Abstract
Membrane protein profiling and characterization is of immense importance for the understanding of vital processes taking place across cellular membranes. Traditional techniques used for soluble proteins, such as 2D gel electrophoresis, are sometimes not entirely applicable to membrane protein targets, due to their low abundance and hydrophobic character. New tools have been developed that will accelerate research on membrane protein targets. Lipid-based protein immobilization (LPI) is the core technology in a new approach that enables immobilization and digestion of native membrane proteins inside a flow cell format. The presented method is described in the context of comparing the method to traditional approaches where the sample amount that is digested and analyzed is the same.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ulmschneider, M. B., Sansom, M. S., and Di Nola, A. (2005) Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 59:252–265.
Terstappen, G. C., and Reggiani, A. (2001) In silico research in drug discovery. Trends Pharmacol Sci 22(1):23–26.
Macher, B. A., Yen, T. Y. (2007) Protein at membrane surfaces-a review of approaches. Mol Biosyst 3:705–713.
Santoni, V., Molloy, M., and Rabilloud, T. (2000) Membrane proteins and proteomics: Un amour impossible? Electrophoresis 21:1054–1070.
Stevens, T. J., and Arkin, I. T. (2000) Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins 39:417–420.
Wallin, E., and Heijine, G. (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029–1038.
Blonder, J., Conrads, T. P., Yu, L. R., Terunuma, A., Janini, G. M., Issaq, H. J., Vogel, J. C., and Veenstra, T. D. (2004) A detergent– and cyanogen bromide- free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 4(1):31–45.
Chen, E. I., Cociorva, D., Norris, J. L., and Yates, J. R. (2007) Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res 6(7):2529–2538.
Mitra, S. K., Gantt, J. A., Ruby, J. F., Clouse, S. D., and Goshe, M. B. (2007) Membrane proteomic analysis of Arabidopsis thaliana using alternative solubilization techniques. J Proteome Res 6(5):1933–1950.
Russell, W. K., Park, Z. Y., and Russel, D. H. (2001) Proteolysis in mixed organic-aqueous solvent systems: applications for peptide mass mapping using mass spectrometry. Anal Chem 73(11):2682–2685.
Soskic, V., and Godovac-Zimmermann, J. (2001) Improvement of an in-gel tryptic digestion method for matrix-assisted laser desorption/ionization-time of flight mass spectrometry peptide mapping by sue of volatile solubilizing agents. Proteomics 1(11):1364–1367.
Zhang, N., Chen, R., Young, N., Wishart, D., Winter, P., Weiner, J. H., and Li, L. (2007) Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 7(4):484–493.
Washburn, M. P., Wolters, D., and Yates, J. R. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242–247.
Martosella, J., Zolotarjova, N., Liu, H., Moyer, S. C., Perkins, P. D., and Boyes, B. E. (2006) High recovery HPLC separation of lipid rafts for membrane proteome analysis. J Proteome Res 5(6):1301–1312.
Da Cruz, S., Xenarios, I., Langridge, J., Vilbois, F., Parone, P. A., and Marinou, J. C. (2003) Proteomic analysis of the mouse liver mitochondrial inner membrane. J Biol Chem 278(42):41566–41571.
Lasonder, E., Ishihama, Y., Andersen, J. S., Vermunt, A. M., Pain, A., Sauerwein, R. W., Eling, W. M., Hall, N., Waters, A. P., Stunnenberg, H. G., and Mann, M. (2002) Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419(6909):537–542.
Mhatre, R., Woodard, J. and Zeng, C. (1999) Strategies for locating disulfide bonds in a monoclonal antibody via mass spectrometry. Rapid Commun Mass Spectrom 13(24):2503–2510.
Zhang, W., Marzilli, L. A., Rouse, J. C., and Czupryn, M. J. (2002) Complete disulfide bond assignment of a recombinant immunoglobulin G4 monoclonal antibody. Anal Biochem 311(1):1–9.
Quach, T. T., Richards, D. P., Zheng, J., Keller, B. O., and Li, L. (2003) Development and applications of in-gel CNBr/tryptic digestion combined with mass spectrometry for the analysis of membrane proteins. J Proteome Res 2(5):543–552.
Ball, L. E., Oatis, J. E. Jr., Dharmasiri, K., Busman, M., Wang, J., Cowden, L. B., Galijatovic, A., Chen, N., Crouch, R. K., and Knapp, D. R. (1998) Mass spectrometric analysis of integral membrane proteins: application to complete mapping of bacteriorhodopsins and rhodopsin. Protein Sci 7(3):758–764.
Wu, C. C., and Yates, J. R. (2003) The application of mass spectrometry to membrane proteomics. Nat Biotechnol 21(3):262–267.
Rodriguez-Ortega, M. J., Norais, N., Bensi, G., Liberatori, S., Capo, S., Mora, M., Scarselli, M., Doro, F., Ferrari, G., Garaguso, I., Maggi, T., Neumann, A., Covre, A., Telford, J. L., and Grandi, G. (2006) Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat Biotechnol 24(2):191–197.
Yu. Y. Q., Gilar, M., and Gebler, J. C. (2004) A complete peptide mapping of membrane proteins: a novel surfactant aiding the enzymatic digestion of bacteriorhodopsin. Rapid Commun Mass Spectrom 18:711–715.
Norris, J. L., Porter, N. A., and Caprioli, R. M. (2003) Mass spectrometry of intracellular and membrane proteins using cleavable detergents. Anal Chem 75(23):6642–6647.
Lochner, N., Pittner, F., Wirth, M., and Gabor, F. (2003) Preparation, characterization and application of artificial Caco-2 cell surfaces in the silver nanoparticle enhanced fluorescence technique. J Control Release 89:249–259.
Speer, A. E. and Wu, C. C. (2007) Proteomics of integral membrane proteins – theory and application. Chem Rev 107:3687–3714.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sui, P., Miliotis, T., Davidson, M., Karlsson, R., Karlsson, A. (2011). Membrane Protein Digestion – Comparison of LPI HexaLane with Traditional Techniques. In: Gevaert, K., Vandekerckhove, J. (eds) Gel-Free Proteomics. Methods in Molecular Biology, vol 753. Humana Press. https://doi.org/10.1007/978-1-61779-148-2_9
Download citation
DOI: https://doi.org/10.1007/978-1-61779-148-2_9
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-147-5
Online ISBN: 978-1-61779-148-2
eBook Packages: Springer Protocols