Title

Analyzing the Packing Specificity of a DNA Binding Protein

Poster Number

10C

Lead Author Major

Biochemistry

Lead Author Status

Senior

Format

Poster Presentation

Faculty Mentor Name

Jerry Tsai

Faculty Mentor Email

jtsai@pacific.edu

Faculty Mentor Department

Chemistry

Abstract/Artist Statement

Identifying the interactions that exist in the leucine zipper DNA binding proteins are crucial for the understanding of disease formation, proliferation, and the development of combative measures against these diseases. Use of the Knob-Socket model for determination of packing structure provides a novel approach to analyze protein-protein as well as protein-nucleic acid interactions. A Knob-Socket analysis of the protein-protein interface provides unique insight into the classical leucine zipper pseudo-7mer repeat. A deeper analysis of longer leucine zippers shows unique packing patterns not indicated by classical representations like the helical wheel. Knob-Socket analysis of the bZIP-DNA interface produces an intuitive mapping of the protein and DNA three-dimensional structure onto a two-dimensional map. This packing map provides a unique insight into the interactions that exist between the nucleotide backbone of the DNA and the α- helical structure of the leucine zipper protein. From analysis of the Knob-Socket packing maps, this research provides evidence of a general framework for a conserved binding site for the DNA-bZIP interaction. This DNA binding site on the protein is bisected by the i+4 ridge of the leucine zipper α-helix: above the ridge interacts with the coding strand, below the ridge interacts with the non-coding strand. The conserved binding model is then determined from the composition of the amino acids that compose the sockets on the protein; and the nucleotide base sequence that act as knobs that fit into these sockets. The results indicate that there exists a conserved binding site for the protein-nucleotide interaction of the leucine zipper as illustrated by the Knob-Socket packing model. This research presents a clear model for the bZIP-DNA interaction and provides the basis for further exploration into these interactions to further our understanding of disease formation and combative techniques against these diseases.

Location

DeRosa University Center, Ballroom

Start Date

29-4-2017 1:00 PM

End Date

29-4-2017 3:00 PM

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Apr 29th, 1:00 PM Apr 29th, 3:00 PM

Analyzing the Packing Specificity of a DNA Binding Protein

DeRosa University Center, Ballroom

Identifying the interactions that exist in the leucine zipper DNA binding proteins are crucial for the understanding of disease formation, proliferation, and the development of combative measures against these diseases. Use of the Knob-Socket model for determination of packing structure provides a novel approach to analyze protein-protein as well as protein-nucleic acid interactions. A Knob-Socket analysis of the protein-protein interface provides unique insight into the classical leucine zipper pseudo-7mer repeat. A deeper analysis of longer leucine zippers shows unique packing patterns not indicated by classical representations like the helical wheel. Knob-Socket analysis of the bZIP-DNA interface produces an intuitive mapping of the protein and DNA three-dimensional structure onto a two-dimensional map. This packing map provides a unique insight into the interactions that exist between the nucleotide backbone of the DNA and the α- helical structure of the leucine zipper protein. From analysis of the Knob-Socket packing maps, this research provides evidence of a general framework for a conserved binding site for the DNA-bZIP interaction. This DNA binding site on the protein is bisected by the i+4 ridge of the leucine zipper α-helix: above the ridge interacts with the coding strand, below the ridge interacts with the non-coding strand. The conserved binding model is then determined from the composition of the amino acids that compose the sockets on the protein; and the nucleotide base sequence that act as knobs that fit into these sockets. The results indicate that there exists a conserved binding site for the protein-nucleotide interaction of the leucine zipper as illustrated by the Knob-Socket packing model. This research presents a clear model for the bZIP-DNA interaction and provides the basis for further exploration into these interactions to further our understanding of disease formation and combative techniques against these diseases.