Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions.

MOTIVATION: The flow of information within cellular pathways largely relies on specific protein-protein interactions. Discovering such interactions that are mostly mediated by peptide recognition modules (PRM) is therefore a fundamental step towards unravelling the complexity of varying pathways. Since peptides can be recognized by more than one PRM and high-throughput experiments are both time consuming and expensive, it would be preferable to narrow down all potential peptide ligands for one specific PRM by a computational method. We at first present Domain Interaction Footprint (DIF) a new approach to predict binding peptides to PRMs merely based on the sequence of the peptides. Second, we show that our method is able to create a multi-classification model that assesses the binding specificity of a given peptide to all examined PRMs at once. RESULTS: We first applied our approach to a previously investigated dataset of different SH3 domains and predicted their appropriate peptide ligands with an exceptionally high accuracy. This result outperforms all recent methods trained on the same dataset. Furthermore, we used our technique to build two multi-classification models (SH3 and PDZ domains) to predict the interaction preference between a peptide and every single domain in the corresponding domain family at once. Predicting the domain specificity most reliably, our proposed approach can be seen as a first step towards a complete multi-domain classification model comprised of all domains of one family. Such a comprehensive domain specificity model would benefit the quest for highly specific peptide ligands interacting solely with the domain of choice. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PGK1 a potential marker for peritoneal dissemination in gastric cancer.

BACKGROUND/AIMS: Peritoneal carcinomatosis, which is caused by the dissemination of cancer cells into the abdominal cavity is a frequent finding in patients with primary gastric cancer, and it is associated with a poor prognosis. The mechanisms that mediate peritoneal carcinomatosis in diffuse primary gastric tumours require definition. METHODS: We therefore compared the gene expression profile in diffuse primary gastric cancer patients with and without peritoneal carcinomatosis (n=13). Human specimens from consecutive gastric cancer patients with and without peritoneal carcinomatosis were investigated using oligonucleotide microarrays. Differentially expressed genes of interest were further evaluated using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS: The results reveal a significant overexpression of phosphoglycerate kinase 1 (PGK1), the chemokine CXCR4 and its ligand CXCL12 in specimens from diffuse gastric cancer patients with peritoneal carcinomatosis. Overexpression of PGK1 is known to increase the expression of CXCR4. CXCR4 on its part can increase CXCL12 expression. Elevated levels of CXCR4 and CXCL12 are associated with an increase in the metastatic rate and play an important role in the metastatic homing of malignant cells. CONCLUSION: The overexpression of PGK1 and its signalling targets may be a expression-pathway in diffuse primary gastric carcinomas promoting peritoneal dissemination and may function as prognostic markers and/or be potential therapeutic targets to prevent the migration of gastric carcinoma cells into the peritoneum.

Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the Shank3 PDZ domain.

Shank is the central scaffolding protein of the postsynaptic density (PSD) protein complex found in cells of the central nervous system. Cellular studies indicate a prominent role of the protein in the organization of the PSD, in the development of neuronal morphology, in neuronal signaling, and in synaptic plasticity, thus linking Shank functions to the molecular basis of learning and memory. Mutations in the Shank gene have been found in several neuronal disorders including mental retardation, typical autism, and Asperger syndrome. Shank is linked to the PSD complex via its PDZ domain that binds to the C-terminus of guanylate-kinase-associated protein (GKAP). Here, small-molecule inhibitors of Shank3 PDZ domain are developed. A fluorescence polarization assay based on an identified high-affinity peptide is established, and tetrahydroquinoline carboxylates are identified as inhibitors of this protein-protein interaction. Chemical synthesis via a hetero-Diels-Alder strategy is employed for hit optimization, and structure-activity relationship studies are performed. Best hits possess K(i) values in the 10 µM range, and binding to the PDZ domain is confirmed by ¹H,¹5N HSQC NMR experiments. One of the hits crystallizes with the Shank3 PDZ domain. The structure, analyzed at a resolution of 1.85 Å, reveals details of the binding mode. Finally, binding to PDZ domains of PSD-95, syntrophin, and DVL3 was studied using ¹H,¹5N HSQC NMR spectroscopy.