Resumen de Methods to model and assess protein-dna and protein-protein interactions in the context of gene regulation
The cells in out body are able of having completely different behaviors and shapes, although they contain the same genetic material. Among the mechanisms that allow this diversity we find transcription factors (TFs). TFs are proteins that bind specific DNA sequences in our genome and modulate the expression of nearby genes. The choice of what genes are regulated by a TF is based in the specificity and affinity of a TF for specific DNA sequences. On the other hand, the effect on gene expression, either it is an increase or a decrease, is usually mediated by interactions between the TF and other proteins. In this thesis we are presenting computational tools to study interactions between TF and DNA, and between TFs and other proteins. For TF-DNA interactions we have developed statistical potentials scoring functions and a platform to make structural models for these interactions. By combining these two tools, we have developed a method to predict the DNA binding preferences of TFs. For interactions between TFs and other proteins we have developed a method to model and estimate the affinity of the interaction.
