Cross-Linking Mass Spectrometry on P-Glycoprotein

Abstract

The ABC transporter P-glycoprotein (Pgp) has been found to be involved in multidrug resistance in tumor cells. Lipids and cholesterol have a pivotal role in Pgp’s conformations; however, it is often difficult to investigate it with conventional structural biology techniques. Here, we applied robust approaches coupled with cross-linking mass spectrometry (XL-MS), where the natural lipid environment remains quasi-intact. Two experimental approaches were carried out using different cross-linkers (i) on living cells, followed by membrane preparation and immunoprecipitation enrichment of Pgp, and (ii) on-bead, subsequent to membrane preparation and immunoprecipitation. Pgp-containing complexes were enriched employing extracellular monoclonal anti-Pgp antibodies on magnetic beads, followed by on-bead enzymatic digestion. The LC-MS/MS results revealed mono-links on Pgp’s solvent-accessible residues, while intraprotein cross-links confirmed a complex interplay between extracellular, transmembrane, and intracellular segments of the protein, of which several have been reported to be connected to cholesterol. Harnessing the MS results and those of molecular docking, we suggest an epitope for the 15D3 cholesterol-dependent mouse monoclonal antibody. Additionally, enriched neighbors of Pgp prove the strong connection of Pgp to the cytoskeleton and other cholesterol-regulated proteins. These findings suggest that XL-MS may be utilized for protein structure and network analyses in such convoluted systems as membrane proteins.

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity

“…The increasing number of cross-linking reagents, different acquisition methods, and various experimental setups led to the implementation of over 20 different software tools (usually denoted as cross-linking search engines) from different research groups specializing in the identification and validation of cross-linked peptides. − It should also be noted here that most traditional database search engines for the identification of linear peptides can be used to detect cross-linked peptides specifically in MS3 scans, in that regard Protein Prospector has been successfully applied, as shown in recent publications. , However, combining the identified peptides to cross-links via their precursor MS2 spectra and subsequent validation is a substantial part of cross-link identification that still needs to be done manually or by another software afterward. Cross-linking search engines typically incorporate all of these steps with very little need for manual work.…”

“… 27 − 34 It should also be noted here that most traditional database search engines for the identification of linear peptides can be used to detect cross-linked peptides specifically in MS3 scans, in that regard Protein Prospector 35 has been successfully applied, as shown in recent publications. 36 , 37 However, combining the identified peptides to cross-links via their precursor MS2 spectra and subsequent validation is a substantial part of cross-link identification that still needs to be done manually or by another software afterward. Cross-linking search engines typically incorporate all of these steps with very little need for manual work.…”