Helical Stabilization on Yap1 Protein Fragments
Poster Number
57
Format
Poster Presentation
Faculty Mentor Name
Michael McCallum
Faculty Mentor Department
Chemistry
Abstract/Artist Statement
Depending on the environment it's in, and it's properties, a protein has the ability to fold to different secondary structures. One such structure is the alpha helix. For hydrophilic proteins, this structure is formed in aqueous (or polar) environments, while hydrophobic proteins form an alpha helix in vacuum (or non-polar) environments. This alpha helix is stabilized by hydrogen bonding between the oxygen (of the carbon - oxygen double bond) and the hydrogen (of the hydrogen - nitrogen bond), from the carbonyl groups and amine groups (from the amino acids which make up the peptide), respectively. Each helix possesses a helical dipole caused by the positive N-Terminus and the negative C-terminus that each amino acid contains. This dipole can be stabilized by placing an ion at either end of the peptide (i.e. a positive cation near the negative C-terminus, or a negative anion near the end of the positive NTerminus). Using molecular dynamics (MD) simulations, the hydrophilic/hydrophobic properties of a protein fragment from the Yap1 protein will be determined. The helical stabilization of an ion will also be determined. Using steered molecular dynamics (SMD) simulations, a force will be applied to the ion, and due to the interaction between the ion and the corresponding terminus of the peptide, the force will be applied on the peptide as well, resulting in an extension of the helix. Using this information, the force associated with the hydrogen bonds - collectively and individually - may be determined.
Location
DeRosa University Center, Ballroom
Start Date
20-4-2013 1:00 PM
End Date
20-4-2013 3:00 PM
Helical Stabilization on Yap1 Protein Fragments
DeRosa University Center, Ballroom
Depending on the environment it's in, and it's properties, a protein has the ability to fold to different secondary structures. One such structure is the alpha helix. For hydrophilic proteins, this structure is formed in aqueous (or polar) environments, while hydrophobic proteins form an alpha helix in vacuum (or non-polar) environments. This alpha helix is stabilized by hydrogen bonding between the oxygen (of the carbon - oxygen double bond) and the hydrogen (of the hydrogen - nitrogen bond), from the carbonyl groups and amine groups (from the amino acids which make up the peptide), respectively. Each helix possesses a helical dipole caused by the positive N-Terminus and the negative C-terminus that each amino acid contains. This dipole can be stabilized by placing an ion at either end of the peptide (i.e. a positive cation near the negative C-terminus, or a negative anion near the end of the positive NTerminus). Using molecular dynamics (MD) simulations, the hydrophilic/hydrophobic properties of a protein fragment from the Yap1 protein will be determined. The helical stabilization of an ion will also be determined. Using steered molecular dynamics (SMD) simulations, a force will be applied to the ion, and due to the interaction between the ion and the corresponding terminus of the peptide, the force will be applied on the peptide as well, resulting in an extension of the helix. Using this information, the force associated with the hydrogen bonds - collectively and individually - may be determined.