How Mutations Can Affect the Binding Affinity of DNA to bZIP Proteins
Poster Number
34
Research or Creativity Area
Natural Sciences
Abstract
The basic leucine binding motif (bZIP) is one of the ways that proteins can bind and recognize DNA bases, where an alpha helical protein’s amino acids bind nucleotide sequences. The crystal structure of the bZIP-DNA binding interaction can be analyzed through the Knob-Socket model, which identifies the packing between a bZIP monomer and its four base half sites of the DNA. This model identifies a conserved quadripartite region on the alpha helix where a set of 9 amino acids recognizes bases on both the positive (P) and negative (N) strands of the DNA half-site. Specifically, the quadripartite binding regions of the DNA on the bZIP alpha sequence are recognized as P1, P2, N1, and N2 by the alpha helices i+4 and i+3 ridges, since the positive and negative bases pack on different parts of the alpha helix. Consistently, in DNA-bZIP binding patterns, half site packing is centered around conserved asparagine and aspartate residues on the i+4 ridge of the alpha helix separated by 8 residues. Binding specificity to multiple target DNA sequences must be modulated by the other 7 residues of the bZIP quadripartite binding region. Therefore, changes in these amino acid positions of the bZIP alpha helix alter half site packing preferences among the quadripartite recognition core for DNA bases. By correlating amino acid residues in the bZIP quadripartite recognition region with DNA half-site sequence composition, the Knob-Socket model allows a direct analysis of bZIP-DNA binding specificity. Hydrophobic packing of the methyl group favors thymine base recognition, but not particularly with non-polar amino acids. Hydrogen bonding networks are implicated with the recognition of other guanine, cytosine, and adenine bases. There are times when mutations to the bZIP alpha helix can result in increased stability, if the amino acids can create additional hydrogen bonds that stabilize the DNA backbone.
Location
Don and Karen DeRosa University Center (DUC) Poster Hall
Start Date
27-4-2024 10:30 AM
End Date
27-4-2024 12:30 PM
How Mutations Can Affect the Binding Affinity of DNA to bZIP Proteins
Don and Karen DeRosa University Center (DUC) Poster Hall
The basic leucine binding motif (bZIP) is one of the ways that proteins can bind and recognize DNA bases, where an alpha helical protein’s amino acids bind nucleotide sequences. The crystal structure of the bZIP-DNA binding interaction can be analyzed through the Knob-Socket model, which identifies the packing between a bZIP monomer and its four base half sites of the DNA. This model identifies a conserved quadripartite region on the alpha helix where a set of 9 amino acids recognizes bases on both the positive (P) and negative (N) strands of the DNA half-site. Specifically, the quadripartite binding regions of the DNA on the bZIP alpha sequence are recognized as P1, P2, N1, and N2 by the alpha helices i+4 and i+3 ridges, since the positive and negative bases pack on different parts of the alpha helix. Consistently, in DNA-bZIP binding patterns, half site packing is centered around conserved asparagine and aspartate residues on the i+4 ridge of the alpha helix separated by 8 residues. Binding specificity to multiple target DNA sequences must be modulated by the other 7 residues of the bZIP quadripartite binding region. Therefore, changes in these amino acid positions of the bZIP alpha helix alter half site packing preferences among the quadripartite recognition core for DNA bases. By correlating amino acid residues in the bZIP quadripartite recognition region with DNA half-site sequence composition, the Knob-Socket model allows a direct analysis of bZIP-DNA binding specificity. Hydrophobic packing of the methyl group favors thymine base recognition, but not particularly with non-polar amino acids. Hydrogen bonding networks are implicated with the recognition of other guanine, cytosine, and adenine bases. There are times when mutations to the bZIP alpha helix can result in increased stability, if the amino acids can create additional hydrogen bonds that stabilize the DNA backbone.
