Abstract
The first mass spectrometry device was made in 1912 by J. J. Thomson. Until the early 1900s, the analysis of small molecules was mainly performed using electronic ionization (EI) and chemical ionization (CI) methods. However, in 1969 Beckey and others developed the electric field desorption (FD) method to analyze the molecular weight distribution of high molecular weight compounds. In subsequent years, electrospray ionization (ESI) and the matrix-assisted laser desorption/ionization (MALDI) methods have been widely used for the analysis of high molecular weight compounds such as proteins and sugars. Significant progress has been made in genomic analysis. For the proteome to be analyzed (e.g., all proteins can be included in an individual sample), mass spectrometry is needed. Recently, mass spectrometry has played an important role in the analysis of protein complexes, particularly in determining the stoichiometry of protein within complexes as well as proteomic analysis. Importantly, the mass measurement of molecular complexes composed of proteins or of proteins and low molecular weight compounds through non-covalent interactions has been enabled, accelerating the understanding of biological phenomena and drug development. In this chapter, we describe the use of mass spectrometry for the analysis of non-covalent protein–protein interactions and protein–low molecular weight compound complexes. We also discuss the validation of the molecular masses of proteins within protein complexes by using mass spectrometry.
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References
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207
Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci U S A 90:5011–5015
Uchiyama S, Kobayashi S, Takata H, Ishihara T, Hori N, Higashi T, Hayashihara K, Sone T, Higo D, Nirasawa T, Takao T, Matsunaga S, Fukui K (2005) Proteome analysis of human metaphase chromosomes. J Biol Chem 280:16994–17004
Kosinska Eriksson U, Fischer G, Friemann R, Enkavi G, Tajkhorshid E, Neutze R (2013) Subangstrom resolution X-ray structure details aquaporin-water interactions. Science 340:1346–1349
Enokizono Y, Kumeta H, Funami K, Kumeta H, Funami K, Horiuchi M, Sarmiento J, Yamashita K, Standley DM, Matsumoto M, Seya T, Inagaki F (2013) Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling. Proc Natl Acad Sci U S A 110:19908–19913
Nogi T, Yasui N, Mihara E, Matsunaga Y, Noda M, Yamashita N, Toyofuku T, Uchiyama S, Goshima Y, Kumanogoh A, Takagi J (2010) Structural basis for semaphorin signalling through the plexin receptor. Nature 467:1123–1127
Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71
Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yohida T (1988) Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2:151–153
Aquilina JA, Benesch JLP, Ding LL, Yaron O, Horwitz J, Robinson CV (2005) Subunit exchange of polydisperse proteins: mass spectrometry reveals consequences of alphaA-crystallin truncation. J Biol Chem 280:14485–14491
Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K (2005) Structure and dynamic properties of nucleosome core particles. FEBS Lett 579:895–898
Gaillard PH, Martini EM, Kaufman PD, Stillman B, Moustacchi E, Almouzni G (1996) Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86:887–896
Hu F, Alcasabas AA, Elledge SJ (2001) Asf1 links Rad53 to control of chromatin assembly. Genes Dev 15:1061–1066
Mosammaparast N, Ewart CS, Pemberton LF (2002) A role for nucleosome assembly protein 1 in the nuclear transport of histones H2A and H2B. EMBO J 21:6527–6538
McBryant SJ, Peersen OB (2004) Self-association of the yeast nucleosome assembly protein 1. Biochemistry 43:10592–10599
Fejes Toth K, Mazurkiewicz J, Rippe K (2005) Association states of nucleosome assembly protein 1 and its complexes with histones. J Biol Chem 280:15690–15699
Noda M, Uchiyama S, McKay AR, Morimoto A, Misawa S, Yoshida A, Shimahara H, Takinowaki H, Nakamura S, Kobayashi Y, Matsunaga S, Ohkubo T, Robinson CV, Fukui K (2011) Assembly states of the nucleosome assembly protein 1 (NAP-1) revealed by sedimentation velocity and non-denaturing mass spectrometry. Biochem J 436:101–112
Kliewer SA, Umesono K, Noonan DJ, Heyman RA, Evans RM (1992) Convergence of 9-cis retinoic acid and peroxisome proliferator signalling pathways through heterodimer formation of their receptors. Nature 358:771–774
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Noda, M., Fukui, K., Uchiyama, S. (2016). Mass Spectrometry. In: Senda, T., Maenaka, K. (eds) Advanced Methods in Structural Biology. Springer Protocols Handbooks. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56030-2_11
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DOI: https://doi.org/10.1007/978-4-431-56030-2_11
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