Applying mass spectrometry to study non‐covalent biomolecule complexes

Abstract

Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.

Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations

“…6 Electrospray ionization (ESI) allows the transfer of proteins and multi-protein complexes into the gas phase. [9][10][11][12] The resulting ions can be analyzed by mass spectrometry (MS), ion mobility spectrometry (IMS), and other gas phase techniques. [13][14][15][16][17][18][19][20] The question whether electrosprayed macromolecules retain their solution structures has attracted considerable attention.…”

Oligonucleotide aptamers: emerging affinity probes for bioanalytical mass spectrometry and biomarker discovery

“…65 Chen and Gulbakan reported that the aptamer-protein interactions could also be studied by high resolution MALDI MS provided that sample preparation conditions were finetuned and -aza-2 thiothymine was used as the MALDI matrix. 66 …”

Interactions of indole alkaloids with myoglobin: A mass spectrometry based spectrometric and computational method

“…UV and fluorescence spectroscopies and other spectroscopic methods can probe the structural changes of protein complexes based on the integral spectra for the analytes of interest, but are lacking in specific information of individual species and chemical stoichiometry. Native electrospray ionization mass spectrometry (native ESI‐MS) has proven to be a powerful tool for studying protein complexes, and it has been used to reveal the existence of noncovalent protein complexes and provide stoichiometric information and association constants . The affinity between proteins and drug molecule ligands is important for physiological and pathological processes, conducive to the development of new treatment methods for associated diseases.…”

“…Native electrospray ionization mass spectrometry (native ESI-MS) has proven to be a powerful tool for studying protein complexes, and it has been used to reveal the existence of noncovalent protein complexes and provide stoichiometric information and association constants. [8][9][10][11][12][13][14] The affinity between proteins and drug molecule ligands is important for physiological and pathological processes, conducive to the development of new treatment methods for associated diseases.…”