Team:UIOWA/Model
Modeling
Protein modeling
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Lys-family regulator proteins are transcription factors that respond to small molecule effectors to regulate downstream genes. We modeled the MmsR and HpdR Lys-family regulator proteins to predict the regions in the protein that bind 3-hydroxypropionic (3-HP). The modelling was done in two parts. First, we identified homologous amino acid sequences to MmsR and HpdR proteins using the program BLASTp. This program uses a residue substitution matrix to find the rate of change of one amino acid in a sequence relative to other amino acids. Using Clustal-Omega, we identified regions in the protein that had high conservation.
Designed process
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The second part was generation of the structural model. We used the PHYRE2 protein fold recognition server to build a homology model of the MmsR or HpdR proteins based on previously determined structures of related Lys-family regulator proteins. The models were found to be reliable according to PHYRE2 metrics. Next, we used the program PyMol (Schrödinger) to visualize the model.
Results:
The model below shows the DNA binding domain (red) and the effector domain (green). 3-HP is predicted to bind in the effector domain.
Next, we focused on the predicted 3-HP binding domain. We painted the conserved residues onto the effector domain model (blue, 35% similarity and red, 55% similarity). The cleft with blue residues is one potential 3-HP binding site.
Rotation of the effector domain by 180◦ in the vertical axis shows a second potential 3-HP binding site.
Current efforts are focused on cloning and expressing full-length and effector domains of mmsR and hpdR proteins to characterize their structures and binding to 3-HP.