Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry
Summary
Presented here is a protocol for a capillary electrophoresis-based hydrogen/deuterium exchange (HDX) approach coupled with top-down mass spectrometry. This approach characterizes the difference in higher-order structures between different protein species, including proteins in different states and different proteoforms, by conducting concurrent differential HDX and electrophoretic separation.
Abstract
Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of protein therapeutics and the determination of the conformational transition pathways critical for biological functions, ranging from molecular recognition to enzymatic catalysis. Hydrogen/deuterium exchange (HDX) reaction coupled with top-down mass spectrometric (MS) analysis provides a means to characterize protein higher-order structures and dynamics in a conformer-specific manner. The conformational resolving power of this technique is highly dependent on the efficiencies of separating protein states at the intact protein level and minimizing the residual non-deuterated protic content during the HDX reactions.
Here we describe a capillary electrophoresis (CE)-based variant of the HDX MS approach that aims to improve the conformational resolution. In this approach, proteins undergo HDX reactions while migrating through a deuterated background electrolyte solution (BGE) during the capillary electrophoretic separation. Different protein states or proteoforms that coexist in solution can be efficiently separated based on their differing charge-to-size ratios. The difference in electrophoretic mobility between proteins and protic solvent molecules minimizes the residual non-deuterated solvent, resulting in a nearly complete deuterating environment during the HDX process. The flow-through microvial CE-MS interface allows efficient electrospray ionization of the eluted protein species following a rapid mixing with the quenching and denaturing modifier solution at the outlet of the sprayer. The online top-down MS analysis measures the global deuteration level of the eluted intact protein species, and subsequently, the deuteration of their gas-phase fragments. This paper demonstrates this approach in differential HDX for systems, including the natural protein variants coexisting in milk.
Introduction
Distinguishing protein species in different conformational, binding, or modification states and characterizing their structural differences are important for monitoring the pathways of transitions between these species involved in biological events, ranging from molecular recognition to enzymatic catalysis, and understanding the mechanisms underlying these events. Conventional biophysical techniques do not provide a complete solution due to the limitations such as insufficient resolution and loss of dynamic information in solution. Hydrogen/deuterium exchange coupled with mass spectrometry (HDX MS) is a technique that labels the structural and conformational features of proteins with deuterium (2H) via the exchange between labile hydrogen atoms of proteins and 2H from the deliberately introduced 2H2O solution. Protons involved in hydrogen bonding or that are sequestered from the solvent in the protein interior do not exchange readily1. Thus, as the exchange rate at an exchangeable site is highly dependent on its involvement in higher-order structures, the protein structures can be revealed at high spatial resolution by MS that probes the extent and rate of 2H-uptake based on the differing atomic masses between 1H and 2H. Over the recent decades, HDX MS has become an outstandingly successful technique for studying protein conformations and dynamics2.
In the classical bottom-up approach of HDX MS, the ensemble of protein species in different conformational, binding, or modification states is proteolyzed without separation at the intact protein level, making it infeasible to characterize individual species by analyzing the resulting proteolytic fragments with convoluted deuterium contents. In contrast, in the top-down approach, different protein states or proteoforms that have incorporated different deuterium contents give rise to multiple distributions of intact protein masses in an MS scan. This allows individual species to be separated by mass-selection of ions corresponding to each mass distribution using a proper mass filter (such as a quadrupole) and the characterization of their conformational differences in the subsequent tandem MS analysis3,4,5,6. However, the efficiency of separating protein states or proteoforms in this strategy is limited by the extent of difference in their corresponding mass distributions.
Capillary electrophoresis (CE) provides a means to separate protein species based on their differing charges and hydrodynamic sizes in the solution phase with high efficiency7. Combining CE with HDX offers additional separation of protein states or proteoforms in the solution phase. In addition, the small volume of the CE capillary allows the utilization of a fully deuterated solution as the background electrolyte solution (BGE), i.e., the running buffer, rendering the capillary as an HDX reactor for protein samples. Due to the difference in electrophoretic mobility between proteins and protic reagents in the electrophoresis process, conducting HDX during CE results in a nearly complete deuterating environment for the protein analytes with minimal residual non-deuterated contents, thereby enhancing the sensitivity of the structural analysis using HDX data. As such, we developed a CE-based differential HDX approach coupled with top-down MS to characterize protein higher-order structures in a state- or proteoform-specific manner8.
This paper describes protocols for this approach by detailing the steps of material preparation, experimental procedure, and data analysis. Factors that may affect the method performance or data quality are listed in short notes. The representative results presented here include differential HDX data of mixtures of different proteins and natural variants of bovine β-lactoglobulin (β-lg), the major whey protein present in milk9. We demonstrate separation efficiency, reproducibility, and 2H-labeling performance of the two abundant variants of β-lg, i.e., A and B10,11 during the CE-based HDX and variant-specific characterization of their conformations.
Protocol
Representative Results
Discussion
The objectives of coating the inner wall of the CE capillary include the minimization of the electroosmotic flow and protein absorption during the CE process13. Although electroosmotic flow is beneficial for conventional CE analysis of small molecules owing to its capability of driving neutral or oppositely charged species to the detector, it compromises the separation efficiency of protein species with similar sizes and net charges in solution. Coating the capillary with HPC minimizes the electro…
Disclosures
The authors have nothing to disclose.
Acknowledgements
This work was supported by grants from the National Natural Science Foundation of China (NSFC 21974069). The authors also received support from the Institute for Cell Analysis, Shenzhen Bay Laboratory, China; Jiangsu Collaborative Innovation Center of Biomedical Functional Materials; and Jiangsu Key Laboratory of Biomedical Materials at Nanjing Normal University, China.
Materials
| ammonium acetate | Fisher Chemical | A/3446/50 | ≥99% |
| CESI 8000 plus capillary electrophoresis system | Sciex, USA | ||
| centrifuge | Eppendorf | 5406000097 | |
| centrifugal filter | Merck | UFC201024 | 10 kDa cutoff |
| deuterium oxide | Energy Chemical | E090001 | 99.9 % D |
| formic acid | Acros Organics | 270480250 | |
| fused silica glass capillary | Polymicro Technologies | 1068150017 | ID 50μm, OD 360μm |
| gas chromatography | Agilent | GC6890N | |
| hydrochloric acid | Sigma Aldrich | 258148 | |
| hydroxypropyl cellulose | Aladdin | H113415 | MW 100000 |
| magnetic stirrers | DLAB | 8030101212 | |
| methanol | Fisher Chemical | A456-4 | MS grade |
| microvolume UV-Vis spectrophotometer | DeNovix | 84677JK7731 | |
| myoglobin | Sigma Aldrich | M1882 | |
| Orbitrap Fusion Lumos mass spectrometer | Thermo Fisher Scientific, USA | ||
| PA 800 Plus Pharmaceutical Analysis CE System | Beckman Coulter, USA | ||
| Q Exactive UHMR mass Spectrometer | Thermo Fisher Scientific, Germany | ||
| sodium hydroxide | Sigma Aldrich | S5881 | |
| ubiquitin | Sigma Aldrich | U6253 | |
| ultrasonicator | SCIENTZ | SB-5200 | |
| β-lactoglobulin | Sigma Aldrich | L0130 | |
References
- Kaltashov, I. A., Bobst, C. E., Pawlowski, J., Wang, G. Mass spectrometry-based methods in characterization of the higher order structure of protein therapeutics. Journal of Pharmaceutical and Biomedical Analysis. 184, 113169 (2020).
- Engen, J. R., Botzanowski, T., Peterle, D., Georgescauld, F., Wales, T. E. Developments in hydrogen/deuterium exchange mass spectrometry. Analytical Chemistry. 93 (1), 567-582 (2021).
- Pan, J., Han, J., Borchers, C. H., Konermann, L. Conformer-specific hydrogen exchange analysis of Abeta(1-42) oligomers by top-down electron capture dissociation mass spectrometry. Analytical Chemistry. 83 (13), 5386-5393 (2011).
- Pan, J., Han, J., Borchers, C. H., Konermann, L. Structure and dynamics of small soluble Abeta(1-40) oligomers studied by top-down hydrogen exchange mass spectrometry. Biochemistry. 51 (17), 3694-3703 (2012).
- Pan, J., Borchers, C. H. Top-down structural analysis of posttranslationally modified proteins by Fourier transform ion cyclotron resonance-MS with hydrogen/deuterium exchange and electron capture dissociation. Proteomics. 13 (6), 974-981 (2013).
- Wang, G., Abzalimov, R. R., Bobst, C. E., Kaltashov, I. A. Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry. Proceedings of the National Academy of Sciences of the United. States of America. 110 (50), 20087-20092 (2013).
- Mironov, G. G., Clouthier, C. M., Akbar, A., Keillor, J. W., Berezovski, M. V. Simultaneous analysis of enzyme structure and activity by kinetic capillary electrophoresis-MS. Nature Chemical Biology. 12 (11), 918-922 (2016).
- Shen, Y., Zhao, X., Wang, G., Chen, D. D. Y. Differential hydrogen/deuterium exchange during proteoform separation enables characterization of conformational differences between coexisting protein states. Analytical Chemistry. 91 (6), 3805-3809 (2019).
- Kontopidis, G., Holt, C., Sawyer, L. Invited review: β-lactoglobulin: binding properties, structure, and function. Journal of Dairy Science. 87 (4), 785-796 (2004).
- Qin, B. Y., et al. Structural basis of the Tanford transition of bovine β-lactoglobulin. Biochemistry. 37 (40), 14014-14023 (1998).
- Qin, B. Y., Bewley, M. C., Creamer, L. K., Baker, E. N., Jameson, G. B. Functional implications of structural differences between variants A and B of bovine beta-lactoglobulin. Protein Science. 8 (1), 75-83 (1999).
- Wang, L., et al. High resolution capillary isoelectric focusing mass spectrometry analysis of peptides, proteins, and monoclonal antibodies with a flow-through microvial interface. Analytical Chemistry. 90 (15), 9495-9503 (2018).
- Busch, M. H. A., Kraak, J. C., Poppe, H. Cellulose acetate-coated fused-silica capillaries for the separation of proteins by capillary zone electrophoresis. Journal of Chromatography A. 1695 (2), 287-296 (1995).
- Zhao, X., Shen, Y., Tong, W., Wang, G., Chen, D. D. Y. Deducing disulfide patterns of cysteine-rich proteins using signature fragments produced by top-down mass spectrometry. Analyst. 143 (4), 817-823 (2018).
- Sutera, S. P., Skalak, R. The history of Poiseuille’s law. Annual Review of Fluid Mechanics. 25 (1), 1-20 (1993).
- Wang, G., Kaltashov, I. A. Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry. Analytical Chemistry. 86 (15), 7293-7298 (2014).
- Wang, G., Johnson, A. J., Kaltashov, I. A. Evaluation of electrospray ionization mass spectrometry as a tool for characterization of small soluble protein aggregates. Analytical Chemistry. 84 (3), 1718-1724 (2012).
- Fellers, R. T., et al. ProSight Lite: graphical software to analyze top-down mass spectrometry data. Proteomics. 15 (7), 1235-1238 (2015).
- Cai, W., et al. MASH Suite Pro: A comprehensive software tool for top-down proteomics. Molecular & Cellular Proteomics. 15 (2), 703-714 (2016).
- Paterson, G. R., Hill, J. P., Otter, D. E. Separation of β-lactoglobulin A, B and C variants of bovine whey using capillary zone electrophoresis. Journal of Chromatography A. 700 (1), 105-110 (1995).
- Wang, G., Kaltashov, I. A. Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry. Analytical Chemistry. 86 (15), 7293-7298 (2014).
- Nicolardi, S., et al. On-line electrochemical reduction of disulfide bonds: improved FTICR-CID and -ETD coverage of oxytocin and hepcidin. Journal of the American Society for Mass Spectrometry. 24 (12), 1980-1987 (2013).
- Adhikari, S., Xia, Y., McLuckey, S. A. Top-down analysis of disulfide-linked proteins using photoinduced radical reactions and ET-DDC. International Journal of Mass Spectrometry. 444, 116173 (2019).
- Rush, M. J. P., Riley, N. M., Westphall, M. S., Coon, J. J. Top-down characterization of proteins with intact disulfide bonds using activated-ion electron transfer dissociation. Analytical Chemistry. 90 (15), 8946-8953 (2018).
- Zhong, X., Maxwell, E. J., Chen, D. D. Y. Mass transport in a micro flow-through vial of a junction-at-the-tip capillary electrophoresis-mass spectrometry interface. Analytical Chemistry. 83 (12), 4916-4923 (2011).
