Membrane Proteomics - Methods and Protocols

The membranes surrounding cells and organelles constitute their interface with the local environment. The functions of membrane proteins include cell/cell and cell/extracellular matrix recognition, the reception and transduction of extracellular signals, and the tra- port of proteins, solutes and water molecules. Abnormal membrane protein expression has profound biological effects and may, for example, underlie phenotypic and functional differences between normal and tumour cells. Moreover the accessibility, particularly of plasma proteins traversing the plasma membrane of cells, makes them of particular ut- ity to the therapeutic intervention in disease. Indeed, it is estimated that of all currently licensed pharmaceuticals, approximately 70% target proteins resident in the plasma m- brane. In theory, unbiased technologies such as proteomics have the power to de?ne patterns of membrane protein expression characteristic of distinct states of cellular development, differentiation or disease, and thereby identify novel markers of, or targets for intervention in, disease. However, although about 25% of open reading frames in fully sequenced genomes are estimated to encode integral membrane proteins, global analysis of membrane protein expression has proved problematic. Membrane protein analysis poses unique challenges at the level of extraction, solubilization, and separation in particular, and to a lesser extent of identi?cation and quantitation. These challenges have, however, fostered creativity, in- vation, and technical advances, many of which are brought together in Membrane P- teomics.

List of contents

In Silico Methods for Prediction of Membrane Protein Hydrophobicity and Topology.- Online Tools for Predicting Integral Membrane Proteins.- In Silico Identification of Novel G Protein Coupled Receptors.- Transcriptome-Based Identification of Candidate Membrane Proteins.- Extraction and Purification of Membrane Proteins.- Separation of Thylakoid Membrane Proteins by Sucrose Gradient Ultracentrifugation or Blue Native-SDS-PAGE Two-Dimensional Electrophoresis.- Extraction of Yeast Mitochondrial Membrane Proteins by Solubilization and Detergent/Polymer Aqueous Two-Phase Partitioning.- 16-BAC/SDS-PAGE Analysis of Membrane Proteins of Yeast Mitochondria Purified by Free Flow Electrophoresis.- Sequential Detergent Extraction Prior to Mass Spectrometry Analysis.- Enrichment of Brain Plasma Membranes by Affinity Two-Phase Partitioning.- Protocol to Enrich and Analyze Plasma Membrane Proteins.- Proteomic Analysis of the Lymphocyte Plasma Membrane Using Cell Surface Biotinylation and Solution-Phase Isoelectric Focusing.- Identification of Target Membrane Proteins as Detected by Phage Antibodies.- Membrane Protease Degradomics: Proteomic Identification and Quantification of Cell Surface Protease Substrates.- Purification of Basolateral Integral Membrane Proteins by Cationic Colloidal Silica-Based Apical Membrane Subtraction.- Moving Closer to the Lipid Raft Proteome Using Quantitative Proteomics.- Use of Sequential Chemical Extractions to Purify Nuclear Membrane Proteins for Proteomics Identification.- Isolation of Extracellular Membranous Vesicles for Proteomic Analysis.- Separation of Membrane Proteins.- Enrichment of Human Platelet Membranes for Proteomic Analysis.- Detergents and Chaotropes for Protein Solubilization Before Two-Dimensional Electrophoresis.- Two-Dimensional Separation of Membrane Proteins by 16-BAC-SDS-PAGE.- Identification and Quantification of Membrane Proteins.- MudPIT Analysis: Application to Human Heart Tissue.- Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis.- Cysteinyl-Tagging of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry.- Quantitative Proteomics Analysis of Pancreatic Zymogen Granule Membrane Proteins.

Summary

The membranes surrounding cells and organelles constitute their interface with the local environment. The functions of membrane proteins include cell/cell and cell/extracellular matrix recognition, the reception and transduction of extracellular signals, and the tra- port of proteins, solutes and water molecules. Abnormal membrane protein expression has profound biological effects and may, for example, underlie phenotypic and functional differences between normal and tumour cells. Moreover the accessibility, particularly of plasma proteins traversing the plasma membrane of cells, makes them of particular ut- ity to the therapeutic intervention in disease. Indeed, it is estimated that of all currently licensed pharmaceuticals, approximately 70% target proteins resident in the plasma m- brane. In theory, unbiased technologies such as proteomics have the power to de?ne patterns of membrane protein expression characteristic of distinct states of cellular development, differentiation or disease, and thereby identify novel markers of, or targets for intervention in, disease. However, although about 25% of open reading frames in fully sequenced genomes are estimated to encode integral membrane proteins, global analysis of membrane protein expression has proved problematic. Membrane protein analysis poses unique challenges at the level of extraction, solubilization, and separation in particular, and to a lesser extent of identi?cation and quantitation. These challenges have, however, fostered creativity, in- vation, and technical advances, many of which are brought together in Membrane P- teomics.

Additional text

From the reviews:

"This is an important resource for investigators interested in understanding patterns of membrane protein expression … which are helpful in the identification of novel markers of, or targets for intervention in, disease. … It will be quite useful for research investigators and students interested in this field. … This book will be a valuable resource for investigators and students interested in learning about membrane proteomic methodologies. … High quality illustrations greatly help the understanding of the material." (Omer Iqbal, Doody’s Review Service, June, 2009)

Report

From the reviews:

"This is an important resource for investigators interested in understanding patterns of membrane protein expression ... which are helpful in the identification of novel markers of, or targets for intervention in, disease. ... It will be quite useful for research investigators and students interested in this field. ... This book will be a valuable resource for investigators and students interested in learning about membrane proteomic methodologies. ... High quality illustrations greatly help the understanding of the material." (Omer Iqbal, Doody's Review Service, June, 2009)

Product details

• Assisted by: Matthe J Peirce (Editor), Matthew J Peirce (Editor), Matthew J. Peirce (Editor), Wait (Editor), Wait (Editor), Robin Wait (Editor)
• Publisher: Springer, Berlin
• Languages: English
• Product format: Paperback / Softback
• Released: 16.03.2011
• EAN: 9781617378898
• ISBN: 978-1-61737-889-8
• No. of pages: 342
• Weight: 871 g
• Illustrations: XIII, 342 p.
• Series: Methods in Molecular Biology; Methods in Molecular Biology
• Subjects: Natural sciences, medicine, IT, technology > Biology > Biochemistry, biophysics; B, Life Sciences, biochemistry, proteins, Biomedical and Life Sciences, Cellular biology (cytology), Biochemistry, general, Membrane Biology, Cell membranes, Membrane Trafficking, Protein Science