Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques.

Although the characterization of proteins cannot solely rely upon sequence similarity, it has been widely proved that all-vs-all massive sequence comparisons may be an effective approach and a good basis for the prediction of biochemical functions or for the delineation of common shared properties. The program Cluster-C presented here enables a stand-alone and efficient construction of protein families within whole proteomes. The algorithm, which is based on the detection of cliques, ensures a high level of connectivity within the clusters.

PHYTOPROT: a database of clusters of plant proteins.

All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related proteins. Within each cluster, the sequences have been submitted to pyramidal classification; in the case where two or several subfamilies have been grouped together, the pyramidal tree helps in finding which sequences make the links between subfamilies. In addition, the 'domains' that are common to two or more sequences within a cluster were determined and displayed à la ProDom.

N-myc regulation of type I insulin-like growth factor receptor in a human neuroblastoma cell line.

Insulin-like growth factors I and II (IGF-I and IGF-II) stimulate proliferation and differentiation in many cell types, including cell lines derived from human neuroblastomas. Their effects are mediated via the IGF-I receptor (IGF-IR) that is essential for growth in these cells. Amplification of the N-myc oncogene is a marker for poor prognosis in neuroblastoma development, and it therefore seemed of interest to analyze the relationships that may exist between IGF-IR and N-myc.

Insulin-like growth factor (IGF) binding protein-3 interacts with the type 1 IGF receptor, reducing the affinity of the receptor for its ligand: an alternative mechanism in the regulation of IGF action.

With a view to determining the mechanisms by which insulin-like growth factor binding protein-3 (IGFBP-3) and its proteolytic fragments modulate IGF action, we used a fibroblast cell line to investigate the possibility of an interaction with the type 1 IGF receptor (IGFR-1). In competitive binding experiments, IGFBP-3 was as potent as unlabelled IGF-I in displacing its truncated analogue, 125I-des(1-3)IGF-I, which has weak affinity for IGFBPs, from its binding to the cell surface. None of the proteolytic fragments of IGFBP-3 tested affected this binding.