Conformational aspects of biological activity of functional fragments of the p21ras oncoproteins. 4. Address fragments of the receptor oncoproteins

Decapeptide fragments of the scr, fgr, fps, and yes oncoproteins were studied by theoretical conformational analysis, and the arrangement of ionized residues in these fragments was found to be complementary to the binding site of p21. The results demonstrated a similarity in conformational properties of these peptides and their structural complementarity to the address fragment of p21. On the basis of this computation, a model of interaction of the p21ras family of oncoproteins with their cellular receptors was suggested.     

Conformational Aspects of Biological Activity of Functional Fragments of the p21ras Oncoproteins: 3. Fragment 34–46 of the Native Oncoprotein and the Decapeptide Corresponding to Its 35–44 Sequence

Theoretical conformational analysis was used to study the spatial structure of a putative binding site responsible for binding of p21 oncoproteins to other oncoproteins. Conformational properties of the isolated address sequence localized in fragment 34–46 of native p21 and of the decapeptide molecule corresponding to the 35–44 sequence in the primary structure of oncoproteins of this family were revealed. Our calculations demonstrated a similarity between spatial structures of the peptides, which confirms the hypothesis on the identity of their biological functions.     

Conformational aspects of biological activity of functional fragments of the p21ras oncoproteins. 3. Fragment 34-46 of the native oncoprotein and the decapeptide corresponding to its 35-44 sequence

Theoretical conformational analysis was used to study the spatial structure of a putative binding site responsible for binding of p21 oncoproteins to other oncoproteins. Conformational properties of the isolated address sequence localized in fragment 34-46 of native p21 and of the decapeptide molecule corresponding to the 35-44 sequence in the primary structure of oncoproteins of this family were revealed. Our calculations demonstrated a similarity between the spatial structures of the peptides, which confirms the hypothesis on the identity of their biological functions.     

Viral Oncoproteins Discriminate between p53 and the p53 Homolog p73

p73 is a recently identified member of the p53 family. Previously it was shown that p73 can, when overproduced in p53-defective tumor cells, activate p53-responsive promoters and induce apoptosis. In this report we describe the generation of anti-p73 monoclonal antibodies and confirm that two previously described p73 isoforms are produced in mammalian cells. Furthermore, we show that these two isoforms can bind to canonical p53 DNA-binding sites in electrophoretic mobility shift assays. Despite the high degree of similarity between p53 and p73, we found that adenovirus E1B 55K, simian virus 40 T, and human papillomavirus E6 do not physically interact with p73. The observation that viral oncoproteins discriminate between p53 and p73 suggests that the functions of these two proteins may differ under physiological conditions. Furthermore, they suggest that inactivation of p73 may not be required for transformation.     

Human Papillomavirus Oncoproteins E6 and E7 Independently Abrogate the Mitotic Spindle Checkpoint

The E6 and E7 genes of the high-risk human papillomavirus (HPV) types encode oncoproteins, and both act by interfering with the activity of cellular tumor suppressor proteins. E7 proteins act by associating with members of the retinoblastoma family, while E6 increases the turnover of p53. p53 has been implicated as a regulator of both the G₁/S cell cycle checkpoint and the mitotic spindle checkpoint. When fibroblasts from p53 knockout mice are treated with the spindle inhibitor nocodazole, a rereplication of DNA occurs without transit through mitosis. We investigated whether E6 or E7 could induce a similar loss of mitotic checkpoint activity in human keratinocytes. Recombinant retroviruses expressing high-risk E6 alone, E7 alone, and E6 in combination with E7 were used to infect normal human foreskin keratinocytes (HFKs). Established cell lines were treated with nocodazole, stained with propidium iodide, and analyzed for DNA content by flow cytometry. Cells infected with high-risk E6 were found to continue to replicate DNA and accumulated an octaploid (8N) population. Surprisingly, expression of E7 alone was also able to bypass this checkpoint. Cells expressing E7 alone exhibited increased levels of p53, while those expressing E6 had significantly reduced levels. The p53 present in the E7 cells was active, as increased levels of p21 were observed. This suggested that E7 bypassed the mitotic checkpoint by a p53-independent mechanism. The levels of MDM2, a cellular oncoprotein also implicated in control of the mitotic checkpoint, were significantly elevated in the E7 cells compared to the normal HFKs. In E6-expressing cells, the levels of MDM2 were undetectable. It is possible that abrogation of Rb function by E7 or increased expression of MDM2 contributes to the loss of mitotic spindle checkpoint control in the E7 cells. These findings suggest mechanisms by which both HPV oncoproteins contribute to genomic instability at the mitotic checkpoint.     

The effect of amino acid substitutions on the 3-dimensional structure of fragment 1--16 of the oncoprotein p21 ras

Using the method of theoretical conformational analysis, spatial structure of fragment 1-16 of active [( Val12-Gly13], [Asp12-Gly13], [Gly12-Asp13]) and passive [( Gly12-Gly13] and [Pro12-Gly13]) modifications of oncoproteins family p21 ras have been investigated. The activation of these proteins has been shown to be accompanied by reorganization of three-dimensional structure of the polypeptide chain.     

Conformational aspects of the biological action of functional fragments of the p21ras oncoprotein family. 1. Fragments 1-11 and 9-16 of the polypeptide chain]

Using theoretical conformational analysis, spatial structures of the N-terminal undecapeptide, common to all p21 modifications, and of the 9-16 fragments of the protein's active and passive analogues have been investigated. The data obtained reveal an essential differences between the predominant backbone forms of the active and passive modifications of the oncoprotein.     

Hydrolysis of GTP by the alpha-chain of Gs and other GTP binding proteins

The functions of G proteins--like those of bacterial elongation factor (EF) Tu and the 21 kDa ras proteins (p21ras)--depend upon their abilities to bind and hydrolyze GTP and to assume different conformations in GTP- and GDP-bound states. Similarities in function and amino acid sequence indicate that EF-Tu, p21ras, and G protein alpha-chains evolved from a primordial GTP-binding protein. Proteins in all three families appear to share common mechanisms for GTP-dependent conformational change and hydrolysis of bound GTP. Biochemical and molecular genetic studies of the alpha-chain of Gs (alpha s) point to key regions that are involved in GTP-dependent conformational change and in hydrolysis of GTP. Tumorigenic mutations of alpha s in human pituitary tumors inhibit the protein's GTPase activity and cause constitutive elevation of adenylyl cyclase activity. One such mutation replaces a Gln residue in alpha s that corresponds to Gln-61 of p21ras; mutational replacements of this residue in both proteins inhibit their GTPase activities. A second class of GTPase inhibiting mutations in alpha s occurs in the codon for an Arg residue whose covalent modification by cholera toxin also inhibits GTP hydrolysis by alpha s. This Arg residue is located in a domain of alpha s not represented in EF-Tu or p21ras. We propose that this domain constitutes an intrinsic activator of GTP hydrolysis, and that it performs a function analogous to that performed for EF-Tu by the programmed ribosome and for p21ras by the recently discovered GTPase-activating protein.(ABSTRACT TRUNCATED AT 250 WORDS)     

Are p27 and p21 Cytoplasmic Oncoproteins?

By causing cytoplasmic mislocation of p27 and p21, the Akt oncogenic kinase functionally inactivates these nuclear tumor suppressor proteins. Is cytoplasmic localization of p27 and p21 simply equivalent to loss of their function or are new functions acquired in the cytoplasm? Indeed, several lines of evidence suggest that cytoplasmic p27 and p21 may be oncoproteins with antiapoptotic activities.     

Are p27 and p21 cytoplasmic oncoproteins?

By causing cytoplasmic mislocation of p27 and p21, the Akt oncogenic kinase functionally inactivates these nuclear tumor suppressor proteins. Is cytoplasmic localization of p27 and p21 simply equivalent to loss of their function or are new functions acquired in the cytoplasm? Indeed, several lines of evidence suggest that cytoplasmic p27 and p21 may be oncoproteins with antiapoptotic activities.     

The p21(WAF1) cyclin-kinase inhibitor: in vivo interaction with E1A adenoviral Ad2 and Ad12 oncoproteins

The capability of adenoviral oncoproteins E1A Ad2 and Ad12 to form complexes in vivo with cyclin-kinase inhibitor p21Waf1 has been analysed. The published data confirming direct interaction between E1A and p21Waf1 are insufficient. In the present work, a yeast two-hybrid SRS system was used to investigate the binding of different fragments of E1A Ad2 and Ad12 polypeptides with p21Waf1. We have shown that the full length product of 12S mRNA E1A Ad2 interacts weekly with p21Waf1, whereas the protein corresponding to 13S mRNA E1A Ad12 does not bind to cyclin-kinase inhibitor protein. Moreover, fragments 1-80 (Ad2), 1-29 (Ad12), 1-79 (Ad12), and 105-194 (Ad12) were able to interact with p21Waf1 to some extent. The difference between interacting regions of adenoviral proteins E1A Ad2/5 and Ad12 gives a new information about the mechanism of p21Waf1 functional inactivation and different transforming activity of Ad2/5 and Ad12.     

A peptide inhibitor of the binding site of oncoproteins of the p21ras family

The method of theoretical conformational analysis was used to study the inverse structural problem to determine the amino acid sequence of the peptide molecule capable of inhibiting the site of binding of p21 to cell receptors. At the first stage of the computational experiment, the spatial structure and the conformational possibilities of the binding sites of protein p21 and its cellular receptors were determined. Then the three-dimensional structures of several peptides containing the Arg-Ala-Ala-Glu-Asp site were studied. By varying the number of alanine residues in the adjacent regions of the molecule, the sequence H-Asp1-Ala2-Ala3-Ala4-Arg5-Ala6-Ala7-Glu8-Asp9-Ala10-Ala11--Lys12-QH was chosen, which most adequately simulates the conformational properties of the address fragments of oncoprotein receptors. The peptide-molecule having this primary structure is capable of forming a complex with p21, i.e., blocking the binding site of the oncoprotein by preventing the signal transduction from the oncoprotein to the cell, thereby breaking the cycle of the carcinogenic process.     

The Conformational Stability/Lability of Peptide Fragments in the Sequence Context of Amino Acids

Biophysics - Criteria for evaluating the conformational stability/lability of peptide fragments referred to fragments of protein structures are formulated. Using the proposed criteria, a...     

Conformational aspects of the biological effect of functional fragments of the p21ras oncoprotein family. 2. Fragment 1-16, various sequences]

The conformational analysis data on active ([Val12-Gly13], [Asp12-Gly13] and [Gly12-Asp13]) and passive ([Gly12-Gly13] and [Pro12-Gly13]) modifications of the p21ras family oncoproteins are presented. The activating amino acid substitutions are shown to be accompanied by essential changes in the secondary structure, resulted in the 9-16 fragment spiralization. The spatial structure of the 1-9 fragment does not vary for all the predominant forms of the active and passive analogues. The results of the conformational analysis have been used for studying the structural-functional relationships.     

腺病毒E1B 55KD癌蛋白与hDaxx的相互作用

为了探讨腺病毒 (adenovirus,Ad)E1B 5 5kD癌蛋白 (AdE1B 5 5kD)打破hDaxx和PML共定位细胞核的作用机制 ,本文利用体内外共免疫沉淀反应研究AdE1B 5 5kD与hDaxx的结合反应 ,并通过酵母双杂交体系测定两种蛋白质的相互作用及其作用的氨基酸残基序列。结果显示 :Ad2E1B 5 5kD通过C端 5 8个氨基酸 (aa)与hDaxx结合并发生相互作用。Ad12E1B 5 5kD与hDaxx结合需全序列aa及其构象。共免疫沉淀反应和Westernblot结果证实Ad2 / 5或Ad12E1B 5 5kD能在体内外与hDaxx直接结合     

Fragments of bovine insulin-like growth factors I and II stimulate proliferation of rat L6 myoblast cells

The active sites of bovine insulin-like growth factor (IGF) I and II fragments were studied. Overlapping fragments of IGF I (residues 1-25, 11-35, 21-45, 31-55, and 41-70) and of IGF II (residues 1-24, 10-34, 20-44, 30-54, and 40-67) were chemically synthesized. The activity of the fragments was measured by stimulating the proliferation of rat L6 myoblast cells. Two fragments of IGF I (residues 21-45 and 31-55) and two fragments of IGF II (residues 20-44 and 30-54) were active while the other fragments were inactive in stimulating cell proliferation. Although the activity of these fragments was observed only at a high concentration of 0.1 mM, the results imply that the active site is located around residues 31-45 for IGF I fragments and residues 30-44 for IGF II fragments. Consequently, an IGF I fragment (residues 26-50) having a five-residue extension to both the N- and C-terminal sites of residues 31-45 also stimulated the proliferation of L6 myoblast cells. Furthermore, the substitution of Ile-35 in two IGF II fragments (residues 21-45 and 31-55) by Ser inactivated these fragments. This suggests that Ile-35 is an essential residue for IGF II fragment activity. Ser-35, which was reported in the original sequencing of bovine IGF II, is incorrect in the sequence and furthermore has been consistently found to be an Ile-35 in our hands.(ABSTRACT TRUNCATED AT 250 WORDS)     

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments

It has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. Here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. We perform replica exchange molecular dynamics (REMD) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the AMBER 96 force field and the OBC implicit solvent model. To analyze the simulations, we compute various contact-based metrics, such as contact probability, and then apply Bayesian classifier methods to infer which metastable contacts are likely to be native vs. non-native. We find that a simple measure, the observed contact probability, is largely more predictive of a peptide''s native structure in the protein than combinations of metrics or multi-body components. Our best classification model is a logistic regression model that can achieve up to 63% correct classifications for 8-mers, 71% for 12-mers, and 76% for 16-mers. We validate these results on fragments of a protein outside our training set. We conclude that local structure provides information to solve some but not all of the conformational search problem. These results help improve our understanding of folding mechanisms, and have implications for improving physics-based conformational sampling and structure prediction using all-atom molecular simulations.     

Comparison of the conformation and GTP hydrolysing ability of N-terminal ras p21 protein segments

Conformational, GTP binding, and GTP hydrolytic studies are carried out with synthetically prepared N-terminal 34 residue segments (residues 2-35) of p21 ras oncogenic (12-Val) and non-oncogenic (12-Gly) proteins. It was found that these N-terminal regions bind nucleotides through their phosphate groups, and that substitution of valine for glycine produces a more pronounced alpha-helical structure and decreases the conformational flexibility. The glycine containing peptide, when compared to the valine containing analog, catalyses the hydrolysis of GTP 6 times more efficiently. Results suggest that restriction of conformational adaptation may contribute to the transforming capacity of the Val-12 p21 protein.