TY - JOUR T1 - Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction A1 - van Dijk, Aalt D. J. A1 - Morabito, Giuseppa A1 - Fiers, Martijn A1 - van Ham, Roeland C. H. J. A1 - Angenent, Gerco C. A1 - Immink, Richard G. H. Y1 - 2010/11/24 N2 - Author Summary Proteins are active in complexes and therefore it is of utmost importance to understand their protein-protein interaction patterns. Over the last decade, various large-scale screening methods have been developed and implemented providing insight into interactomes for a number of model species. Despite all these efforts, our knowledge about molecular mechanisms determining interaction specificity and underlying protein network formation is limited. Here, we applied an integrated computational and experimental approach to identify short sequence motifs that determine interaction specificity for members of the large and important MADS domain transcription factor family. We show that the method is able to predict MADS domain transcription factor interaction networks for non-model plant species with a reasonable accuracy. Subsequently performed experiments revealed the possibility to rewire protein-protein interaction networks in a desired manner by generating small dedicated mutations in predicted interaction motifs. Additional bioinformatics analyses led to interesting hypotheses about protein-protein interaction network evolution. All together, these results provide insight in the way protein-protein interaction specificity is laid down in primary protein sequences and open the road towards a better understanding of protein complex formation and the possibility to control this important process. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 6 IS - 11 UR - https://doi.org/10.1371/journal.pcbi.1001017 SP - e1001017 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1001017 ER -