Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene.

BACKGROUND: Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD, indicating a potential tumor suppressor function for this gene. The molecular mechanism, however, by which PTPRD renders a tumor suppressor effect in neuroblastoma is unknown. RESULTS: As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. CONCLUSIONS: PTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma.

Differential binding of ICln in platelets to integrin-derived activating and inhibitory peptides.

The capacity of platelets to form a thrombus is mediated by integrin alpha(IIb)beta(3). The cytoplasmic tail of alpha(IIb) contains a highly conserved motif, (989)KVGFFKR(995), which plays a critical role in regulating integrin activation and acts as a recognition site for various intracellular proteins, e.g. CIB1, PP1, ICln and RN181. Previously, we demonstrated that a cell-permeable integrin-derived activating (IDA) peptide, KVGFFKR, induces platelet activation, whereas an integrin-derived inhibitory (IDI) peptide, KVGAAKR, is antithrombotic. To elucidate the molecular mechanism underlying these opposite effects we investigate the affinity of known integrin alpha(IIb) binding proteins for the two immobilized peptides in dependence on the activation state of platelets by means of peptide-affinity chromatography, blotting techniques and protein:peptide docking studies. Our results provide a model for the inhibition of ICln interaction with the integrin in activated platelets by the IDI-peptide. Thus, ICln:IDI-peptide interaction profiles can have a pivotal purpose in the search for consensus pharmacophores specifically inhibiting ICln function in platelets potentially leading to the development of integrin-derived antithrombotic drugs.

fac-Tris(4-amino-benzohydroxamato)iron(III) ethanol solvate.

In the structure of the title compound, [Fe(C(7)H(7)N(2)O(2))(3)]·CH(3)CH(2)OH, the Fe(III) atom is in a distorted octa-hedral O(6) environment with the three hydroxamate O atoms (and the three carbonyl O atoms) arranged in a fac configuration and one of the hydroxamate ligands being puckered. The methyl C atom of the ethanol solvent mol-ecule is disordered over two positions with occupancies of 0.626 (13) and 0.374 (13), respectively. The cocrystallized ethanol mol-ecule is hydrogen bonded to one of the hydroxamate O atoms. O-H⋯O and N-H⋯O inter-actions generate infinite three-dimensional networks along [100], [010] and [001].

CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.

The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database.

Ligand switching in cell-permeable peptides: manipulation of the alpha-integrin signature motif.

A synthetic cell-permeable peptide corresponding to the highly conserved alpha-integrin signature motif, Palmityl-K(989)VGFFKR(995) (Pal-FF), induces integrin activation and aggregation in human platelets. Systematic replacement of the F(992)-F(993) with amino acids of greater or lesser hydrophobicity to create Pal-KVGxxKR peptides demonstrate that hydrophobic amino acids (isoleucine, phenylalanine, tyrosine, tryptophan) are essential for agonist potency. In marked contrast, substitution with small and/or hydrophilic amino acids (glycine, alanine, serine) causes a switch in the biological activity resulting in inhibition of platelet aggregation, adhesion, ADP secretion, and thromboxane synthesis. These substituted, hydrophilic peptides are not true pharmacological antagonists, as they actively induce a phosphotyrosine signaling cascade in platelets. Singly substituted peptides (Pal-AF and Pal-FA) cause preferential retention of pro- or anti-thrombotic properties, respectively. Because the alpha-integrin signature motif is an established docking site for a number of diverse cytoplasmic proteins, we conclude that eliminating critical protein-protein interactions mediated through the hydrophobic amino acids, especially F(993), favors an anti-thrombotic pathway in platelets. Agents derived from the inhibitory peptides described in this study may represent a new therapeutic strategy for anti-platelet or anti-integrin drug development.

Approved drug mimics of short peptide ligands from protein interaction motifs.

Most biological functions are regulated through complex networks of transient protein interactions, and, thus, finding effective ways to modulate them would represent an important step towards defining the next generation of drugs. In this study, we set out to determine if existing approved drugs may represent a good source of compounds from which initial lead inhibitors of protein-protein interactions mediated by short peptide regions may be drawn. Peptide structures were defined in terms of pharmacophores and searched against U.S. Food and Drug Administration (FDA)-approved drugs to identify similar compounds. The top ranking matches (using a score that corrects root-mean-square deviation (rmsd) for the number of matched pharmacophores and for the number of drug rotatable bonds) included a number of nuclear receptor ligands that matched allosterically to the corepressor binding site of peroxisome proliferator-activated receptor alpha (PPARalpha). The top ranking drug matches were docked to the peptide-binding site using AUTODOCK. The majority of the top-ranking matches showed a negative estimated free energy change upon binding that is comparable to, or greater than, that of the original peptide. We conclude that the usage of certain approved drugs may represent a useful strategy in inhibiting specific protein-protein interactions. Such a strategy may benefit from the increased likelihood that developed compounds might have favorable bioactivity and safety profiles in clinical use.

Identification of potential small molecule peptidomimetics similar to motifs in proteins.

Protein-protein interactions are central to most biological processes and represent a large and important class of targets for human therapeutics. Small molecules containing peptide substituents may mimic regions of interacting proteins and inhibit their interactions. We set out to develop efficient methods to screen for similarities between known peptide structures within proteins and small molecules. We developed a method to rank peptide-compound similarities, that is restricted to small linear motifs in proteins, and to compounds containing amino acid substituents. Application to a search of the PubChem database (5.4 million compounds) using all short motifs on accessible surface areas in a nonredundant set of 11 488 peptides from the protein structure database PDB demonstrated the feasibility of the method for high throughput comparisons and the availability of compounds with comparable substituents: over 6 million compound-peptide pairs shared at least three amino acid substituents, approximately 100 000 of which had an rmsd score of less than 1 A. A Z-score function was developed that compares matches of a compound to different instances of the peptide motif in PDB, providing an appropriate scoring function for comparison among peptide-compound similarities involving different numbers of atoms (while simultaneously enriching for similarities that are likely to be more specific for the protein of interest). We applied the method to searches of known short protein motifs against the National Cancer Institute Developmental Therapeutic Program compound database, identifying a known true positive.

Absolute net charge and the biological activity of oligopeptides.

Sequences of human proteins are frequently prepared as synthetic oligopeptides to assess their functional ability to act as compounds modulating pathways involving the parent protein. Our objective was to analyze a set of oligopeptides, to determine if their solubility or activity correlated with features of their primary sequence, or with features of properties inferred from three-dimensional structural models derived by conformational searches. We generated a conformational database for a set of 78 oligopeptides, derived from human proteins, and correlated their 3D structures with solubility and biological assay activity (as measured by platelet activation and inhibition). Parameters of these conformers (frequency of coil, frequency of turns, the degree of packing, and the energy) did not correlate with solubility, which was instead partly predicted by two measures obtained from primary sequence analysis, that is, the hydrophobic moment and the number of charges. The platelet activity of peptides was correlated with a parameter derived from the structural modeling; this was the second virial coefficient (a measure of the tendency for a structure to autoaggregate). This could be explained by an excess among the active peptides of those which had either a large number of positive charges or in some cases a large number of negative charges, with a corresponding deficit of peptides with a mixture of negative and positive charges. We subsequently determined that a panel of 523 commercially available (and biologically active) peptides shared this elevation of absolute net charge: there were significantly lower frequencies of peptides of mixed charges compared to expectations. We conclude that the design of biologically active peptides should consider favoring those with a higher absolute net charge.