1
|
Feng H, Yamaguchi T. Effects of Different Adduct Ions, Ionization Temperatures, and Solvents on the Ion Mobility of Glycans. Molecules 2025; 30:2177. [PMID: 40430350 PMCID: PMC12114495 DOI: 10.3390/molecules30102177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2025] [Revised: 05/10/2025] [Accepted: 05/14/2025] [Indexed: 05/29/2025] Open
Abstract
The structural analysis of glycans remains a major challenge due to their high isomeric complexity and conformational flexibility arising from diverse glycosidic linkages and dynamic three-dimensional structures. Ion mobility-mass spectrometry (IM-MS) has been attracting attention as a way to develop the structural analysis of glycans. In this study, the effects of ionization conditions-including different types of adduct ions, ionization temperatures, and solvent environments-on the ion mobility behavior of glycans were systematically investigated. IM-MS measurements of ethylamine-tagged glycans showed broad arrival time distributions of monoprotonated ions indicating the presence of multiple conformers of glycans. Increased ionization temperatures and the use of methanol as a solvent further broadened the distribution, suggesting the enhanced conformational dynamics of the glycan ions. In contrast, sodium adduct ions yielded narrower distributions, implying that the interactions between sodium ions and glycans constrained structural flexibility. These results demonstrate that ionization parameters have a significant impact on glycan conformational behavior and mobility in the gas phase. This study provides insights into the analytical conditions for IM-MS measurements of glycans and highlights the utility of this method as a powerful tool for elucidating glycan structure and dynamics.
Collapse
Affiliation(s)
- Hao Feng
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 9231292, Japan
| | - Takumi Yamaguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 9231292, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 4678603, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 4448787, Japan
| |
Collapse
|
2
|
Kato K, Yanaka S, Yamaguchi T. The synergy of experimental and computational approaches for visualizing glycoprotein dynamics: Exploring order within the apparent disorder of glycan conformational ensembles. Curr Opin Struct Biol 2025; 92:103049. [PMID: 40306228 DOI: 10.1016/j.sbi.2025.103049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/25/2025] [Accepted: 03/29/2025] [Indexed: 05/02/2025]
Abstract
Understanding the dynamic behavior of glycoproteins is crucial for deciphering their biological roles. This review explores the synergistic use of experimental and computational methods to address this complex challenge. Glycans, with their inherent flexibility and structural diversity, pose significant obstacles to traditional structural analysis. Innovative experimental techniques offer valuable snapshots of glycan conformations, but often lack the context of a physiological environment. Computational simulations provide atomic-level detail and explore the full range of dynamic motions, but require extensive resources and validation. Integrating these approaches, by using experimental data to refine and validate computational models, is essential for accurately capturing the complex interplay between glycans and proteins. This combined strategy promises to unlock a deeper understanding of glycoprotein function and inform the design of novel therapeutics.
Collapse
Affiliation(s)
- Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Core for Spin Life Sciences, Okazaki Collaborative Platform, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Core for Spin Life Sciences, Okazaki Collaborative Platform, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; Materials and Structures Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Takumi Yamaguchi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Core for Spin Life Sciences, Okazaki Collaborative Platform, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| |
Collapse
|
3
|
Ruda A, Aytenfisu AH, Angles d’Ortoli T, MacKerell AD, Widmalm G. Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields. Phys Chem Chem Phys 2023; 25:3042-3060. [PMID: 36607620 PMCID: PMC9890503 DOI: 10.1039/d2cp05203b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D 1H,1H-NOESY and 1D 1H,1H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly 13C-isotope labeled α-D-[1,2-13C2]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on 13C,13C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.
Collapse
Affiliation(s)
- Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Asaminew H. Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| |
Collapse
|
4
|
Watanabe T, Yagi H, Yanaka S, Yamaguchi T, Kato K. Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space. Phys Chem Chem Phys 2021; 23:9753-9760. [PMID: 33881019 DOI: 10.1039/d0cp06448c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oligosaccharides play versatile roles in various biological systems but are difficult to characterize from a structural viewpoint due to their remarkable degrees of freedom in internal motion. Therefore, molecular dynamics simulations have been widely used to delineate the dynamic conformations of oligosaccharides. However, hardly any methods have thus far been available for the comprehensive characterization of simulation-derived conformational ensembles of oligosaccharides. In this research, we attempted to develop a non-linear multivariate analysis by employing a kernel method using two homologous high-mannose-type oligosaccharides composed of ten and eleven residues as model molecules. These oligosaccharides' conformers derived from simulations were mapped into reproductive kernel Hilbert space with a positive definite function in which all required non-redundant variables for describing the oligosaccharide conformations can be treated in a non-biased manner. By applying Gaussian mixture model clustering, the oligosaccharide conformers were successfully classified by different funnels in the free-energy landscape, enabling a systematic comparison of conformational ensembles of the homologous oligosaccharides. The results shed light on the contributions of intraresidue conformational factors such as the hydroxyl group orientation and/or ring puckering state to their global conformational dynamics. Our methodology will open opportunities to explore oligosaccharides' conformational spaces, and more generally, molecules with high degrees of motional freedom.
Collapse
Affiliation(s)
- Tokio Watanabe
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-Dori, Mizuho-Ku, Nagoya, Aichi 467-8603, Japan.
| | | | | | | | | |
Collapse
|