lack of even a marginal similarity between the two aminoacyl-tRNA synthetase (aaRS) classes suggests their independent origins (Eriani et al., 1990; Nagel and Doolittle, 1991). Yet, this independence is a puzzle inconsistent with the common origin of transfer RNAs, the coevolutionary theory of the genetic code (Wong, 1975, 1981) and other associated data and ideas. We present here the results of antiparallel 'class I versus class II' comparisons of aaRSs within their signature sequences. The two main HIGH- and KMSKS-containing motifs of class I appeared to be complementary to the class II motifs 2 and 1, respectively. The above sequence complementarity along with the mirror-image between crystal structures of complexes formed by the opposite aaRSs and their cognate tRNAs (Ruff et al., 1991), and the generally mirror ('head-to-tail') mapping of the basic functional sites in the sequences of aaRSs from the opposite two classes led us to conclude that these two synthetases emerged synchronously as complementary strands of the same primordial nucleic acid. This conclusion, combined with the hypothesis of tRNA concerted origin (Rodin et al., 1993a,b), may explain many intriguing features of aaRSs and favor the elucidation of the origin of the genetic code.

Sense in antisense?

A correspondence between open reading frames in sense and antisense strands is expected from the hypothesis that the prototypic triplet code was of general form RNY, where R is a purine base, N is any base, and Y is a pyrimidine. A deficit of stop codons in the antisense strand (and thus long open reading frames) is predicted for organisms with high G + C percentages; however, two bacteria (Azotobacter vinelandii, Rhodobacter capsulatum) have larger average antisense strand open reading frames than predicted from (G + C)%. The similar codon frequencies found in sense and antisense strands can be attributed to the wide distribution of inverted repeats (stem-loop potential) in natural DNA sequences.

The antisense homology box: a new motif within proteins that encodes biologically active peptides

Amphiphilic peptides approximately fifteen amino acids in length and their corresponding antisense peptides exist within protein molecules. These regions (termed antisense homology boxes) are separated by approximately fifty amino acids. Because many sense-antisense peptide pairs have been reported to recognize and bind to each other, antisense homology boxes may be involved in folding, chaperoning and oligomer formation of proteins. The antisense homology box-derived peptide CALSVDRYRAVASW, a fragment of human endothelin A receptor, proved to be a specific inhibitor of endothelin peptide (ET-1) in a smooth muscle relaxation assay. The peptide was able to block endotoxin-induced shock in rats as well. Our finding of endothelin receptor inhibitor among antisense homology box-derived peptides indicates that searching proteins for this new motif may be useful in finding biologically active peptides.

Antisense overlapping open reading frames in genes from bacteria to humans

Long Open Reading Frames (ORFs) in antisense DNA strands have been reported in the literature as being rare events. However, an extensive analysis of the GenBank database revealed that a substantial number of genes from several species contain an in-phase ORF in the antisense strand, that overlaps entirely the coding sequence of the sense strand, or even extends beyond. The findings described in this paper show that this is a frequent, non-random phenomenon, which is primarily dependent on codon usage, and to a lesser extent on gene size and GC content. Examination of the sequence database for several prokaryotic and eukaryotic organisms, demonstrates that coding sequences with in-phase, 100% overlapping antisense ORFs are present in every genome studied so far.

Canine parietal cell binding by antibodies to the complementary peptide of somatostatin

Using antibodies to a complementary peptide of somatostatin, putative somatostatin binding proteins were characterized on canine parietal cells. A synthetic peptide (S-C1) was derived from the complementary mRNA sequence for somatostatin-14. Antiserum containing antibodies to S-C1 inhibited competitively 125I-Tyr11-somatostatin binding to canine oxyntic mucosal membranes. Canine parietal cell preparations were incubated with carbachol in the presence or absence of somatostatin and antisera to S-C1. Antibodies to S-C1 produced a decrease in carbachol-stimulated 14C-aminopyrine uptake comparable with that produced by 10(-6) M somatostatin. In immunocytochemical studies by light microscopy, antibodies to S-C1 produced positive staining of parietal cells throughout the oxyntic gland area. By electron microscopy using immunogold techniques, binding by antibodies to somatostatin C-1 was localized ultrastructurally to basolateral and intracellular membranes and to secretory canalicular membranes of parietal cells. These studies support the conclusion that antibodies to the somatostatin complementary peptide demonstrate properties similar to those of somatostatin in that they inhibit carbachol-stimulated aminopyrine uptake and 125I-somatostatin binding. Furthermore, these antibodies localize to specific regions on plasma membranes of parietal cells, which may represent somatostatin binding sites.

Making sense from antisense: a review of experimental data and developing ideas on sense--antisense peptide recognition

Peptides encoded in the antisense strand of DNA have been predicted and found experimentally to bind to sense peptides and proteins with significant selectivity and affinity. Such sense--antisense peptide recognition has been observed in many systems, most often by detecting binding between immobilized and soluble interaction partners. Data obtained so far on sequence and solvent dependence of interaction support a hydrophobic-hydrophilic (amphipathic) model of peptide recognition. Nonetheless, the mechanistic understanding of this type of molecular recognition remains incomplete. Improving this understanding likely will require expanding the types of characteristics measured for sense--antisense peptide complexes and hence the types of analytical methods applied to such interactions. Understanding the mechanism of sense--antisense peptide recognition also may provide insights into mechanisms of native (sense) peptide and protein interactions and protein folding. Such insight may be helpful to learn how to design macromolecular recognition agents in technology for separation, diagnostics and therapeutics.

Antagonist effect of a receptor-mimicking peptide encoded by human angiotensin II complementary RNA

This article reports on the binding and the angiotensin II (Ang II) antagonistic properties of a peptide, referred to as hIIA, encoded by an RNA strand complementary to the human Ang II messenger RNA. Although Ang II and hIIA (H2N-Glu-Gly-Val-Tyr-Val-His-Pro-Val-COOH) share four amino acids, the iodinated and tritiated forms of hIIA were unreactive with seven monoclonal antibodies defining four distinct epitopes on the Ang II molecule and failed to bind to Ang II hepatic and mesangial receptors. However, hIIA did inhibit binding of 125I-Ang II to rat hepatocyte membranes (IC50, 2 x 10(-7) M) and to the various monoclonal antibodies. The lowest IC50 (5 x 10(-7) M) was measured with the monoclonal antibody specific for the Ang II sequence generally considered as implicated in receptor recognition. As predicted from the binding studies, hIIA was further shown to antagonize some biological properties of Ang II. On mesangial cells, hIIA alone had no effect on intracellular calcium concentration ([Ca2+]i) and prostaglandin E2 synthesis but did abolish the transient increase in [Ca2+]i in response to 100 nM Ang II and did induce a specific dose-dependent inhibition of the Ang II-stimulated prostaglandin E2 release. Furthermore, intravenous infusion of hIIA (200 micrograms.kg-1.min-1) inhibited by 66 +/- 3% the rat hypertensive response to 100 ng.kg-1 Ang II but had no effect on the pressor activity of agents such as alpha 1-adrenergic and HT2 serotonin agonists. Our data suggest that the "complementary" peptide hIIA interacts directly with Ang II by mimicking the Ang II complementary site on the receptor and can inhibit the physiological effects of Ang II. This type of Ang II complementary peptide may serve as a model for a new class of antihypertensive drugs.

Affinity chromatography purification of angiotensin II receptor using photoactivable biotinylated probes

We have developed biotinylated photoactivable probes that are suitable for covalent labeling of angiotensin II (AII) receptors and the subsequent purification of covalent complexes through immobilized avidin or streptavidin. One of these probes, biotin-NH(CH2)2SS(CH2)2CO-[Ala1,Phe(4N3)8]AII, which contains a cleavable disulfide bridge in its spacer arm and which displays, in its radioiodinated form, very high affinity for AII receptors (Kd approximately 1 nM), proved to be suitable for indirect affinity chromatography of rat liver receptor with facilitated recovery from avidin gels by use of reducing agents. This constituted the central step of an efficient partial purification scheme involving hydroxylapatite chromatography, streptavidin chromatography, and thiopropyl-Sepharose chromatography. SDS-PAGE analysis and autoradiography established the identity of the purified entity (molecular weight 65K) as the AII receptor. Possible ways of completing purification to homogeneity and extrapolation of the protocols to a preparative scale are discussed, as well as the potential contribution of our new probes to the study of the structural properties of angiotensin receptors.

NMR study of the possible interaction in solution of angiotensin II with a peptide encoded by angiotensin II complementary RNA

The potential binding of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) (AII) to a peptide encoded by its complementary RNA (Lys-Gly-Val-Asp-Val-Tyr-Ala-Val) (IIA) has been studied by monitoring the 1H NMR spectrum of IIA in aqueous phosphate or Tris.HCl buffer (2H2O) as it is titrated with AII. For molar ratios of AII/IIA ranging from 0.2 to 1.8, the NMR spectra are unchanged as compared to the spectra of the isolated peptides. Based on these findings, the Kd for the putative biomolecular complex of the two peptides under these conditions is calculated to be greater than 10(-4) M. This result does not support the suggestion of Elton et al. [Elton, T. S., Dion, L.D., Bost, K. L., Oparil, S. & Blalock, J. E. (1988) Proc. Natl. Acad. Sci. USA 85, 2518-2522] that AII and IIA engage in high-affinity binding (Kd approximately 5 x 10(-8) M) with each other.