Self-complementary regions in human albumin mRNA encode important structural regions within the human albumin protein

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.

Prediction of homologous binding sites on RB and p107 common for viral oncoproteins and cellular ligands

Hydropathic anticomplementarity of amino acids specifies that peptides translated from complementary DNA strands may acquire amphiphilic conformations and bind to each other. This concept has been coined 'Molecular Recognition Theory' (MRT) or 'complementary peptide theory'. Inactivation of retinoblastoma protein (RB), a tumor suppressor gene product, has been shown to be involved in the pathogenesis of many tumors and to be due to either mutation of the RB gene, hyperphosphorylation or complex formation with viral oncoproteins. The viral oncoproteins share a common RB binding motif with cellular ligands. The exact site on RB associating with this common RB binding motif of viral oncoproteins and cellular ligands has not been identified yet. This study is the first to predict putative binding sites on RB and p107, a cellular protein with RB sequence homology, respectively, by using the hydropathic complementarity approach. These sites are residues 649-654 of RB and 657-662 of p107. Moreover, this paper proposes a structure for a potential antineoplastic agent based on the amino acid sequence of the predicted RB binding site. The data presented herein should have important implications both for the understanding of cancer pathophysiology and for the drug design of antineoplastic compounds.

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.

Design and recognition properties of a hydropathically complementary peptide to human interleukin 1 beta

A computer-designed hydropathically complementary peptide to human interleukin 1 beta (IL1 beta) precursor sequence 204-215 recognized the 204-215 peptide as well the entire IL1 beta protein with binding affinities in the micromolar range. Interaction between the complementary pair was characterized by analytical high-performance liquid affinity chromatography on columns derivatized with the computer-generated peptide. Recognition selectivity was clearly shown by the ability of the computer-generated complementary peptide columns to purify the IL1 beta-(204-215)-peptide from complex synthetic mixtures with high yields, independently of the type of solid support used. Recognition specificity was demonstrated by the inability of the IL1 beta-(204-215)-peptide and IL1 beta molecules to interact with blank columns or columns derivatized with other non-related peptides. Furthermore, scrambling the sequence of the computer-generated peptide or the IL1 beta-(204-215)-peptide in such a way as to alter their hydropathic profiles had the effect of abolishing binding. The complementary pair failed to interact in the presence of competing peptide, thus providing further evidence of specificity. Computer-generated complementary peptide affinity columns also proved useful for purification of recombinant human IL1 beta protein directly from crude Escherichia coli lysates.