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Chapter B2 - Structure function studies

from Part B - Mass spectrometry

Published online by Cambridge University Press:  05 November 2012

Igor N. Serdyuk ,
Nathan R. Zaccai  and
Joseph Zaccai
Igor N. Serdyuk
Affiliation:
Institute of Protein Research, Moscow
Nathan R. Zaccai
Affiliation:
University of Bristol
Joseph Zaccai
Affiliation:
Institut de Biologie Structurale, Grenoble
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Summary

Protein structure and function

ESI and MALDI have become increasingly useful for the mass spectrometric analysis of proteins. The two ionisation techniques have been exploited to study protein folding, to characterise non-covalent protein complexes, to map protein function and for many other applications (Comment B2.1).

Comment B2.1: Mass spectrometry and X-ray crystallography

It is very useful to use mass spectrometry prior to X-ray crystallography. Indeed, the determination of a protein structure at atomic resolution takes a considerable investment of time and effort (see Chapter G3). Mass spectrometry permits a rapid check of the correctness of the accepted primary structure of a protein, and high-resolution determination of the purity of protein preparations. The information is particularly important for proteins obtained by recombinant techniques, which are subject to a number a special sources of error, including unanticipated mutations, modifications, termination and proteolitic degradation. A simple molecular mass measurement is so informative and time saving that there is a reason to obtain the mass spectrum of virtually every protein before it is subject to X-ray crystallography. It is especially important for proteins produced with special amino acid residues (e.g. selenomethionine), for NMR with 13C and/or 15N enrichment and for neutron small-angle scattering with specific deuteration. In the last case the incorporation of deuterium into biological macromolecules by biosynthetic methods is routinely determined by mass spectrometry measurements.

Mass determination

ESI and MALDI have made the mass analysis of proteins a routine procedure.

Type
Chapter
Information
Methods in Molecular Biophysics
Structure, Dynamics, Function
 , pp. 136 - 170
Publisher: Cambridge University Press
Print publication year: 2007

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References

Chait, B. T. (1994). Mass spectrometry – useful tool for protein X-ray crystallographer and NMR spectroscopist. Structure, 2, 465–467.CrossRefGoogle ScholarPubMed
Winston, R. L., and Fitzgerald, M. C. (1997). Mass spectrometry as a readout of protein structure and function. Mass Spectr. Rev., 16, 165–179.3.0.CO;2-F>CrossRefGoogle ScholarPubMed
Rostom, A. A., and Robinson, C. V. (1999). Disassembly of protein complexes in the gas phase. Curr. Opin. Struct. Biol., 9, 135–141.CrossRefGoogle ScholarPubMed
Miranker, A. D. (2000). Protein complexes and analysis of their assembly by mass spectrometry. Curr. Opin. Struct. Biol., 10, 601–606.CrossRefGoogle ScholarPubMed
Dobo, A., and Kaltashov, I. A. (2001). Detection of multiple protein conformational ensembles in solution via deconvolution of charge-state distribution in ESI MS. Anal. Chem., 73, 4763–4772.CrossRefGoogle Scholar
Nielsen, M. L., Bennet, K. L., Larsen, B., Monniate, M., and Mann, M. (2002). Peptide end sequencing by orthogonal MALDI tandem mass spectroscopy. J. Proteome Res., 1, 63–71.CrossRefGoogle Scholar
Link, A. J., Eng, J., et al. (1999). Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol., 17, 676–682.CrossRefGoogle ScholarPubMed
Jungblut, P., and Thiede, B. (1997). Protein identification from 2-DE gels by MALDI mass spectrometry.Mass Spectr. Rev., 16, 145–162.3.0.CO;2-H>CrossRefGoogle ScholarPubMed
Godovach-Zimmermann, J., and Brown, L. R. (2001). Perspectives for mass spectrometry and functional proteomics. Mass Spectr. Rev., 20, 1–57.3.0.CO;2-J>CrossRefGoogle Scholar
Ogorzalek Loo, R. R., Cavalcoli, J. D., et al. (2001). Virtual 2-D gel electrophoresis: visualization and analysis of the E. coli proteome by mass spectrometry. Anal. Chem., 73, 4063–4070.CrossRefGoogle Scholar
Nordhoff, E., Kirpekar, F., and Roepstorff, P. (1996). Mass spectrometry of nucleic acids. Mass Spectr. Rev., 15, 67–138.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Murray, K. K. (1996). DNA sequencing by mass spectrometry. J. Mass Spectr., 31, 1203–1215.3.0.CO;2-3>CrossRefGoogle ScholarPubMed
Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. (1998). Infrared MALDI mass spectrometry of large nucleic acids. Science, 281, 260–262.CrossRefGoogle ScholarPubMed
Crain, P. F., and McCloskay, J. A. (1998). Application of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Curr. Opin. Biotechnol., 9, 25–34.CrossRefGoogle Scholar
Karlsson, K. A. (1989). Animal glycosphingolipids as membrane attachment sites for bacteria. Ann. Rev. Biochem., 58, 309–350.CrossRefGoogle ScholarPubMed
Solouki, T., Reinhold, B. B., et al. (1998). Electrospray ionization and matrix-assisted laser desorption/ionisation Fourier transform ion cyclotron resonance mass spectrometry of permethylated oligosaccarides. Anal. Chem., 70, 857–864.CrossRefGoogle Scholar
Rostom, A., Fucini, P., et al. (2000). Detection and selective dissociation of intact ribosomes in a mass spectrometer. Proc. Natl. Acad. Sci. USA, 97, 5185–5190.CrossRefGoogle Scholar
Lay, J. O. (2001). MALDI-TOF mass spectrometry of bacteria. Mass Spectr. Rev., 20, 172–194.CrossRefGoogle Scholar
Guo, B. (1999). Mass spectrometry in DNA analysis. Anal. Chem., 71, 333–337R.CrossRefGoogle ScholarPubMed
Pacholski, M. L., and Winograd, N. (1999). Imaging with mass spectrometry. Chem. Rev., 99, 2977–3005.CrossRefGoogle ScholarPubMed
Chait, B. T. (1994). Mass spectrometry – useful tool for protein X-ray crystallographer and NMR spectroscopist. Structure, 2, 465–467.CrossRefGoogle ScholarPubMed
Winston, R. L., and Fitzgerald, M. C. (1997). Mass spectrometry as a readout of protein structure and function. Mass Spectr. Rev., 16, 165–179.3.0.CO;2-F>CrossRefGoogle ScholarPubMed
Rostom, A. A., and Robinson, C. V. (1999). Disassembly of protein complexes in the gas phase. Curr. Opin. Struct. Biol., 9, 135–141.CrossRefGoogle ScholarPubMed
Miranker, A. D. (2000). Protein complexes and analysis of their assembly by mass spectrometry. Curr. Opin. Struct. Biol., 10, 601–606.CrossRefGoogle ScholarPubMed
Dobo, A., and Kaltashov, I. A. (2001). Detection of multiple protein conformational ensembles in solution via deconvolution of charge-state distribution in ESI MS. Anal. Chem., 73, 4763–4772.CrossRefGoogle Scholar
Nielsen, M. L., Bennet, K. L., Larsen, B., Monniate, M., and Mann, M. (2002). Peptide end sequencing by orthogonal MALDI tandem mass spectroscopy. J. Proteome Res., 1, 63–71.CrossRefGoogle Scholar
Link, A. J., Eng, J., et al. (1999). Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol., 17, 676–682.CrossRefGoogle ScholarPubMed
Jungblut, P., and Thiede, B. (1997). Protein identification from 2-DE gels by MALDI mass spectrometry.Mass Spectr. Rev., 16, 145–162.3.0.CO;2-H>CrossRefGoogle ScholarPubMed
Godovach-Zimmermann, J., and Brown, L. R. (2001). Perspectives for mass spectrometry and functional proteomics. Mass Spectr. Rev., 20, 1–57.3.0.CO;2-J>CrossRefGoogle Scholar
Ogorzalek Loo, R. R., Cavalcoli, J. D., et al. (2001). Virtual 2-D gel electrophoresis: visualization and analysis of the E. coli proteome by mass spectrometry. Anal. Chem., 73, 4063–4070.CrossRefGoogle Scholar
Nordhoff, E., Kirpekar, F., and Roepstorff, P. (1996). Mass spectrometry of nucleic acids. Mass Spectr. Rev., 15, 67–138.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Murray, K. K. (1996). DNA sequencing by mass spectrometry. J. Mass Spectr., 31, 1203–1215.3.0.CO;2-3>CrossRefGoogle ScholarPubMed
Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. (1998). Infrared MALDI mass spectrometry of large nucleic acids. Science, 281, 260–262.CrossRefGoogle ScholarPubMed
Crain, P. F., and McCloskay, J. A. (1998). Application of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Curr. Opin. Biotechnol., 9, 25–34.CrossRefGoogle Scholar
Karlsson, K. A. (1989). Animal glycosphingolipids as membrane attachment sites for bacteria. Ann. Rev. Biochem., 58, 309–350.CrossRefGoogle ScholarPubMed
Solouki, T., Reinhold, B. B., et al. (1998). Electrospray ionization and matrix-assisted laser desorption/ionisation Fourier transform ion cyclotron resonance mass spectrometry of permethylated oligosaccarides. Anal. Chem., 70, 857–864.CrossRefGoogle Scholar
Rostom, A., Fucini, P., et al. (2000). Detection and selective dissociation of intact ribosomes in a mass spectrometer. Proc. Natl. Acad. Sci. USA, 97, 5185–5190.CrossRefGoogle Scholar
Lay, J. O. (2001). MALDI-TOF mass spectrometry of bacteria. Mass Spectr. Rev., 20, 172–194.CrossRefGoogle Scholar
Guo, B. (1999). Mass spectrometry in DNA analysis. Anal. Chem., 71, 333–337R.CrossRefGoogle ScholarPubMed
Pacholski, M. L., and Winograd, N. (1999). Imaging with mass spectrometry. Chem. Rev., 99, 2977–3005.CrossRefGoogle ScholarPubMed

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