Synopses & Reviews
With the great cellular and therapeutic importance of plasma membrane proteins, unbiased technologies such as proteomics become even more vital as they have the power to define 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. In Membrane Proteomics: Methods and Protocols, leading experts in the field compile a laboratory bench resource which provides a comprehensive toolkit of proven methods. The volume delves into various modifications to standard two-dimensional gel electrophoresis protocols as well as liquid chromatographic methods, protocols for the enrichment of diverse classes of plasma membrane proteins, in silico approaches, and cutting-edge techniques for quantitative membrane protein profiling. Written in the highly successful Methods in Molecular Biology™ series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and easy-to-use, Membrane Proteomics: Methods and Protocols is an ideal guide for investigators wishing to apply state of the art membrane proteomic methodologies in their own research programs.
Review
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)
Review
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)
Synopsis
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.
Synopsis
This book collects together in one volume the diverse practical approaches to analyzing membrane proteins. This is an ideal guide for investigators wishing to apply state-of-the-art membrane proteomic methodologies in their own research programs.
Table of Contents
Section I: In silico Methods for Prediction of Membrane Protein Hydrophobicity and Topology
1. Online Tools for Predicting Integral Membrane Proteins
Henry Bigelow and Burkhard Rost
2. In silico Identification of Novel G Protein Coupled Receptors
Matthew N. Davies and Darren R. Flower
3. Transcriptome-Based Identification of Candidate Membrane Proteins
Edward J. Evans, Lawrence Hene, Mai Vuong, S. Hussain I. Abidi, and Simon J. Davis
Section II: Extraction and Purification of Membrane Proteins
Subsection 1: Plant Membrane Proteins
4. Separation of Thylakoid Membrane Proteins by Sucrose Ultracentrifugation Gradient or Blue Native-SDS-PAGE Two Dimensional Electrophoresis
Gian Maria D'Amici, Christian G. Huber, and Lello Zolla
Subsection 2: Prokaryotic Membrane Proteins
5. Extraction of Yeast Mitochondrial Membrane Proteins by Solubilization and Detergent/Polymer Aqueous Two-Phase Partitioning
Henrik Everberg, Niklas Gustavsson, and Folke Tjerneld
6. 16-BAC/SDS-PAGE Analysis of Membrane Proteins of Yeast Mitochondria Purified by Free Flow Electrophoresis
Ralf J. Braun, Norbert Kinkl, Hans Zischka, and Marius Ueffing
Subsection 3: Mammalian Membrane Proteins
7. Sequential Detergent Extraction Prior to Mass Spectrometry Analysis
Fiona M. McCarthy, Amanda M. Cooksey, and Shane C. Burgess
8. Enrichment of Brain Plasma Membranes by Affinity Two-Phase Partitioning
Jens Schindler and Hans Gerd Nothwang
9. Protocol to Enrich and Analyze Plasma Membrane Proteins
Jacek R. Wisniewski
10. Proteomic Analysis of the Lymphocyte Plasma Membrane Using Cell Surface Biotinylation and Solution-Phase Iso-Electric Focusing
Matthew J. Peirce, Andrew P. Cope, and Robin Wait
11. Identification of Target Membrane Proteins as Detected by Phage Antibodies
Cecile A.W. Geuijen, Arjen Q. Bakker, and John de Kruif
12. Membrane Protease Degradomics: Proteomic Identification and Quantification of Cell Surface Protease Substrates
Georgina S. Butler, Richard A. Dean, Derek Smith, and Christopher M. Overall
13. Purification of Basolateral Integral Membrane Proteins by Cationic Colloidal Silica-Based Apical Membrane Subtraction
Robert J.A. Goode and Richard J. Simpson
14. Moving Closer to the Lipid Raft Proteome Using Quantitative Proteomics
Leonard J. Foster
15. Use of Sequential Chemical Extractions to Purify Nuclear Membrane Proteins for Proteomics Identification
Nadia Korfali, Elizabeth A.L. Fairley, Selene K. Swanson, Laurence Florens, and Eric C. Schirmer
16. Isolation of Extracellular Membranous Vesicles for Proteomic Analysis
Rommel A. Mathias, Justin W. Lim, Hong Ji, and Richard J. Simpson
Section III: Separation of Membrane Proteins
17. Enrichment of Human Platelet Membranes for Proteomic Analysis
David W. Greening, Kristen M. Glenister, Rosemary L. Sparrow, and Richard J. Simpson
18. Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis
Thierry Rabilloud
19. Two-Dimensional Separation of Membrane Proteins by 16-BAC-SDS-PAGE
Hans Gerd Nothwang and Jens Schindler
Section IV: Identification and Quantification of Membrane Proteins
20. MudPIT Analysis: Application to Human Heart Tissue
Kelli G. Kline and Christine C. Wu
21. Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis
Nan Wang, Bryce Young, and Liang Li
22. Cysteinyl-Tagging of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry
Srijeet K. Mitra and Michael B. Goshe
23. Quantitative Proteomics Analysis of Pancreatic Zymogen Granule Membrane Proteins
Xuequn Chen and Philip C. Andrews