DNA-binding proteins (DBP) are the primary molecules regulating the expression of DNA. The goal of this proposal is to develop a model of protein-DNA binding and recognition. A recently solved x-ray crystal structure of the modular, all-helical protein human mitochondrial transcription termination factor-1 (MTERF1)1 shows that it binds the major groove of DNA, making it a prototypical DBP. We hypothesize that three processes drive binding and recognition. First, (i), an open unbound MTERF1 binds B-like DNA. Second, (ii), nonspecific MTERF1-DNA interactions and indirect readout shift the equilibrium to a closed conformation. Nonspecific interactions allow MTERF1 to scan the DNA for its target cognate sequence. Third, (iii), specific MTERF1-DNA interaction, shift the equilibrium to a fully closed conformation: the x-ray crystal structure. Three specifics aims will test our hypothesis and achieve our goal.
In Aim 1, we will model the structure of unbound MTERF1, which has not been crystallized to date.
In Aim 2, we will determine the sequence of events that lead to the protein- DNA interactions that are seen in the MTERF1-DNA crystal structure.
In Aim 3, we will determine the importance of sequence dependent DNA deformability during MTERF1-DNA binding and recognition.
The goal of this proposal is to develop a model of protein-DNA binding and recognition, based on dynamics, structure and energy, so that a more complete understanding of protein-DNA interaction can lead to the broadening our knowledge of the processes of DNA repair, recombination, replication, and transcription. Computational chemistry adds dynamics to the static information obtained in the experimental laboratory, enabling predictions of observables and recommendations for experimental collaborators to be made, which for this proposal will be the prediction of the sequence of events as a model protein, human mitochondrial transcription termination factor-1 (MTERF1), binds its target sequence of DNA. We hypothesize that the protein can extend into a wide-open conformation, use a clamping motion to bind and deform DNA, and that sequence dependent elasticity of DNA during clamping is part of the recognition process.