The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.

Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/.

Contribution of C-tail residues of potato carboxypeptidase inhibitor to the binding to carboxypeptidase A A mutagenesis analysis.

The role of each residue of the potato carboxypeptidase inhibitor (PCI) C-terminal tail, in the interaction with carboxypeptidase A (CPA), has been studied by the analysis of two main kinds of site-directed mutants: the point substitution of each C-terminal residue by glycine and the sequential deletions of the C-terminal residues. The mutant PCI-CPA interactions have been characterized by the measurement of their inhibition constant, Ki, in several cases, by their kinetic association and dissociation constants determined by presteady-state analysis, and by computational approaches. The role of Pro36 appears to be mainly the restriction of the mobility of the PCI C-tail. In addition, and unexpectedly, both Gly35 and Pro36 have been found to be important for folding of the protein core. Val38 has the greatest enthalpic contribution to the PCI-CPA interaction. Although Tyr37 has a minor contribution to the binding energy of the whole inhibitor, it has been found to be essential for the interaction with the enzyme following the cleavage of the C-terminal Gly39 by CPA. The energetic contribution of the PCI secondary binding site has been evaluated to be about half of the total free energy of dissociation of the PCI-CPA complex.

Structural domains of the insulin receptor and IGF receptor required for dimerisation and ligand binding.

We investigated structural requirements for dimerisation and ligand binding of insulin/IGF receptors. Soluble receptor fragments consisting of N-terminal domains (L1/CYS/L2, L1/CYS/L2/F0) or fibronectin domains (F0/F1/F2, F1/F2) were expressed in CHO cells. Fragments containing F0 or F1 domains were secreted as disulphide-linked dimers, and those consisting of L1/CYS/L2 domains as monomers. None of these proteins bound ligand. However, when a peptide of 16 amino acids from the alpha-subunit C-terminus was fused to the C-terminus of L1/CYS/L2, the monomeric insulin and IGF receptor constructs bound their respective ligands with affinity only 10-fold lower than native receptors.

The insulin receptor: from protein sequence to structure.

Sequences of the insulin receptor (IR), the type-I insulin-like growth-factor receptor (IGFR) and the insulin-receptor-related receptor show that they belong to a homologous family but, until recently, have given few clues about their structures. Three repeats of fibronectin type III have been identified close to the membrane. Although the N-terminal L1, Cys-rich and L2 domains of the IGFR have been identified from their sequences and their structures determined by X-ray crystallography, little is known of their relative positions in the complete receptor in vivo. Here, we ask what can be learnt further from the analysis of sequences, about the structure, organization and function of the extracellular regions of the IR family.

A third fibronectin type III domain in the extracellular region of the insulin receptor family.

The insulin receptor family consists of the homologous tyrosine kinase receptors, insulin receptor (IR), insulin-like growth factor 1 receptor (IGF1R) and insulin receptor-related receptor. The three-dimensional structures of the tyrosine kinase domain of the IR and the first three extracellular domains (L1, Cys-rich and L2) of the IGF1R are known. Here we present evidence that the connecting domain of the IR family is a member of the fibronectin type II (FnIII) superfamily. Structure-based alignment of FnIII domains reveals several key residues that are also conserved in the sequence of the connecting domain. The alignment of the connecting domain with FnIII domains is in good agreement with secondary structure prediction. A model of the connecting domain shows a hydrophobic core formed by the conserved residues and is consistent with previously known biochemical data. This suggests that the IR family contains three FnIII domains in tandem in the extracellular juxtamembrane region.