Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
Highlights
Carbohydrates are ubiquitous components of living organisms
molecular dynamics (MD) simulations have revealed that the protonation state as well as the conformational ensemble are important determinants for collision cross section (CCS) of gas-phase N-glycans
In the studied N-glycans, single conformers of either globular or rod-like shapes dominate and their CCSs are sufficiently different for identification of isomeric N-glycan structures
Summary
Carbohydrates are ubiquitous components of living organisms. As over 50% of eukaryotic proteins and most of membrane proteins are glycosylated[1], their roles in biological processes, ranging from protein folding to biomolecular recognition events, have received considerable attention[2,3,4]. Ion mobility mass spectrometry (IM-MS) is an analytical method increasingly used for obtaining information of conformational changes in polyatomic ions, such as unfolding or aggregation[7,8,9] This method separates gas-phase ions based on the collision cross section (CCS) that reflects their sizes and shapes. We previously reported a combined IM-MS and molecular dynamics (MD) simulation study on the identification of isomeric N-glycan structures[23]. We computationally investigated CCS determinants of N-glycans to predict CCSs from the structural information. To this end, we extended the previous simulation study in several ways.
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