Molecular models of acidic peptides from pea bud chromatin and seminal plasma. Divalent cations-mediated interaction with DNA

Water-Soluble Nanoparticle Receptors Supramolecularly Coded for Acidic Peptides

Sequence-specific recognition of peptides is of enormous importance to many chemical and biological applications, but has been difficult to achieve due to the minute differences in the side chains of amino acids. Acidic peptides are known to play important roles in cell growth and gene expression. In this work, we report molecularly imprinted micelles coded with molecular recognition information for the acidic and hydrophobic side chains of acidic peptides. The imprinted receptors could distinguish acidic amino acids from other polar and nonpolar amino acids, with dissociation constants of tens of nanomolar for biologically active peptides containing up to 18 amino acids.

A pool of peptides extracted from wheat bud chromatin inhibits tumor cell growth by causing defective DNA synthesis

Background

We previously reported that a pool of low molecular weight peptides can be extracted by alkali treatment of DNA preparations obtained from prokaryotic and eukaryotic cells after intensive deproteinization. This class of peptides, isolated from wheat bud chromatin, induces growth inhibition, DNA damage, G2 checkpoint activation and apoptosis in HeLa cells. In this work we studied their mechanism of action by investigating their ability to interfere with DNA synthesis.

Methods

BrdUrd comet assays were used to detect DNA replication defects during S phase. DNA synthesis, cell proliferation, cell cycle progression and DNA damage response pathway activation were assessed using 3H-thymidine incorporation, DNA flow cytometry and Western blotting, respectively.

Results

BrdUrd labelling close to DNA strand discontinuities (comet tails) detects the number of active replicons. This number was significantly higher in treated cells (compared to controls) from entry until mid S phase, but markedly lower in late S phase, indicating the occurrence of defective DNA synthesis. In mid S phase the treated cells showed less 3H-thymidine incorporation with respect to the controls, which supports an early arrest of DNA synthesis. DNA damage response activation was also shown in both p53-defective HeLa cells and p53-proficient U2OS cells by the detection of the phosphorylated form of H2AX after peptide treatment. These events were accompanied in both cell lines by an increase in p21 levels and, in U2OS cells, of phospho-p53 (Ser15) levels. At 24 h of recovery after peptide treatment the cell cycle phase distribution was similar to that seen in controls and CDK1 kinase accumulation was not detected.

Conclusion

The data reported here show that the antiproliferative effect exhibited by these chromatin peptides results from their ability to induce genomic stress during DNA synthesis. This effect seems to be S-phase specific since surviving cells are able to progress through their normal cell cycle when the peptide fraction is removed from the culture medium. It is likely that the subsequent apoptosis is a consequence of the failed attempt of the tumour cells to repair the DNA damage induced by the peptides.

A class of DNA-binding peptides from wheat bud causes growth inhibition, G2 cell cycle arrest and apoptosis induction in HeLa cells

Background

Deproteinized DNA from eukaryotic and prokaryotic cells still contains a low-molecular weight peptidic fraction which can be dissociated by alkalinization of the medium. This fraction inhibits RNA transcription and tumor cell growth. Removal from DNA of normal cells causes amplification of DNA template activity. This effect is lower or absent in several cancer cell lines. Likewise, the amount of active peptides in cancer cell DNA extracts is lower than in DNA preparation of the corresponding normal cells. Such evidence, and their ubiquitous presence, suggests that they are a regulatory, conserved factor involved in the control of normal cell growth and gene expression.

Results

We report that peptides extracted from wheat bud chromatin induce growth inhibition, G₂ arrest and caspase-dependent apoptosis in HeLa cells. The growth rate is decreased in cells treated during the S phase only and it is accompanied by DNA damage and DNA synthesis inhibition. In G₂ cells, this treatment induces inactivation of the CDK1-cyclin B1 complex and an increase of active chk1 kinase expression.

Conclusion

The data indicate that the chromatin peptidic pool inhibits HeLa cell growth by causing defective DNA replication which, in turn, arrests cell cycle progression to mitosis via G₂ checkpoint pathway activation.

Interaction of DDSDEEN peptide with N-CAM protein. Possible mechanism enhancing neuronal differentiation

DDSDEEN chromatin peptide, after dansylation, was studied for its ability to bind N-CAM protein. The binding causes a quenching of the Dns-peptide fluorescence emission. Dose- and time-dependent binding of Dns-peptide with N-CAM has been shown. Fluorescence quenching is completely lost if the Dns-peptide is subjected to carboxypeptidase digestion. Moreover the undansylated peptide pEDDSDEEN competes with the DnsDDSDEEN peptide for the binding with the N-CAM protein. The Dns-peptide-N-CAM bond has been related to the peptide biological activity probably involved in the promotion of neuronal differentiation. An attempt to recognize a possible N-CAM binding site for Dns-peptide was performed by alignment of N-CAM from various sources with some sequences that have been previously reported as binding sites for the pEDDSDEEN and DDSDEEN peptides. Interestingly, the alignment of N-CAM from various sources with the peptides WHPREGWAL and WFPRWAGQA recognizes on rat and human N-CAM a unique sequence that could be the specific binding site for chromatin peptide: WHSKWYDAK. This sequence is present in fibronectin type-III domain of N-CAM. In addition molecular modeling studies indicate the N-CAM sequence WHSKWYDAK as, probably, the main active site for DnsDDSDEEN (or pEDDSDEEN) peptide ligand. Accordingly the binding experiments show a high affinity between WHSKWYDAK and DnsDDSDEEN peptides.

Synthetic seminal plasma peptide inhibits testosterone production in frog testis in vitro

The role of synthetic seminal plasma peptide, designed using biochemical and mass spectroscopy analyses of native peptides extracted from seminal plasma, was studied in amphibian (Rana esculenta) testicular steroidogenesis. Production of testosterone and prostaglandin F(2alpha) was determined by incubating frog testes with synthetic peptide in vitro. Analysis of the data showed a dose-dependent inhibition of testosterone production (43% at 10(-5) M concentration) without prostaglandin F(2alpha) synthesis being affected. Determination of the peptide activity during the annual R. esculenta reproductive cycle showed inhibition of testosterone production in post-reproductive and recovery periods, suggesting a possible involvement of peptide in gonad steroidogenesis.

Short acidic peptides isolated from wheat sprout chromatin and involved in the control of cell proliferation. Characterization by infrared spectroscopy and mass spectrometry

Low molecular weight peptides were isolated from the chromatin of wheat sprouts. Following gel filtration the peptide fraction shows a sharp inhibiting activity on the growth of HeLa cancer cells. Infrared (IR) spectroscopy and mass spectrometry have been utilized to characterize the wheat sprout peptides in an attempt to recognize the peptide sequence involved in the control of cell growth. The quantitative presence of a peptide with MH+=572 appears proportional to the cell growth inhibition activity. This compound has been subjected to extensive mass spectrometry analysis. The automatic computational analysis of the ions of second, third and fourth generations indicate a peptide sequence, AcHis-Asp-Ser-Glu-, that binds at the C-terminal a molecule of ethanolamine. Moreover, the results show that some sequences of the wheat sprout peptide family are present in the peptide fractions isolated from several other tissues, thus supporting the hypothesis of ubiquitous regulatory peptides.

Aging reversibility: from thymus graft to vegetable extract treatment-- application to cure an age-associated pathology

Neonatal thymus graft and thymus calf extract (TME) in vivo treatment exert similar corrective actions on different mouse age-related alterations. The aim of the present paper is to investigate whether a vegetal extract, wheat sprout extract (WESPRE), could mimic the thymus action on recovering age-related alterations and if this extract can cure an age-associated pathology, the cataract in dogs. Present experiments were carried out by using WESPRE and TME in vivo in old mice to check their ability to recover the altered DNA synthesis in hepatocyte primary cultures. Old mice treated with WESPRE and TME showed a recovery of hepatocyte DNA synthesis levels when compared with the old untreated ones. The increase of DNA and protein contents observed in aged animals is reduced by WESPRE treatments to levels observed in young mice hepatocytes. We measured also WESPRE phosphorylation activity by endogenous kinase: it was from 10 to 40 times higher with respect to wheat seeds. Old dogs were orally treated for a month and the lens opacity analysed before and after the treatment. Results showed a reduction from 25 to 40% of lens opacity. The efficacy of wheat sprouts in the recovery of age-related alterations and in treating age-associated pathologies could be due to the contemporary presence of small regulatory acid peptides, a remarkable level of highly energetic phosphoric radicals and antioxidant molecules, peculiarities that may be, to some extent, related to the aging process regulation.

On peptidede novo sequencing: a new approach

A procedure is presented for the automatic determination of the amino acid sequence of peptides by processing data obtained from mass spectrometry analysis. This is a basic and relevant problem in the field of proteomics. Furthermore, it has an even higher conceptual and applicative interest in peptide research, as well as in other connected fields. The analysis does not rely on known protein databases, but on the computation of all amino acid sequences compatible with the given spectral data. By formulating a mathematical model for such combinatorial problems, the structural limitations of known methods are overcome, and efficient solution algorithms can be developed. The results are very encouraging both from the accuracy and computational points of view.

Synthesis of antioxidants in wheat sprouts

Aqueous and ethanolic extracts from wheat (Triticum aestivum) sprout powder were analyzed to determine its reduction and antioxidant activities. Mean and standard deviation of five independent samples were reported. The results showed that the micromoles of potassium ferricyanide reduced by aqueous and ethanolic extracts corresponding to 1 g of sprout powder (80.6 +/- 11.2 and 9.7 +/- 1.8, respectively) were higher than that reduced by 1 mg of other reducing compounds: ascorbic acid, rutin, quercetin, and reduced gluthatione (4.8 +/- 0.7, 3.8 +/- 1.2, 4.8 +/- 1.7, and 1.6 +/- 0.4, respectively). In addition, the oxygen superoxide scavenging activity performed by sprout extracts (from 1 g of powder) is comparable to that shown by 10 mg of antioxidant pure compounds (rutin and quercetin). Biochemical analysis of the sprout extracts shows that the antioxidant activity is mainly due to reducing glycoside and polyphenolic compounds.

Nutritional relevance of wheat sprouts containing high levels of organic phosphates and antioxidant compounds

Wheat sprouts contain a very high level of organic phosphates and a powerful cocktail of antioxidant molecules. Catalase and peroxidase activity appears very strong. Regarding low-molecular weight antioxidant molecules, TLC and other biochemical analysis show the presence of several classes of antioxidant compounds such as reducing glycosides, polyphenols, and -SH groups. Antioxidant activity has been measured by potassium ferricyanide reduction and by means of superoxide scavenging NBT. It has also been observed that the oral assumption of wheat sprout powder induces in old dogs a significant reduction of senile cataract. These results clearly confirm that the administration of natural antioxidant compounds can prevent or delay senile cataract. Moreover, it is evident that wheat sprout biologically active substances can be at least partially absorbed during the digestion process. Our research is now directed to the recovery of large amounts of wheat sprout biologically active substances that could also be used in the formulation of nutritional complements.

N-CAM expression and localization in PC12 cells modulated by extracellular peptides

The neural cell adhesion molecules (N-CAMs) play an important role in mediating cell-cell interactions in the nervous system. Different isoforms of these membrane proteins are involved in the formation of the neuronal network and in the dynamic phases of neuronal plasticity. We studied the early stages of the pseudo neuronal differentiation of PC12 cells induced by a class of small acidic peptides capable of modulating gene expression in these cells. The data presented here indicate that peptides with specific sequences induce an increase in N-CAM mRNA expression and protein translocation to the plasma membrane to a comparable degree as NGF.

Chromatin-derived acidic peptides modulate catecholamine release in the hypothalamus

We have studied the neuromodulatory effects of three synthetic peptides, structurally related to chromatin-derived acidic peptides (ACPs): ACP-1 (Asp-Asp-Ser-Asp-Glu-Glu-Asn), corresponding to the C-terminal fragment of the largest subunit of eukaryotic RNA polymerase II; a more lipophilic derivative, ACP-2 (Ala-Ile-Ser-Pro-Asp-Asp-Ser-Asp-Glu-Glu-Asn); and its phosphorylated form ACP-3 (Ala-Ile-Ser-Pro-Asp-Asp-Ser(P)-Asp-Glu-Glu-Asn). Rat hypothalamic synaptosomes, loaded with [(3)H]norepinephrine or [(3)H]dopamine, were perfused with the above peptides, both basally and during a depolarizing stimulus. We have found: ACP-1 inhibited both dopamine and norepinephrine release; ACP-2 inhibited dopamine release, without affecting norepinephrine release; ACP-3 was almost ineffective, except for a weak dopamine inhibiting effect only at a higher concentration.

Binding citrate/DNA in presence of divalent cations. Potential mimicry of acidic peptides/DNA interactions

Citric acid whose structure is comparable to that of small acidic peptides, can bind to DNA in the presence of divalent cations (Cu2+, Fe2+, Zn2+, Mg2+). Citrate-DNA interaction occurs also in a cell homogenate and in this experimental model too requires the presence of natural divalent cations. In fact the addition of 2 mM EDTA to cell homogenate strongly decreases the DNA-citrate binding. The results demonstrate that divalent cations can act as bridges between two acidic molecules and that citric acid can mimic the structure of acidic peptides.