Conformations and Energetics of B- and Y-Ions in Peptoid Fragmentation
Format
Poster Presentation
Faculty Mentor Name
Jianhua Ren
Faculty Mentor Department
Chemistry
Graduate Student Mentor Name
Yuntao Zhang
Graduate Student Mentor Department
Chemistry
Abstract/Artist Statement
Peptoids, peptide-mimicking polymers, are man-made molecules that are not susceptible to protease degradation. It has shown high potential in pharmaceutics, such as artificial pulmonary surfactants and Alzheimer’s treatment. Unfortunately, the broadening of applications has been hindered by the lack of optimal ways to efficiently sequence peptoids. To gain knowledge about their fragmentation pathways and help develop peptoid sequencing methods, a series of model peptoids have been designed, and their fragmentation patterns have been investigated thoroughly. The energetics and structures of the N-terminal fragments, B-ions, and C-terminal fragments, Y-ions, were also examined to rationalize experimental observations.
A series of peptoids varying in length were designed. The initial conformations of B-ions, Y-ions, and their “neutral” pairs were generated based on “chemistry intuition.” Conformer search using MMFF method was completed, and sequential optimizations were executed. With the energetics and conformations, the computational outputs were used to examine the differences between channels to form each observed ion.
Y-ions were generally found in higher abundance compared to B-ions, and the energy differences between the Y- and B-ion channels (E(Y) – E(B)) at each amide position were calculated. For positions where different sizes of Y- and B-ions are formed, the larger ion tends to be energetically favored. As the amide bond cleavage moves from C-terminus to N-terminus, the Y-ion channel becomes more favored. In longer Y-ions, more hydrogen bonding interactions allow for adequate stabilization of the charged cation, while oxazolone ring stabilization has less importance for longer B-ions. Based on this research endeavor, we have found that peptoid fragmentation patterns can be correlated to the energetics of peptoid fragmentation using computational chemistry.
Location
Virtual
Start Date
25-4-2020 1:00 PM
End Date
25-4-2020 3:00 PM
Conformations and Energetics of B- and Y-Ions in Peptoid Fragmentation
Virtual
Peptoids, peptide-mimicking polymers, are man-made molecules that are not susceptible to protease degradation. It has shown high potential in pharmaceutics, such as artificial pulmonary surfactants and Alzheimer’s treatment. Unfortunately, the broadening of applications has been hindered by the lack of optimal ways to efficiently sequence peptoids. To gain knowledge about their fragmentation pathways and help develop peptoid sequencing methods, a series of model peptoids have been designed, and their fragmentation patterns have been investigated thoroughly. The energetics and structures of the N-terminal fragments, B-ions, and C-terminal fragments, Y-ions, were also examined to rationalize experimental observations.
A series of peptoids varying in length were designed. The initial conformations of B-ions, Y-ions, and their “neutral” pairs were generated based on “chemistry intuition.” Conformer search using MMFF method was completed, and sequential optimizations were executed. With the energetics and conformations, the computational outputs were used to examine the differences between channels to form each observed ion.
Y-ions were generally found in higher abundance compared to B-ions, and the energy differences between the Y- and B-ion channels (E(Y) – E(B)) at each amide position were calculated. For positions where different sizes of Y- and B-ions are formed, the larger ion tends to be energetically favored. As the amide bond cleavage moves from C-terminus to N-terminus, the Y-ion channel becomes more favored. In longer Y-ions, more hydrogen bonding interactions allow for adequate stabilization of the charged cation, while oxazolone ring stabilization has less importance for longer B-ions. Based on this research endeavor, we have found that peptoid fragmentation patterns can be correlated to the energetics of peptoid fragmentation using computational chemistry.