Mass spectrometry noncovalent protein analysis

Benkestock, K. Sundqvist, G. Edlund, P. O. Roeraade, J. Influence of droplet size, capillary-cone distance and selected instrumental parameters for the analysis of noncovalent protein-ligand complexes by nanoelectrospray ionization mass spectrometry. J. Mass Spectrom. 2004, 39,1059-1067. 

Characterization of noncovalent bonding of the proteins can also be done using MS. For example MALDI MS has been used in measurement of the molecular mass of the noncovalendy linked tetramer of glucose isomerase, a complex consisting of identical monomers of 43.1 kDa each. MALDI-TOFF peptide mass fingerprinting combined with electrospray tandem mass spectrometry can efficiently solve many complicated peptide protein analysis problems. 

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To benefit general readers, the discussion has been limited to methodologies that are accessible to nonspecialists and that can be carried out on commercially available spectrometers without special modifications. The chapter illustrates the principles of mass spectrometry by demonstrating how various techniques [MALDI, ESI, Fourier transform ion cyclotron resonance (FT-ICR), ion traps, and tandem mass spectrometry (MS-MS)] work. It also provides examples of utilizing mass spectrometry to solve biological and biochemical problems in the field of protein analysis, protein folding, and noncovalent interactions of protein-DNA complexes. 

Electrospray mass spectrometry has developed into a well-established method of wide scope and potential over the past 15 years. The softness of electrospray ionization has made this technique an indispensable tool for biochemical and biomedical research. Electrospray ionization has revolutionized the analysis of labile biopolymers, with applications ranging from the analysis of DNA, RNA, oligonucleotides, proteins as well as glycoproteins to carbohydrates, lipids, gly-colipids, and lipopolysaccharides, often in combination with state-of-the-art separation techniques like liquid chromatography or capillary electrophoresis [1,2]. Beyond mere analytical applications, electrospray ionization mass spectrometry (ESMS) has proven to be a powerful tool for collision-induced dissociation (CID) and multiple-stage mass spectrometric (MSn) analysis, and - beyond the elucidation of primary structures - even for the study of noncovalent macromolecular complexes [3]. 

A particular advantage of ESTMS for biomolecule analysis is realized by generating the analyte ions from solution conditions that retain the secondary, tertiary and even quaternary structure of the biomoT ecules. Noncovalent binding of biomolecules has been observed in the ESI mass spectrum and, when operated under the appropriate conditions, the mass spectral data are a direct probe of the solution-phase biomolecule assembly. Protein assemblies, protein-nucleic acid complexes, duplex DNA and other non-covalently bound biomolecule assemblies have been studied using mass spectrometry. 

The use of cross-linkers for the study of noncovalent interactions by mass spectrometry helps to circumvent one of the major issues of the analysis dissociation of the interactions during analysis. Even if the use of chemical cross-linkers and mass spectrometry is a rapidly growing area, it is still not yet a generally applicable technique for characterizing protein complexes. The synthesis of new cross-linkers and the improvement of emichment strategies for the cross-linked species are needed to further develop this promising technique. 

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