Attributes of short linear motifs.
- BiologyMolecular bioSystems
Analysis of curated instances currently available in the Eukaryotic Linear Motif database suggest that functional SLiMs have higher levels of conservation than their surrounding residues, frequently evolve convergently, preferentially occur in disordered regions and often form a secondary structure when bound to their interaction partner.
Local structural disorder imparts plasticity on linear motifs
It is demonstrated that LMs in average are embedded in locally unstructured regions, while their amino acid composition and charge/hydropathy properties exhibit a mixture characteristic of folded and disordered proteins.
Short linear motifs – ex nihilo evolution of protein regulation
- BiologyCell Communication and Signaling
A mechanism of ex nihilo SLiM evolution is proposed – the evolution of a novelSLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence to create a large functional motif space.
A million peptide motifs for the molecular biologist.
- BiologyMolecular cell
Computational prediction of short linear motifs from protein sequences.
- BiologyMethods in molecular biology
This review explores the current knowledge of SLiMs and how it can be applied to the task of predicting them computationally from protein sequences and highlights the importance of correctly modelling evolutionary relationships and the probability of false positive predictions.
Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions
- BiologyPloS one
The results suggest that flanking regions are relevant for linear motif–mediated interactions, both at the structural and sequence level, and indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here.
DILIMOT: discovery of linear motifs in proteins
- BiologyNucleic Acids Res.
DILIMOT (DIscovery of LInear MOTifs), a server for the prediction of these short linear motifs within a set of proteins, finds statistically over-represented motifs likely to be responsible for it.
Classification of protein protein interactions
- Biology, Computer Science
PiType is reported, a method for classifying protein interactions into obligate/non-obligate as well as into SP/ME based exclusively on sequence and network information.
Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks
- BiologyPLoS biology
The approach based on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others that will give molecular insight into protein networks and greatly illuminate cellular processes.
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
- BiologyBMC Bioinformatics
The conservation score improves the prediction of linear motifs, by discarding those matches that are unlikely to be functional because they have not been conserved during the evolution of the protein sequences.
SHOWING 1-10 OF 41 REFERENCES
Intrinsically unstructured proteins and their functions
- BiologyNature Reviews Molecular Cell Biology
Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold, whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.
Discovering novel cis-regulatory motifs using functional networks.
- BiologyGenome research
A new scoring metric was developed and used in motif discovery to predict cis-regulatory motifs in the upstream region of genes, showing that interacting proteins are often coordinated at the level of transcription, even in the absence of obvious coregulation in gene expression data sets.
A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules
A strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests is developed, resulting in a strategy containing 59 highly likely interactions common to both networks.
The natural history of protein domains.
- BiologyAnnual review of biophysics and biomolecular structure
The evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains are discussed, and when and how analysis of domains can be used to understand details of protein function are discussed.
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
- BiologyNucleic Acids Res.
ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryosis proteins, aiming to fill the void in bio informatics tools.
Kinetic studies of protein-protein interactions.
- Biology, ChemistryCurrent opinion in structural biology
Protein Interaction Networks by Proteome Peptide Scanning
- BiologyPLoS biology
This work has developed an approach, named WISE (whole interactome scanning experiment), that permits rapid and reliable identification of the partners of any peptide recognition module by peptide scanning of a proteome, thereby offering a powerful proteomic tool to help completing a full description of the cell interactome.
Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination
This work engineered variants of the actin regulatory protein N-WASP (neuronal Wiskott-Aldrich syndrome protein) in which the “output” domain of N- WASP was recombined with heterologous autoinhibitory “input” domains to facilitate the evolution or engineering of cellular signaling circuits.
SH3 domains: complexity in moderation.
- BiologyJournal of cell science
The SH3 domain is perhaps the best-characterized member of the growing family of protein-interaction modules, and its processes raise important questions about the nature of specificity and the overall logic governing networks of protein interactions.