Knob-Socket To 'Em: Investigating Protein/DNA Binding Interactions Using the Knob Socket Model
Poster Number
2
Format
Poster Presentation
Faculty Mentor Name
Jerry Tsai
Faculty Mentor Department
Chemistry
Additional Faculty Mentor Name
Hyun Joo
Abstract/Artist Statement
Understanding how proteins specifically bind and recognize DNA has important implications in the understanding of many diseases and how to combat them. The Knob-Socket model of packing structure provides a novel approach to analyzing protein-nucleic acid interactions. A Knob-Socket analysis of the protein-DNA interface produces an intuitive mapping of the protein and DNA three dimensional structure onto a two dimensional map. This topological packing maps allows for unique insight into the specificity of how proteins and DNA recognize each other. From an analysis of the Knob- Socket surface topology maps, this research illustrates a general framework for how the classic basic leucine zipper alpha-helices bind to DNA. DNA packing is divided into specific interactions with the nucleic acid bases and nonspecific interactions with the phosphate backbone groups. The i±4 ridge of the protein divides the binding of the alpha-helix into two regions of sockets that recognize the DNA bases: one on the coding strand and the other on the non-coding strand. The pocket pattern and amino acid composition on the alpha-helices determine specificity for DNA base recognition. Therefore, this general framework not only explains the specificity and recognition of protein and DNA binding, but also provides a predictive model. The results demonstrate that the knob-socket model can rationally investigate and produce clear insight into protein-DNA binding interfaces. This research presents a clear understanding in the fundamentals of binding interactions, which provide the framework for further work in investigating the biochemical mechanics of disease and drugs to combat them.
Location
DeRosa University Center, Ballroom
Start Date
30-4-2016 1:30 AM
End Date
30-4-2016 3:30 PM
Knob-Socket To 'Em: Investigating Protein/DNA Binding Interactions Using the Knob Socket Model
DeRosa University Center, Ballroom
Understanding how proteins specifically bind and recognize DNA has important implications in the understanding of many diseases and how to combat them. The Knob-Socket model of packing structure provides a novel approach to analyzing protein-nucleic acid interactions. A Knob-Socket analysis of the protein-DNA interface produces an intuitive mapping of the protein and DNA three dimensional structure onto a two dimensional map. This topological packing maps allows for unique insight into the specificity of how proteins and DNA recognize each other. From an analysis of the Knob- Socket surface topology maps, this research illustrates a general framework for how the classic basic leucine zipper alpha-helices bind to DNA. DNA packing is divided into specific interactions with the nucleic acid bases and nonspecific interactions with the phosphate backbone groups. The i±4 ridge of the protein divides the binding of the alpha-helix into two regions of sockets that recognize the DNA bases: one on the coding strand and the other on the non-coding strand. The pocket pattern and amino acid composition on the alpha-helices determine specificity for DNA base recognition. Therefore, this general framework not only explains the specificity and recognition of protein and DNA binding, but also provides a predictive model. The results demonstrate that the knob-socket model can rationally investigate and produce clear insight into protein-DNA binding interfaces. This research presents a clear understanding in the fundamentals of binding interactions, which provide the framework for further work in investigating the biochemical mechanics of disease and drugs to combat them.