Abstract
Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal phenotype. This protocol describes how ancestral protein-protein interaction patterns can be inferred using a set of known protein interactions from phylogenetically informative species. Although this protocol focuses on protein-protein interaction data, character-state reconstructions can in general be performed with other kinds of binary data in the same way.
Keywords: Protein-protein interaction, Phylogeny, Character-state reconstruction, Mesquite, Markov model
Data
Software
Procedure
Representative data
Figure 4. Mirror tree comparing results of character-state reconstruction for homodimerization (left) and heterodimerization (right) of a subfamily of plant transcription factors. Pie charts at internal nodes indicate the probability of the presence (yellow) or absence (black) of an interaction. Hatched circles at terminal positions (e.g. Petunia hybrida PHTM6 on the left tree) and grey circles at internal nodes designate an unknown interaction status.
Acknowledgments
This protocol was adapted from a previously published study (Melzer et al., 2014). This research was supported by a DFG grant to G. T. and R. M. (TH417/5–2). R. M. was supported by a post-doctoral fellowship of the Carl-Zeiss-Foundation.
References
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