Computational Investigation of the Fixed Charge Derivative Tris[(2,4,6-trimethoxyphenyl) phosphonium]
EMSL Project ID
3691
Abstract
Proteomic studies often rely upon liquid chromatography (LC)/tandem mass spectrometry (MS) measurements in conjunction with sequencing algorithms for the identification of proteins. When a peptide fragments, it most commonly cleaves at the peptide bond, resulting in an/bn ions if the side containing the amino terminus is charged, and xn/yn ions if the side containing the carboxy terminus is charged. The subscript ?n? denotes the amino acid position of fragmentation. A more thorough understanding of why certain cleavages occur in the dissociation process and the incorporation of this information in the identification process may help improve the performance of current sequencing algorithms, and thereby protein identification. Methods to investigate the gas-conformation, protonation site, and intramolecular interactions of peptides containing functional groups and structural motifs of interest include gas phase hydrogen/deuterium (H/D) exchange, ion mobility, molecular modeling and charge solvation studies. Information gained from these studies aids in the understanding of how the intramolecular interactions preceding the fragmentation event affect the mechanism of cleavage.Peptide fragmentation is thought to proceed through either charge-directed or charge-remote processes, depending on the conditions of the fragmentation event and the characteristics of the peptide. Charge-remote cleavage occurs under high-energy dissociation conditions or when peptides are modified with a fixed charge, while charge-directed cleavage is consistent with low energy dissociation and a mobile charge.
The derivative Tris[(2,4,6-trimethoxyphenyl) phosphonium] (TMPP) may be attached to the amino terminus of a peptide, resulting in a fixed charge carried by the TMPP. Fragmentation of a peptide containing this fixed charge derivative results in fragment ions carrying the charge at the N-terminus, therefore mainly an/bn ions are observed. By contrast, charge-directed fragmentation with a mobile proton usually results in abundant xn/yn and an/bn fragment ions. It is assumed that because of steric hindrance resulting from the 2,4,6-trimethoxyphenyl groups that the phosphorus atom is unable to initiate charge-directed cleavage at the peptide bonds. However, it may be sterically possible for one of the methoxy groups to initiate charge-directed cleavage if the oxygen atom carries enough partial charge. The purpose of this proposal, therefore, is to utilize the PNNL-EMSL computational modeling facilities, under the direction of Dr. Erich Vorpagel, to determine the charge distribution of TMPP attached to a small model peptide, such as Ala-Ala. If the majority of the charge is carried by the phosphorous atom, then presumably the TMPP derivative undergoes fragmentation only via a charge-remote process, validating the use of TMPP to study charge-remote fragmentation.
Project Details
Project type
Exploratory Research
Start Date
2003-09-15
End Date
2003-12-31
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members