Membrane Proteomics: Methods and Protocols (Methods in Molecular Biology, 528)

✍ Scribed by Matthew J. Peirce (editor), Robin Wait (editor)

• Publisher: Humana
• Year: 2009
• Tongue: English
• Leaves: 339
• Category: Library

✦ 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.

✦ Table of Contents

Preface
Contents
Contributors
Part I. In Silico Methods for Prediction of Membrane Protein Hydrophobicity and Topology
Online Tools for Predicting Integral Membrane Proteins
Henry Bigelow and Burkhard Rost
In Silico Identification of Novel G ProteinCoupled Receptors
Matthew N. Davies and Darren R. Flower
Transcriptome-Based Identification of CandidateMembrane Proteins
Edward J. Evans, Lawrence Hene, Mai Vuong, S. Hussain I. Abidi,and Simon J. Davis
Part II. Extraction and Purification of Membrane Proteins
Part A. Plant Membrane Proteins
Separation of Thylakoid Membrane Proteins by Sucrose Gradient Ultracentrifugation or Blue Native-SDS-PAGE Two-Dimensional Electrophoresis
Gian Maria D'Amici, Christian G. Huber, and Lello Zolla
Part B. Prokaryotic Membrane Proteins
Extraction of Yeast Mitochondrial Membrane Proteins by Solubilization and Detergent/Polymer Aqueous Two-Phase Partitioning
Henrik Everberg, Niklas Gustavsson, and Folke Tjerneld
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
Part C. Mammalian Membrane Proteins
Sequential Detergent Extraction Prior to Mass Spectrometry Analysis
Fiona M. McCarthy, Amanda M. Cooksey, and Shane C. Burgess
Enrichment of Brain Plasma Membranes by Affinity Two-Phase Partitioning
Jens Schindler and Hans Gerd Nothwang
Protocol to Enrich and Analyze Plasma Membrane Proteins
Jacek R. Wisniewski
Proteomic Analysis of the Lymphocyte Plasma Membrane Using Cell Surface Biotinylation and Solution-Phase Isoelectric Focusing
Matthew J. Peirce, Andrew P. Cope, and Robin Wait
Identification of Target Membrane Proteins as Detected by Phage Antibodies
Cecile A.W. Geuijen, Arjen Q. Bakker, and John de Kruif
Membrane Protease Degradomics: Proteomic Identification and Quantification of Cell Surface Protease Substrates
Georgina S. Butler, Richard A. Dean, Derek Smith, and Christopher M. Overall
Purification of Basolateral Integral Membrane Proteins by Cationic Colloidal Silica-Based Apical Membrane Subtraction
Robert J.A. Goode and Richard J. Simpson
Moving Closer to the Lipid Raft Proteome Using Quantitative Proteomics
Leonard J. Foster
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
Isolation of Extracellular Membranous Vesicles for Proteomic Analysis
Rommel A. Mathias, Justin W. Lim, Hong Ji, and Richard J. Simpson
Part III. Separation of Membrane Proteins
Enrichment of Human Platelet Membranes for Proteomic Analysis
David W. Greening, Kristen M. Glenister, Rosemary L. Sparrow, and Richard J. Simpson
Detergents and Chaotropes for Protein Solubilization Before Two-Dimensional Electrophoresis
Thierry Rabilloud
Two-Dimensional Separation of Membrane Proteins by 16-BAC-SDS-PAGE
Hans Gerd Nothwang and Jens Schindler
Part IV. Identification and Quantification of Membrane Proteins
MudPIT Analysis: Application to Human Heart Tissue
Kelli G. Kline and Christine C. Wu
Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis
Nan Wang, J. Bryce Young and Liang Li
Cysteinyl-Tagging of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry
Srijeet K. Mitra and Michael B. Goshe
Quantitative Proteomics Analysis of Pancreatic Zymogen Granule Membrane Proteins
Xuequn Chen and Philip C. Andrews
978-1-60327-310-7_BookBackmatter_OnlinePDF.pdf
Index