ArticlePloS one2009
Evidence for the concerted evolution between short linear protein motifs and their flanking regions.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Article
- Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes.Molecular biology and evolution · 2024Article
- In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences.iScience · 2019Article
- Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.Proteomics · 2018Review
- PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.Nucleic acids research · 2018Article
- Functions of intrinsic disorder in transmembrane proteins.Cellular and molecular life sciences : CMLS · 2017Review
- Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution.Nucleic acids research · 2015Article
- Efficient prediction of human protein-protein interactions at a global scale.BMC bioinformatics · 2014Article
- MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation.BMC bioinformatics · 2013Article
- Coupled folding-binding in a hydrophobic/polar protein model: impact of synergistic folding and disordered flanks.Biophysical journal · 2012Article
- Article
- A dynamic view of domain-motif interactions.PLoS computational biology · 2012Article
- Article
- Proline rich motifs as drug targets in immune mediated disorders.International journal of peptides · 2012Article
- Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition.PloS one · 2012Article
- Sequence evolution of the intrinsically disordered and globular domains of a model viral oncoprotein.PloS one · 2012Article
- The sequence, structure and evolutionary features of HOTAIR in mammals.BMC evolutionary biology · 2011Article
- A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions.Proteins · 2011Article
- Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures.PLoS computational biology · 2010Article
- ELM: the status of the 2010 eukaryotic linear motif resource.Nucleic acids research · 2010Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLinear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids.
resultsThe evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co-evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif-mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions.
conclusionThe results suggest that flanking regions are relevant for linear motif-mediated interactions, both at the structural and sequence level. More interestingly, they 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. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network where they arise.
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