Computational Analysis of Electronic Effects of Protonated Ubiquitin Carbonyl
Poster Number
22B
Format
Poster Presentation
Faculty Mentor Name
Anthony Dutoi
Faculty Mentor Department
Department of Chemistry
Abstract/Artist Statement
Ubiquitin is a regulatory protein prevalent in almost all eukaryotic life forms with high identity conservation across all species found to contain it. Structural and functional signatures of ubiquitin are its 7 lysine residues and C-terminus tail. Ubiquitin’s role as a tagging protein for amino acids that require regulation or degradation is carried out by its linkage processes. We focused on the electronic effects of electrophilic attack on the C-terminus’s carbonyl oxygen in relationship to the thioester’s alkyl group which creates a molecule that can undergo transesterification-like reactions. By using quantum chemical calculations, we compared bonding energy curves of molecules with a hydrogen bound to a carbonyl of an aminated thioester, an approximation of ubiquitin’s C-terminus where the amine group acts as a simplified lysine, with varied dihedral angles of the hydrogen and a methyl attached to the sulfur depending on bond distances of the amine group and of the approaching hydrogen. Graphing this data showed a narrow spread of binding curves for each dihedral angle of the methyl group. This could indicate a lack of electronic influence from the sulfur-linked alkyl group or that the methyl group is an insufficient theoretical model for ubiquitin’s thioester structures.
Location
Information Commons, William Knox Holt Memorial Library and Learning Center
Start Date
29-4-2023 10:00 AM
End Date
29-4-2023 1:00 PM
Computational Analysis of Electronic Effects of Protonated Ubiquitin Carbonyl
Information Commons, William Knox Holt Memorial Library and Learning Center
Ubiquitin is a regulatory protein prevalent in almost all eukaryotic life forms with high identity conservation across all species found to contain it. Structural and functional signatures of ubiquitin are its 7 lysine residues and C-terminus tail. Ubiquitin’s role as a tagging protein for amino acids that require regulation or degradation is carried out by its linkage processes. We focused on the electronic effects of electrophilic attack on the C-terminus’s carbonyl oxygen in relationship to the thioester’s alkyl group which creates a molecule that can undergo transesterification-like reactions. By using quantum chemical calculations, we compared bonding energy curves of molecules with a hydrogen bound to a carbonyl of an aminated thioester, an approximation of ubiquitin’s C-terminus where the amine group acts as a simplified lysine, with varied dihedral angles of the hydrogen and a methyl attached to the sulfur depending on bond distances of the amine group and of the approaching hydrogen. Graphing this data showed a narrow spread of binding curves for each dihedral angle of the methyl group. This could indicate a lack of electronic influence from the sulfur-linked alkyl group or that the methyl group is an insufficient theoretical model for ubiquitin’s thioester structures.