Mutant conformation of p53. Precise epitope mapping using a filamentous phage epitope library

Reproducing the immune response against the Plasmodium vivax merozoite surface protein 1 with mimotopes selected from a phage-displayed peptide library

We have used phage display technology to identify peptides binding D14-3, a monoclonal antibody raised against the M(r) 42,000 C-terminal fragment of Plasmodium vivax merozoite surface protein 1 (PvMSP1). By screening a constrained hexapeptide library, seven independent clones binding D14-3 were isolated. The reactivity of D14-3 for these peptides was lower than for the natural antigen and the antibody binding was strictly associated with the viral context and the peptide conformation. Sequence analysis showed that five of them shared homology with the M(r) 42,000 C-terminal fragment (Pv42) and therefore appears to identify the D14-3 epitope. However, the other two peptides, while related to each other, did not correspond to any sequence in the Pv42 molecules. To evaluate their immunological interest, these phagotopes were injected into mice belonging to Balb/c, IC57BI/6 and Biozzi strains. All animals developed a strong immune response against phage particles but only Biozzi mice produced antibodies cross-reacting with Pv42. All phagotopes in Biozzi mice elicited a specific response against Pv42, even those sharing no sequence similarity with the antigen. Moreover, the avidities of these immune sera and the polyclonal response against Pv42 were comparable, suggesting phagotopes could be used as components of a subunit vaccine based on the C-terminal fragment of MSP1.

A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage

It has been suggested that recombination and shuffling between exons has been a key feature in the evolution of proteins. We propose that this strategy could also be used for the artificial evolution of proteins in bacteria. As a first step, we illustrate the use of a self-splicing group I intron with inserted lox-Cre recombination site to assemble a very large combinatorial repertoire (> 10(11) members) of peptides from two different exons. Each exon comprised a repertoire of 10 random amino acids residues; after splicing, the repertoires were joined together through a central five-residue spacer to give a combinatorial repertoire of 25-residue peptides. The repertoire was displayed on filamentous bacteriophage by fusion to the pIII phage coat protein and selected by binding to several proteins, including beta-glucuronidase. One of the peptides selected against beta-glucuronidase was chemically synthesized and shown to inhibit the enzymatic activity (inhibition constant: 17 nM); by further exon shuffling, an improved inhibitor was isolated (inhibition constant: 7 nM). Not only does this approach provide the means for making very large peptide repertoires, but we anticipate that by introducing constraints in the sequences of the peptides and of the linker, it may be possible to evolve small folded peptides and proteins.

Permissive residues within the minimal epitopes of neutralizing monoclonal antibodies to the V3 loop of HIV-1

Neutralizing monoclonal antibodies (mAb) specific for the third variable (V3) domain of gp120, the HIV-1 surface envelope protein, are mainly isolate specific. We have studied the composition and the permissivity of the minimal epitopes interacting with two of these, the 110-A and 19.26.4 mAb, which are strictly LAI isolate specific. Screening a hexapeptide phage library displayed on the surface of filamentous phage with the 110-A mAb has allowed selection of 49 phage sequences, permitting the definition of a consensus sequence. Based on this sequence, substituted synthetic peptides were prepared and used in binding assays. Our results show that both mAb interact with the same narrow region (316-320) of the V3 domain. The minimal epitope of the 110-A mAb was identified as a five amino acid sequence, Hy x R G p, where Hy represents any non-aromatic hydrophobic amino acid. By contrast, the minimal epitope of the 19.26.4 mAb was identified as x Q Pos G P, where Pos is any positively charged amino acid. Core residues of the epitope, critical for the binding to the mAb (written in uppercase letters), were set apart from permissive amino acid positions that tolerate substitutions (written in lowercase letters). Interestingly, the identified core residues Q2/317 (19.26.4 mAb) and R3/318 (110-A mAb) do not tolerate substitution and correspond to the QR insertion in the V3 domain, characteristic of the LAI isolate as compared to other isolates. This result may explain the strict isolate specificity of most anti-V3 LAI mAb. The two epitopes have totally different patterns of permissivity; thus, the effect of substitutions will differ depending on the mAb involved in the interaction. This suggests that the diversity of the antibody response is high enough to delay the emergence of HIV-1 variants resistant to neutralization by V3-specific antibodies.

Heat shock protein 84 forms a complex with mutant p53 protein predominantly within a cytoplasmic compartment of the cell

Cellular DNA damage results in the increased expression and accumulation of the p53 tumor suppressor protein within the nucleus which leads to cell cycle arrest or apoptosis. In some cases, however, wild-type p53 and some mutant forms of p53 reside in the cytoplasm of cancer cells. To understand the mechanism responsible for its cytoplasmic retention, studies were undertaken to determine if unique proteins form a complex with mutant p53 within the cytoplasm of transformed cells. One protein, with an apparent molecular mass of 92 kDa (p92), was observed to form a complex with a temperature-sensitive mutant p53 (TSp53(Val-135)) in the cytoplasm of transformed rat embryo fibroblasts at the non-permissive temperature. p92 copurified with TSp53(Val-135) on a p53-specific immunoaffinity column and a gel filtration column. The protein was purified to homogeneity and identified as hsp84 by partial amino acid sequence analysis. hsp84 is a member of the hsp90 class of proteins. At the non-permissive temperature, TSp53(Val-135) and hsp84 colocalized in the cytoplasm near the nuclear envelope. At the permissive temperature, TSp53(Val-135) resides in the nucleus and expresses a "wild-type like" conformation. Under these conditions hsp84 continued to reside in the cytoplasm and little or no hsp84 formed a complex with p53. The results suggest that hsp84 binds mutant p53 in a spatial and/or conformation dependent manner.

Conformational effects in the p53 protein of mutations induced during chemical carcinogenesis: molecular dynamic and immunologic analyses

The tumor suppressor gene p53 has been identified as the most frequent target of genetic alterations in human cancers. Vinyl chloride, a known human carcinogen that induces the rare sentinel neoplasm angiosarcoma of the liver, has been associated with specific A-->T transversions at the first base of codons 249 and 255 of the p53 gene. These mutations result in an Arg-->Trp amino acid substitution at residue 249 and an Ile-->Phe amino acid substitution at residue 255 in a highly conserved region in the DNA-binding core domain of the p53 protein. To determine the effects of these substitutions on the three-dimensional structure of the p53 protein, we have performed molecular dynamics calculations on this core domain of the wild-type and the Trp-249 and Phe-255 mutants to compute the average structures of each of the three forms. Comparisons of the computed average structures show that both mutants differ substantially from the wild-type structure in certain common, discrete regions. One of these regions (residues 204-217) contains the epitope for the monoclonal antibody PAb240, which is concealed in the wild-type structure but accessible in both mutant structures. In order to confirm this conformational shift, tumor tissue and serum from vinyl chloride-exposed individuals with angiosarcomas of the liver were examined by immunohistochemistry and enzyme-linked immunosorbent assay. Individuals with tumors that contained the p53 mutations were found to have detectable mutant p53 protein in their tumor tissue and serum, whereas individuals with tumors without mutations and normal controls did not.

Identification of polyclonal serum specificities with phage-display libraries

A random hexapeptide fusion-phage library was screened to isolate phage that bound antibodies in a serum induced by hepatitis B virus surface antigen (HBsAg). Analysis of the isolated phage and comparison of their displayed peptide sequences with the primary sequence of HBsAg revealed areas where three and four amino acid matches accumulated. Differential binding studies of individual phage clones with immune and pre-immune sera identified phage carrying sequences that matched with region 117-122 of HBsAg which may represent a linear epitope or part of a larger antigenic determinant. Synthetic hexapeptides representing this region competed for binding with the matching phage clones.

Identification of the peptides that stimulate the phosphoinositide hydrolysis in lymphocyte cell lines from peptide libraries

Peptides which stimulate the formation of inositol phosphates (InoPs) in lymphocyte cell lines were identified by screening synthetic peptide libraries composed of random sequences of hexapeptides. The peptides containing the consensus sequence XKYX(P/V)M were found to be most active in the phospholipase C (PLC)-mediated formation of InoPs in a human B myeloma cell line, U266. The peptides also stimulated the phosphoinositide hydrolysis and the release of [Ca2+]i in HL60 and U937 cell lines. On the other hand, these peptides showed no effect in the following cell lines: NIH3T3, PC12, Daudi, Sp2, Jurkat, H9, Molt-4, SupT-1, K562, and RBL-2H3. The result suggests the possibility that the peptides may have cell type specificity. Experiments with one of the active peptides, WKYMVM-NH2 showed that its action mimics the effect of AlF4- which is a G-protein activator in the InoPs generation, and pertussis toxin partially blocked the InoPs accumulation and [Ca2+]i release induced by the peptide in the U266 cells. Binding assays with the peptide labeled with 125I showed that U266 cells have a saturable number of binding sites for the peptide. Taken together, these results suggest that the peptides could activate PLC-mediated signal transduction via a pertussis toxin-sensitive G-protein coupled receptor in certain cell types.

Use of specific ELISA for the detection of antibodies directed against p53 protein in patients with hepatocellular carcinoma

AIMS

To analyse the significance of antibodies to p53 protein as a serological marker for changes in p53 gene expression in patients with hepatocellular carcinoma.

METHODS

Thirty eight patients with hepatocellular carcinoma, 19 showing accumulation of p53 protein by immunohistochemistry and 19 having no accumulation, were studied. The presence of anti-p53 was tested using a novel ELISA utilising a recombinant p53 protein as a capture system and verified by western blotting. p53 gene mutations were sought by single strand conformational polymorphism and DNA sequencing analyses.

RESULTS

Of 19 patients with p53 protein accumulation in tumour tissue, 10 (52%) had antibodies to p53 in serum by ELISA. Four patients with p53 negative immunohistochemistry also had detectable anti-p53. Western blot analysis confirmed the specificity of the ELISA positive serum samples. The presence of anti-p53 was independent of serum alpha-fetoprotein and was detected in 50% of small tumours while only 8% were alpha-fetoprotein positive. Mutations affecting exons 5 and 6 seem to be more frequently associated with development of anti-p53, than mutations in exons 7 or 8.

CONCLUSIONS

The ELISA for anti-p53 is a convenient and specific tet for the detection of humoral response to alterations in p53 gene expression and could be of value in the diagnosis and characterisation of patients with hepatocellular carcinoma.

Identification of a decapeptide with the binding reactivity for tumor-associated TAG72 antigen from a phage displayed library

Peptide ligands for tumor-associated TAG72 antigen were identified by screening a large, diverse decapeptide library expressed on the surface of filamentous phages. Fifty-eight clones of phages were selected from the eluates after the third round of biopanning and their DNA inserts were sequenced. A dominant decapeptide HYVSIELPDH (14/58) was found with the binding reactivity for TAG72 antigen in the TAG72-binding ELISA and Western dot blotting. It also showed a preferential binding to colonic adenocarcinomatous cells expressing the TAG72 antigen in the histochemical study. Therefore, this anti-TAG72 decapeptide may be useful in serving as the starting point with regard to further designing peptidomimetics for potential pharmaceuticals.

Comparative evaluation of p53-protein expression and the PCNA and Ki-67 proliferating cell indices in human astrocytomas

Mutations of the p53 gene are one of the most frequent genomic alterations of human tumours of astrocytic lineage. Because the physiological role of this gene is a suppression of cellular proliferation and growth, the overexpression of p53-protein may correlate with the expression of PCNA or Ki-67, established markers of cell proliferation. Paraffin-embedded surgical specimens from 60 human astrocytomas (9 pilocytic tumours, 12 WHO grade II, 9 anaplastic astrocytomas [WHO grade III] and 30 glioblastomas [WHO grade IV]) were stained with anti-PCNA (PC10), anti-p53(DO-7) and anti-Ki-67 antibodies (DAKO). Approximately 40% of all the cases were p53-protein immunopositive (53.3% glioblastomas, 33.3% anaplastic, 41.7% low grade astrocytomas but no pilocytic tumor). Statistical analysis did not reveal statistically significant correlation between p53-immunopositivity and PCNA or Ki-67 labeling indices. The Ki-67- and PCNA LI-s were statistically correlated, and the former better discriminated groups of different grades of malignancy.

Allosteric regulation of the thermostability and DNA binding activity of human p53 by specific interacting proteins. CRC Cell Transformation Group

Conformational stability is a prerequisite for the physiological activity of the tumor suppressor protein p53. p53 protein can be allosterically activated for DNA binding by phosphorylation or through noncovalent interaction with proteins such as DnaK, the Escherichia coli homologue of the heat shock protein Hsp70. We present in vitro evidence for a rapid temperature-dependent change in the conformation and tetrameric nature of wild-type p53 upon incubation at 37 degrees C, which correlates with a permanent loss in DNA binding activity. We show that p53 is allosterically regulated for stabilization of the wild-type conformation and DNA binding activity at 37 degrees C by binding of two classes of ligands to regulatory sites on the N and C terminus of the molecule through which an intrinsic instability of p53 is neutralized. Deletion of the domain conferring instability at the C terminus is sufficient to confer enhanced stability to the total protein. DnaK binding to the C terminus can profoundly protect p53 at 37 degrees C from a temperature-dependent loss of the DNA binding activity but does not renature or activate denatured p53. In contrast, another activator of the DNA binding activity of latent p53, the monoclonal antibody PAb421, which also interacts with the C terminus of the protein, is not able to protect p53 from thermal denaturation. Two monoclonal antibodies to the N terminus of p53, PAb1801 and DO-1, do not activate the latent DNA binding function of p53 but can protect the p53 wild-type conformation at 37 degrees C. Thus, activation of the DNA binding function of p53 is not synonymous with protection from thermal denaturation, and therefore, both of these pathways may be used in cells to control the physiological activity of p53. The protection of p53 conformation from heat denaturation by interacting proteins suggests a novel mechanism by which p53 function could be regulated in vivo.

Identification of epitope recognized by an anti-c-myc monoclonal antibody that cross-reacts with E. coli sigma factor using phage display libraries

BACKGROUND

During the epitope mapping of monoclonal antibodies specific for myc proteins, two E. coli proteins cross-reactive with an anti-c-myc monoclonal antibody (MYC-X-5/1) were identified. One of the proteins is approximately 90 kDa and the other is over 150 kDa in apparent molecular mass. The molecular masses of these cross-reactive proteins suggested that they may be subunits of E. coli RNA polymerase.

OBJECTIVES

We have investigated whether or not the proteins cross-reactive with MYC-X-5/1 are subunits of E. coli RNA polymerase. In addition, we have attempted to determine the epitope of MYC-X-5/1.

STUDY DESIGN

The reactivity of MYC-X-5/1 antibody was tested against highly purified E. coli RNA polymerase holo-enzyme preparations and the cell lysate made from E. coli carrying a multi-copy plasmid with an insert of the rpoD gene, the structural gene for the E. coli sigma subunit. The epitope of MYC-X-5/1 was determined by use of phage display of random peptide libraries.

RESULTS

On immunoblotting assays, MYC-X-5/1 reacted with the 90-kDa protein in the E. coli RNA polymerase preparations and with the 90-kDa protein over-expressed in E. coli carrying the plasmid with the rpoD insert. In addition, we have deduced the epitope of the MYC-X-5/1 antibody to be residues 235-245 of the human c-myc protein. A highly similar sequence to this was also identified in residues 62-72 of the sigma subunit of E. coli RNA polymerase.

CONCLUSION

These data demonstrated that the 90-kDa protein cross-reactive with MYC-X-5/1 is the sigma subunit of E. coli RNA polymerase. Furthermore, this study shows that random peptide libraries displayed on filamentous phage are useful tools for epitope mapping and defining cross-reactivities of monoclonal antibodies.

Early p53 alterations in mouse skin carcinogenesis by UVB radiation: immunohistochemical detection of mutant p53 protein in clusters of preneoplastic epidermal cells

High levels of the p53 protein are immunohistochemically detectable in a majority of human nonmelanoma skin cancers and UVB-induced murine skin tumors. These increased protein levels are often associated with mutations in the conserved domains of the p53 gene. To investigate the timing of the p53 alterations in the process of UVB carcinogenesis, we used a well defined murine model (SKH:HR1 hairless mice) in which the time that tumors appear is predictable from the UVB exposures. The mice were subjected to a series of daily UVB exposures, either for 17 days or for 30 days, which would cause skin tumors to appear around 80 or 30 weeks, respectively. In the epidermis of these mice, we detected clusters of cells showing a strong immunostaining of the p53 protein, as measured with the CM-5 polyclonal antiserum. This cannot be explained by transient accumulation of the normal p53 protein as a physiological response to UVB-induced DNA damage. In single exposure experiments the observed transient CM-5 immunoreactivity lasted for only 3 days and was not clustered, whereas these clusters were still detectable as long as 56 days after 17 days of UVB exposure. In addition, approximately 70% of these patches reacted with the mutant-specific monoclonal antibody PAb240, whereas transiently induced p53-positive cells did not. In line with indicative human data, these experimental results in the hairless mouse model unambiguously demonstrate that constitutive p53 alterations are causally related to chronic UVB exposure and that they are a very early event in the induction of skin cancer by UVB radiation.

The p53 gene and its role in human brain tumors

Mutation of the p53 gene is among the most common lesions in a variety of human tumors, including those of the central nervous system. In most instances, mutation of one p53 allele is followed by loss of the remaining wild-type allele, resulting in cells with a complete absence of functional wild-type p53 protein. However, in some situations, such as at initiation of spontaneously arising gliomas or as the germline configuration of patients with the Li-Fraumeni syndrome, cells clearly carry both wild-type and mutant p53 alleles. These observations lead to the hypothesis that p53 mutations can give rise to loss of tumor suppressor functions as well as to gain of oncogenic transformation capabilities. In this review, we define the types of mutations that occur in the p53 gene in various glial tumors, contrast that with the spectra described in other human tumor types, and discuss the biochemistry and physiology of the p53 protein and its ability to regulate and be regulated by other gene products. We use this information to propose roles for p53 in the initiation and progression of human gliomas.

Phage display

Phage display is a powerful method for the selection and evolution of proteins and peptides. Applications include the generation of potent and novel antibodies, the in vitro improvement of protein affinity and function, epitope discovery, the development of leads for vaccine research and the identification of interacting proteins using cDNA libraries.

Levels of p53 antigen in the plasma of patients with adenomas and carcinomas of the colon

Plasma levels of p53 protein were examined by an enzyme linked immunosorbent assay in 184 patients enrolled in a colonoscopy study. The mean levels among 47 individuals with normal colonoscopic examinations and no prior history of colonic neoplasia (0.12 ng/ml) and among 61 individuals with normal colonoscopic examinations and a prior history of colonic neoplasia (0.09 ng/ml) were similar. However, the mean levels among 54 individuals with newly diagnosed colonic adenomas (0.44 ng/ml) and 22 individuals with newly diagnosed colonic carcinomas (0.55 ng/ml) were statistically significantly elevated compared to the normal controls (P < 0.02). Among these tumor patients, the plasma levels tended to increase with increasing adenoma size and with increasing carcinoma stage, although these trends were not statistically significant. Defining a significant positive plasma level as any value greater than ten times background, the percentage of positive samples increased from 4% in the controls to 20% in the adenoma cases to 32% in the carcinoma cases. These results demonstrate that plasma p53 protein levels are elevated in a subgroup of individuals with colonic neoplasia.

The usage of oligopeptides in proteins correlates negatively with molecular weight

We scanned the Swissprot databank to study the distribution of oligopeptides in sequenced proteins. We observed that in 7839,000 amino acids in the bank, the frequency is strongly and negatively correlated with molecular weight. The correlation coefficient is -0.63 for single amino acids, -0.58 for dipeptides, -0.54 for tri- and -0.46 for tetrapeptides. In subsets of proteins of man, mouse, rat drosophila, yeast and E. coli, the correlations were very similar to those for the total database. The intensity of the correlation diminishes linearly with the length of the peptide. We attributed the loss of dominance of molecular weight in determining the frequency of oligopeptides of higher order, to the emergence of function in longer oligopeptides. In the case of dipeptides, we observed that those composed of the same amino acid are in great excess in comparison with their expectation. The WW dipeptide is singular, in the sense that is observed/expected ratio is 13.5 standard deviations above the average ratio.

Accumulation of wild-type p53 in meningiomas

The p53 tumour suppressor gene contributes to the regulation of DNA repair and the initiation of apoptosis. Mutations of this gene and nuclear accumulation of its protein product are features of a large variety of tumours. A histological spectrum of meningiomas, including anaplastic examples and a meningosarcoma, was analysed for accumulation of the p53 protein and mutations in exons 4-9 of the p53 gene. No mutations were found, but 9/34 (26%) tumours showed accumulation of the p53 protein. The p53-positive meningiomas came from across the histological spectrum and were not restricted to the anaplastic group. The accumulation of wild-type p53 in a proportion of meningiomas may reflect this gene's role in DNA repair, or its enhanced stability when bound to cellular proteins such as the mdm-2 gene product.

Protein-protein interactions: methods for detection and analysis

The function and activity of a protein are often modulated by other proteins with which it interacts. This review is intended as a practical guide to the analysis of such protein-protein interactions. We discuss biochemical methods such as protein affinity chromatography, affinity blotting, coimmunoprecipitation, and cross-linking; molecular biological methods such as protein probing, the two-hybrid system, and phage display: and genetic methods such as the isolation of extragenic suppressors, synthetic mutants, and unlinked noncomplementing mutants. We next describe how binding affinities can be evaluated by techniques including protein affinity chromatography, sedimentation, gel filtration, fluorescence methods, solid-phase sampling of equilibrium solutions, and surface plasmon resonance. Finally, three examples of well-characterized domains involved in multiple protein-protein interactions are examined. The emphasis of the discussion is on variations in the approaches, concerns in evaluating the results, and advantages and disadvantages of the techniques.

Screening a monoclonal antibody with a fusion-phage display library shows a discontinuity in a linear epitope within PreS1 of hepatitis B virus

The epitope recognized by the monoclonal antibody MA18/7, specific for the PreS1-domain of the hepatitis B virus surface antigen, has been defined precisely by means of a library of fusion-phage carrying random hexapeptides on the tip of filamentous phage fd particles. Phage, isolated after only one round of affinity selection, displayed hexapeptides showing strong conservation of the PreS1 primary sequence in the region 19-23 with three noncontiguous residues, DP (20 and 21) and F (23) appearing in phage that bound the antibody. The importance of these core residues was supported by comparing the antibody binding of individual phage in solution, which provided relative dissociation constants for these interactions. Replacement of F (23) by Y was the only substitution observed in the three core residues, and resulted in somewhat weaker binding. Synthetic tetra- and hexapeptides containing these key residues inhibited the reaction between the phage and the antibody.

Binding epitope of somatostatin defined by phage-displayed peptide libraries

We have developed a versatile phagemid system to display peptides on the surface of M13 bacteriophage at a copy number which approaches monovalency. In this system, a phagemid encodes a peptide fused to the amino-terminus of the second domain (dII) of the minor coat protein pIII under control of the inducible lac promoter. The fusion protein is displayed in combination with several copies of wild-type pIII on the surface of phage. Two diverse random octapeptide libraries, one linear and one which contained flanking cysteines capable of forming disulfide bridges, were were generated using an in vitro mutagenesis approach and affinity selected on an anti-somatostatin mAb. Peptides with high affinity for the mAb were enriched only from the cyclic library and the tetrapeptide, FWKT, was identified by consensus as the binding epitope. The selected peptides exhibited not only the primary amino acid sequence but also shared structural features with somatostatin. One peptide, CRFWKTWC, also exhibited nanomolar affinities for the five known somatostatin receptor subtypes. This system can easily be adapted to display individual peptides or a wide range of custom peptide libraries.

Temperature sensitivity for conformation is an intrinsic property of wild-type p53

The tumour-suppressor protein p53 is a metal-binding transcription factor with sequence-specific DNA-binding capacity. In cancer, mutation of p53 disrupts protein conformation with consequent loss of DNA binding and associated tumour-suppressor function. In vitro, the conformation and DNA-binding activity of wild-type p53 are subject to redox modulation and are abrogated by exposure to metal chelators. In the present study, we have used the chelator 1, 10-phenanthroline (OP) to probe the effect of temperature on the conformational stability of p53 translated in vitro. Whereas low temperature (30 degrees C) stabilised wild-type p53 conformation and protected against chelation, high temperature (41 degrees C) promoted destabilisation and enhanced chelation, indicating that temperature influences the folding of wild-type p53. Destabilisation of p53 tertiary structure induced protein aggregation through hydrophobic interactions, consistent with the notion that wild-type p53 contains a hydrophobic core which may become exposed by metal chelation. These results indicate that temperature sensitivity for conformation is an intrinsic property of wild-type p53 and suggests that small changes in temperature may directly affect p53 function.

Identification of biologically active peptides using random libraries displayed on phage

The construction of new and increasingly diverse libraries, as well as the implementation of more powerful selection schemes, has led to the identification of linear peptides that mimic complex epitopes. Phage display techniques are allowing the selection of disease-related peptides, which reproduce the antigenic and immunogenic properties of natural antigens, using whole sera from patients. The range of applications of phage technology has been extended to include the search for peptides binding to molecules other than antibodies, such as cell receptors and enzymes.

Mutation and expression of TP53 in malignant melanomas

Mutations of the TP53 gene are the most common genetic alterations in human malignancies. Overexpression of the p53 protein has been reported in high frequencies in all types of skin cancer. To determine the role of TP53 in the pathogenesis of malignant melanoma, we investigated the expression of p53 in 12 cell lines and 145 primary and metastatic lesions by immunohistochemistry. Overexpression of p53 was predominantly detected in the cytoplasm of the cells in 96 (66%) tumor and 12 (93%) cell lines. In contrast to findings in other tumor types, in melanomas immunoreactive cells were found in clusters or as scattered single cells. In primary melanomas, the frequency of p53 overexpression did not correlate with tumor thickness. Nucleotide sequencing of TP53 genes of 24 melanoma tumors/cell lines demonstrated point mutations in seven samples, all coding for mutant p53 protein species. The frequency of TP53 alterations of 20%-30% is lower than in other skin tumor types. Notably, immunohistochemistry was not a suitable method to distinguish overexpression of wild-type p53 from mutant species, since cell lines/tumors with TP53 mutations did not show distinctive staining patterns. The mutation pattern in six out of seven lesions was similar to that caused by ultraviolet light damage. This finding may be regarded a further indication for a pathogenetic role of UV light damage in at least a subgroup of malignant melanomas.

Giant leap for p53, small step for drug design

We review the findings of Cho et al. on the crystal structure of a p53 tumor suppressor-DNA complex. The core DNA binding domain of p53 folds into a structure termed a beta-sandwich, which organizes two loops and a loop-sheet-helix structure on one surface of p53 to interact with the consensus DNA recognition sequence of p53. These structures help to explain the functions of wild-type p53 and the effects of tumor-associated mutations on p53 DNA binding, transactivation and suppression of cellular proliferation.

Tumor suppressor p53 mutations and breast cancer: a critical analysis

Alterations in the tumor suppressor gene p53 are the most commonly identified changes in cancer, including neoplasia of the breast. The activity of p53 is regulated post-translationally. Phosphorylation state, subcellular localization, and interaction with any of a number of cellular proteins are likely to influence the function of p53. The exact effect of p53-mediated growth suppression seems to be cell-type specific but appears to be directly related to the ability of p53 to act as a specific transcriptional activator. The role that transcriptional repression plays in the function of WT p53 is less clear. It is also possible that p53 has a more direct activity in DNA replication and repair. Most documented p53 mutations result in single amino acid substitutions which may confer one or more of a spectrum of transforming abilities on the protein. Mutation may lead to nuclear accumulation of p53 protein; however, inactivation of p53 by nuclear exclusion and interaction with the mdm2 protein also appear to be important in tumorigenesis. Used in conjunction with other established factors, accumulation of cellular p53 may be a useful prognostic indicator in breast cancer. A syngeneic mouse model system yielded evidence that p53 mutations are important in the early, preneoplastic stages of mammary tumorigenesis. This murine system may provide the ability to investigate the functions of p53 in the early stages of breast cancer which are technically difficult to examine in the human system.

Identification of the core residues of the epitope of a monoclonal antibody raised against glycoprotein D of herpes simplex virus type 1 by screening of a random peptide library

Random peptide libraries (RPL) displayed on the surface of a filamentous bacteriophage can be used to identify peptide ligands that interact with target molecules. We have used a 15-amino acid residue RPL displayed on bacteriophage M13 to identify the core residues within the epitope of a monoclonal antibody (mAb) A16 which interacts with a continuous epitope restricted to amino acid residues 9 to 19 in the N-terminal region of glycoprotein D of herpes simplex virus type 1 (gD-1). The single peptide sequence obtained after three rounds of selection contained identical residues at three positions compared to the authentic gD-1 sequence. Synthetic peptides were prepared based on the sequence of the original epitope and the phage-derived epitope. The binding constants (Ka) with mAb A16 were determined using surface plasmon resonance (SPR) biosensor technology. The RPL-derived peptide and peptide 9-19 of gD-1 had approximately the same affinity for mAb A16. This suggests that those residues within the epitope that are essential for binding were identified. The synthesis of shorter versions of the RPL-derived peptide restricted the binding region to seven amino acid residues. These results show that minimal information retrieved from the screening of an RPL combined with peptide synthesis can characterize the epitope of an mAb with high resolution. Immunization of mice with the phage-derived peptide protected against a challenge with a lethal dose of herpes simplex virus type 1 equally well as the gD-1 derived peptide.

The characterisation of p53 binding phage isolated from phage peptide display libraries

Peptide phage display libraries were screened for peptides that bind to the tumour suppressor protein, human p53. Three p53 binding peptides were isolated respectively from hexamer (6-mer), dodecamer (12-mer) and icosomer (20-mer) libraries. We have characterised their interaction with p53 in detail. The phage appear to bind regions on native p53 common between mouse and man. Two conformation-specific anti-p53 monoclonal antibodies were used to dissect the phage-p53 interaction, the phage were found to preferentially bind the PAb1620-p53 conformation rather than the PAb240-p53 conformation. Mapping experiments indicated the C-terminal 30 amino acid residues of p53 were dispensable for phage binding and that the binding of SV40 large T-antigen and the phage were not mutually exclusive. Interestingly the phage were seen to exhibit differential binding to wild-type human p53 over the two point mutant p53 proteins, His175 and Trp248. Ultimately the phage appear to selectively target native wild-type p53, mimicking the specificity of SV40 large T-antigen. The ability to target specific sub-populations of p53 could be an important step in the development of therapeutics for the treatment of p53-based human malignancy.

Analysis of idiotope structure of ovarian cancer antibodies: recognition of the same epitope by two monoclonal antibodies differing mainly in their heavy chain variable sequences

Two MoAbs, independently raised against ovarian carcinoma cells and referred to as OV-TL3 and OV-TL16, display an identical reaction pattern with a membrane-associated protein in both normal and malignant ovarian cells. Also, a similar binding affinity constant and a similar number of binding sites per cell indicate that both MoAbs bind to the same antigen. Competition assays reveal that OV-TL16 is able to compete with OV-TL3 for binding to OVCAR-3 cells. Epitope mapping using a filamentous phage hexapeptide epitope library showed that both MoAbs are able to select identical phages, suggesting that their epitopes are identical or at least overlapping. However, purified polyclonal and monoclonal anti-idiotypic antibodies directed against OV-TL3 failed to recognize the OV-TL16 idiotype, indicating that the structure of the antigen-binding regions of both antibodies is distinct. This was corroborated by molecular cloning and sequencing of the variable heavy (VH) and light (VL) chain immunoglobulin regions of both MoAbs. The VH regions of both antibodies were found to be distinct, whereas the VL regions are almost identical. Computer modelling of the idiotypes suggests that the complementarity determining regions (CDR), with the exception of VHCDR3, have (almost) identical spatial configurations. Our data indicate that, although structurally different in their VH regions, OV-TL3 and OV-TL16 are able to bind to identical epitopic regions on the antigen, because differences in primary structure do not exclude the formation of sufficient and similar spatial structures for the interaction with an epitope.

Allosteric activation of latent p53 tetramers

BACKGROUND

The DNA-binding activity of p53 is essential to its function as a tumour suppressor. Point mutations that abolish this activity have been found to occur frequently in the p53 genes of human cancer cells. Wild-type p53 protein assembles into oligomers with latent DNA-binding activity that can be activated in vitro by phosphorylation of a carboxy-terminal regulatory region, catalyzed by protein kinase C or casein kinase II. We have investigated the mechanism underlying this post-translational regulation of p53. Specifically, we have asked the following questions. First, whether the carboxy-terminal regulatory site contributes to p53's ability to form tetramers. Second, whether the latent DNA-binding activity of p53 can be activated in vivo. And third, whether the activation of p53 is reversible.

RESULTS

Biophysical molecular-sizing analysis shows that both latent and activated forms of p53 are tetramers. Using a novel method, we have further established that p53 remains tetrameric when bound to DNA. We have also found that p53 can indeed be activated in vivo: p53 prepared from cells can be separated into activated and latent forms. Finally, we generated a monoclonal antibody specific for the casein kinase II target site in the carboxy-terminal regulatory region of p53, and used it to demonstrate the allosteric inhibition of in vitro and in vivo activated forms of p53.

CONCLUSIONS

p53 protein assembles naturally as a tetramer that can be converted between latent and activated forms by a concerted, allosteric transition. The highly purified, reconstituted system that we have developed, in which the DNA-binding activity of p53 can be reversibly regulated, should facilitate the discovery of agents that can modulate the DNA-binding activity of p53--particularly those that can activate mutant p53 proteins and that may have potential in the design of anti-cancer drugs.

Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations

Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues 102-292), and they result in loss of DNA binding. The crystal structure of a complex containing the core domain of human p53 and a DNA binding site has been determined at 2.2 angstroms resolution and refined to a crystallographic R factor of 20.5 percent. The core domain structure consists of a beta sandwich that serves as a scaffold for two large loops and a loop-sheet-helix motif. The two loops, which are held together in part by a tetrahedrally coordinated zinc atom, and the loop-sheet-helix motif form the DNA binding surface of p53. Residues from the loop-sheet-helix motif interact in the major groove of the DNA, while an arginine from one of the two large loops interacts in the minor groove. The loops and the loop-sheet-helix motif consist of the conserved regions of the core domain and contain the majority of the p53 mutations identified in tumors. The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it.

Loss of cell cycle controls in apoptotic lymphoblasts of the bursa of Fabricius

Lymphoblasts of the normal embryonic follicles of the chicken bursa of Fabricius undergo rapid apoptosis when exposed to gamma-radiation or when cell-cell contacts are disrupted by mechanical dispersion in short term culture. We have observed previously that overexpression of v-myc sensitizes preneoplastic bursal lymphoblasts to induction of cell death, whereas resistance to induced cell death is acquired during progression to neoplasia. In this study we observed extensive DNA degradation in the large majority of the lymphoblast population within the first hour after dispersion-induced apoptosis. Paradoxically these cells continued to progress into S-phase with the bulk of DNA cleavage and death occurring in S-phase cells (i.e., in cells with more than 2C and less than 4C DNA content). We confirmed the S phase status of apoptotic cells by determining that detection of nuclear cyclin A in individual cells also corresponded with detection of DNA breakage. Levels of cyclin E, cyclin E-dependent H1 histone kinase, and p53 proteins were maintained during dispersion-induced DNA cleavage. gamma-radiation failed either to inhibit cell cycle progression or to raise p53 levels in dispersed bursal lymphoblasts. In intact bursal follicles low doses of gamma-radiation induced p53 whereas higher, apoptosis-inducing doses failed to induce p53 or prevent G1 to S-phase progression. These results suggest that normal DNA damage-induced cell cycle checkpoint controls are lost or overridden when apoptosis is induced in bursal lymphoblasts.

Conformational change of p53 protein in growth factor-stimulated human myelogenous leukemia cells

Frequent point mutations of the p53 tumor suppressor gene have been detected in solid tumors but not in acute myelogenous leukemia (AML). The inactivation of the suppressor function of the p53 protein in AML cells may be achieved through the acquisition of a mutant-like conformation. We provide evidence in this report that the p53 protein in AML cells switches to a mutant-like conformation in response to growth factor stimulation, and we propose that the conformation of p53 protein is one of the molecular mechanisms in determining whether the cells proliferate or enter apoptosis. We also show that wild-type p53 with mutant-like conformation is not equivalent to mutant p53 in their stability, which is consistent with the fact they have very different biological activities in the cells.

Epitope discovery using peptide libraries displayed on phage

Peptides displayed on phage, which mimic continuous and discontinuous epitopes, can be selected using purified antibodies or preparations of polyclonal serum. This review describes recent advances in this field, discusses the application of phage-display technology to the diagnosis of human diseases, and presents new ideas for the preparation of vaccines directed against specific epitopes on a pathogen.

A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera

A strategy to identify disease-specific epitopes from phage-displayed random peptide libraries using human sera is described. Peptides on phage (phagotopes) that react with antibodies present in patient sera are purified from > 10(7) different sequences by affinity selection and immunological screening of plaques. Disease-specific phagotopes can be identified out of this pool through an 'antigen independent' procedure which avails itself only of patient and normal human sera. Using this strategy, we have selected antigenic mimics (mimotopes) of two different epitopes from the human hepatitis B virus envelope protein (HBsAg). We could show that a humoral response to these mimotopes is widespread in the immunized population, suggesting that the strategy identifies phagotopes that have a potential role as diagnostic reagents. Immunization of mice with the selected phagotopes elicited a strong specific response against the HBsAg. These results open new inroads into disease-related epitope discovery and provide the potential for vaccine development without a requirement for the use of, or even information about, the aetiological agent or its antigens.

Endogenous p53 protein generated from wild-type alternatively spliced p53 RNA in mouse epidermal cells

We previously demonstrated that a wild-type alternatively spliced p53 (p53as) RNA exists in mouse cultured cells and normal mouse tissues at approximately 25 to 33% of the level of the major p53 RNA form. The alternative RNA transcript is 96 nucleotides longer than the major transcript as a result of alternative splicing of intron 10 sequences. The protein expected to be generated from the p53as transcript is 9 amino acids shorter than the major p53 protein and has 17 different amino acids at the carboxyl terminus. We report here that p53as protein exists in nontransformed and malignant epidermal cells and is localized to the nucleus. In addition, p53as protein is preferentially expressed during the G2 phase of the cell cycle and in cells with greater than G2 DNA content compared with the major p53 protein, which is preferentially expressed in G1. The p53as immunoreactivity is elevated and shifted to the G1 phase of the cell cycle following actinomycin D treatment of nontransformed cells but not malignant cells. In view of the dimerization and tetramerization of p53 protein which may be necessary for its DNA binding and transcriptional activation activities, the presence of p53as protein in cells has important implications for understanding the physiological function(s) of the p53 gene.

Endogenous p53 protein generated from wild-type alternatively spliced p53 RNA in mouse epidermal cells

We previously demonstrated that a wild-type alternatively spliced p53 (p53as) RNA exists in mouse cultured cells and normal mouse tissues at approximately 25 to 33% of the level of the major p53 RNA form. The alternative RNA transcript is 96 nucleotides longer than the major transcript as a result of alternative splicing of intron 10 sequences. The protein expected to be generated from the p53as transcript is 9 amino acids shorter than the major p53 protein and has 17 different amino acids at the carboxyl terminus. We report here that p53as protein exists in nontransformed and malignant epidermal cells and is localized to the nucleus. In addition, p53as protein is preferentially expressed during the G2 phase of the cell cycle and in cells with greater than G2 DNA content compared with the major p53 protein, which is preferentially expressed in G1. The p53as immunoreactivity is elevated and shifted to the G1 phase of the cell cycle following actinomycin D treatment of nontransformed cells but not malignant cells. In view of the dimerization and tetramerization of p53 protein which may be necessary for its DNA binding and transcriptional activation activities, the presence of p53as protein in cells has important implications for understanding the physiological function(s) of the p53 gene.

Random peptide libraries

Over the past year, great strides have been made in the design of peptide libraries, and new approaches have been developed for identifying peptide ligands. The libraries comprise large collections of peptides, ranging from 1 million to 1 billion different sequences, which can be screened using monoclonal and polyclonal antibodies, receptors, enzymes or other target molecules. The power of this technology stems from the chemical diversity of the amino acids coupled with the large number of sequences in a library. As such, peptide libraries may be useful for finding ligands that can serve as leads for pharmaceutical development and other purposes.

A monoclonal antibody epitope on keratin 8 identified using a phage peptide library

A bacteriophage random hexapeptide library was used to define the epitope of a monoclonal anti-keratin antibody. Phage selected by the keratin 8-specific antibody LE41 displayed highly related sequences on their pIII coat protein. The consensus sequence S(X)LNP allowed the precise localization of an LE41 epitope (SLLSP) within the head domain (H1 subdomain) of human keratin 8, known to be important for correct filament polymerisation. By sequencing the immunizing antigen, keratin 8 from Potorous tridactylis, it was shown that the natural epitope of LE41 is the pentapeptide SLLNP, which confirmed predictions from the phage library results. An SLL(X)P motif is found in the H1 region of all type II keratins (keratins 1 to 8) in different species, but mutational analysis revealed that LE41 can only bind to keratin 8 when Asn (N) or Ser (S) is found in the (X) position. Thus the monoclonal antibody LE41 retains its specificity for keratin 8, dependent on a single amino acid residue, even though it recognizes an epitope within the highly conserved H1 subdomain of the head region. Six other monoclonal antibodies tested on the phage library failed to select motifs.

Identification of a hexapeptide that mimics a conformation-dependent binding site of acetylcholine receptor by use of a phage-epitope library

Monoclonal antibody (mAb) 5.5 is directed against the ligand-binding site of the nicotinic acetylcholine receptor. The epitope for this antibody is conformation-dependent, and the antibody does not react with synthetic peptides derived from the receptor sequence. We have identified a ligand peptide that mimics this conformation-dependent epitope from a phage-epitope library composed of filamentous phage displaying random hexapeptides. Among 38 positive phage clones, individually selected from the library, 34 positive clones carried the sequence Asp-Leu-Val-Trp-Leu-Leu (DLVWLL), 1 positive clone had the sequence Asp-Ile-Val-Trp-Leu-Leu (DIVWLL), and 3 positive clones expressed the sequence Leu-Ile-Glu-Trp-Leu-Leu (LIEWLL), none of which are significantly homologous with the nicotinic acetylcholine receptor alpha subunit sequence. All of these phages bind specifically to mAb 5.5. The synthetic peptide DLVWLL inhibits binding of mAb 5.5 to the related peptide-presenting phage and to the nicotinic acetylcholine receptor in a concentration-dependent manner; the IC50 value is of the order of 10(-4) M. Bioactivity of the peptide "mimotope" DLVWLL was demonstrated in vivo in hatched chickens by inhibition of the mAb 5.5 effect by the peptide. The neuromuscular block and myasthenia gravis-like symptoms that are induced in chicken by passive transfer of mAb 5.5 were specifically abolished by DLVWLL. This study shows the potential of a random peptide phage-epitope library for selecting a mimotope for an antibody that recognizes a folded form of the protein, where peptides from the linear amino acid sequence of the protein are not applicable.

Recent advances in phage display

The selection of peptides and proteins from libraries expressed on the surface of filamentous phage is becoming an important tool in biotechnology. Recent developments have shown that peptides can be selected to bind receptors and antibodies, while semisynthetic antibodies can be selected to bind almost any target. Phage display has allowed the routine isolation of therapeutically interesting human antibodies. Phage are also being utilized to examine the specificities of natural enzymes as well as to evolve novel enzymes de novo.