Can Mass Spectrometry Determine Protein Structure?
In protein research, determining protein structure is critical for understanding its function, interactions, and role in diseases. As a powerful analytical tool, mass spectrometry has become an increasingly important method in protein studies. But can mass spectrometry determine protein structure?
Traditionally, X-ray crystallography and nuclear magnetic resonance (NMR) have been the primary techniques for determining protein structures. X-ray crystallography provides high-resolution three-dimensional structures, but requires protein crystallization, which is not feasible for many proteins. NMR can be used to determine protein structures in solution, but it has limitations when studying large proteins.
Mass spectrometry offers unique advantages in protein structure analysis. It can precisely measure the molecular weight of proteins, and by measuring the molecular weights of both intact proteins and their enzymatic fragments, it provides amino acid sequence information. For instance, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry can ionize proteins and measure their mass-to-charge ratio, enabling accurate molecular weight calculations. In proteomics, mass spectrometry is widely used to measure molecular weights and sequence large numbers of proteins, allowing for high-throughput identification.
Additionally, mass spectrometry provides detailed insights into protein modifications. Post-translational modifications (PTMs), such as phosphorylation and glycosylation, play crucial roles in regulating protein function. By detecting changes in molecular weight before and after modifications, mass spectrometry helps identify modification sites and types. Tandem mass spectrometry (MS/MS) enables further fragmentation of peptide segments after protein digestion, allowing precise localization of modification sites and providing strong evidence for understanding the relationship between modifications and protein function.
Mass spectrometry has also made significant advancements in the study of higher-order protein structures. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique for studying protein conformation and dynamics. Hydrogen atoms in proteins exchange with deuterium atoms at different rates, depending on the protein's environment. By measuring the changes in peptide molecular weight before and after exchange, HDX-MS can reveal information about protein secondary and tertiary structures, as well as domain interactions. For example, in studies of protein-small molecule interactions, HDX-MS can identify drug-binding sites and conformational changes in proteins, providing important structural insights for drug development.
However, there are limitations to using mass spectrometry to determine protein structure. While mass spectrometry provides valuable information on sequence, modifications, and some higher-order structural features, it cannot yet determine the complete atomic-resolution three-dimensional structure of a protein on its own. It is more often used in combination with other techniques, such as X-ray crystallography and NMR, to achieve comprehensive protein structural analysis. For example, in the study of membrane proteins, which are difficult to crystallize, mass spectrometry can be used for sequence analysis, modification identification, and initial structural domain studies, which can then be complemented by other techniques to determine the full three-dimensional structure.
Mass spectrometry plays an indispensable role in protein structure research. It provides critical information on protein sequence, modifications, and some aspects of higher-order structure. While it cannot yet independently determine atomic-resolution three-dimensional structures, when used in conjunction with other techniques, it greatly advances protein structure research. This has significant implications for understanding protein function, addressing related diseases, and developing new biologic drugs, making mass spectrometry a pivotal tool in modern protein science.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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