Protein-Protein Surface Modeling of Double-Stranded Break Complexes
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Date
2019-05
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The Ohio State University
Abstract
The purpose of this study is to computationally model proteins to view double-stranded break repair complexes. Double-strand breaks (DSBs) in DNA are extremely problematic and require intricate, complicated repair. DSBs also have an unknown mechanism. A lack of repair can result in a loss of a region of chromosome, while incorrect repairs result in cancer development. In order to prevent cancer development, the mechanism must be more well understood. Protein-protein docking, the modeling technique used in this study, is a snapshot of two proteins interacting with each other on their surfaces and was used to look at a combination of the yeast proteins RAD52, MST1, and HIP1. Comparing computational data with experimental results will give better insights as to what is happening among the protein complexes involved with DSB repair. Tertiary yeast structures (RAD52, MST1, and HIP1) were generated using homology modeling of the corresponding primary sequences in the yeast strain s. pombe. Each of the protein- protein docking calculations provided ten solutions with different intermolecular interactions to be analyzed. Interactions between side chains, such as hydrogen bonding, become extremely important in order to predict residues of interaction needed for experimentation. In the future, these computational methods could predict the outcomes of yeast experimentation with mutational analysis. Once the mechanism is well understood, further studies may find a way to ensure DSBs are repaired correctly.
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Keywords
double-strand break, molecular modeling, protein-protein interaction, cancer