Proteomics for drug discovery : methods and protocols

✍ Scribed by Kontoyianni, Maria.; Lazar, Alexandru C.; Lazar, Iulia M

• Publisher: Humana Press : Springer
• Year: 2017
• Tongue: English
• Leaves: 304
• Series: Methods in molecular biology 1647
• Category: Library

✦ Synopsis

This book reflects the drug development communitys interest in proteomics methods by providing researchers with the necessary knowledge for the implementation of a number of basic experimental and bioinformatics protocols in the drug discovery research laboratory. The focus of the collection is on select protocols and methodologies that address the analysis of post-translational modifications, targeted protein quantification, protein-protein, protein-lipid, or protein-ATP interactions, in silicolead identification, protein arrays, tissue and cell extract preparation, labeling, chemoproteomics, and drug efficacy assessment. Emphasis was placed not just on methods that describe large-scale protein analysis, but also on ones that are amenable to future implementation in a high-throughput format. Written in the highly successfulMethods in Molecular Biologyseries format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative,Proteomics for Drug Discovery: Methods and Protocolsaims to provide a deep knowledge of the fundamentals of disease biology as well the means that were developed for probing the complex biological milieu. Read more...

Abstract:

This book reflects the drug development community's interest in proteomics methods by providing researchers with the necessary knowledge for the implementation of a number of basic experimental and bioinformatics protocols in the drug discovery research laboratory. Read more...

✦ Table of Contents

Front Matter ....Pages i-xi
A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates (Jason R. Thomas, Scott M. Brittain, Jennifer Lipps, Luis Llamas, Rishi K. Jain, Markus Schirle)....Pages 1-18
Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins (Yi Chen, Kate J. Fisher, Mark Lloyd, Elizabeth R. Wood, Domenico Coppola, Erin Siegel et al.)....Pages 19-45
Monitoring Dynamic Changes of the Cell Surface Glycoproteome by Quantitative Proteomics (Mathias Kalxdorf, Hans Christian Eberl, Marcus Bantscheff)....Pages 47-59
High-Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics: An Application to Study the Quantitative Changes Induced by Histone Modifying Enzyme Inhibitors and Activators (Michael J. Sweredoski, Annie Moradian, Sonja Hess)....Pages 61-69
Preparation and Immunoaffinity Depletion of Fresh Frozen Tissue Homogenates for Mass Spectrometry-Based Proteomics in the Context of Drug Target/Biomarker Discovery (DaRue A. Prieto, King C. Chan, Donald J. Johann Jr, Xiaoying Ye, Gordon Whitely, Josip Blonder)....Pages 71-90
Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules (Jacqui L. Mendez-Johnson, Danette L. Daniels, Marjeta Urh, Rachel Friedman Ohana)....Pages 91-108
Microfluidics-Mass Spectrometry of Protein-Carbohydrate Interactions: Applications to the Development of Therapeutics and Biomarker Discovery (Alina D. Zamfir)....Pages 109-128
Studying Protein–Protein Interactions by Biotin AP-Tagged Pulldown and LTQ-Orbitrap Mass Spectrometry (Zhongqiu Xie, Yuemeng Jia, Hui Li)....Pages 129-138
Post-Translational Modification Profiling-Functional Proteomics for the Analysis of Immune Regulation (Avital Eisenberg-Lerner, Ifat Regev, Yifat Merbl)....Pages 139-152
Reverse Phase Protein Arrays and Drug Discovery (Kenneth G. Macleod, Bryan Serrels, Neil O. Carragher)....Pages 153-169
Probing Protein Kinase-ATP Interactions Using a Fluorescent ATP Analog (Leslie E. W. LaConte, Sarika Srivastava, Konark Mukherjee)....Pages 171-183
Preparation of Disease-Related Protein Assemblies for Single Particle Electron Microscopy (A. Cameron Varano, Naoe Harafuji, William Dearnaley, Lisa Guay-Woodford, Deborah F. Kelly)....Pages 185-196
Identification of Lipid Binding Modulators Using the Protein-Lipid Overlay Assay (Tuo-Xian Tang, Wen Xiong, Carla V. Finkielstein, Daniel G. S. Capelluto)....Pages 197-206
Resazurin Live Cell Assay: Setup and Fine-Tuning for Reliable Cytotoxicity Results (José Á. Rodríguez-Corrales, Jatinder S. Josan)....Pages 207-219
Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows (Alexander Goncearenco, Minghui Li, Franco L. Simonetti, Benjamin A. Shoemaker, Anna R. Panchenko)....Pages 221-236
Method to Identify Silent Codon Mutations That May Alter Peptide Elongation Kinetics and Co-translational Protein Folding (Ronald Worthington, Elijah Ball, Brentsen Wolf, Gregory Takacs)....Pages 237-243
In Silico Design of Anticancer Peptides (Shailesh Kumar, Hui Li)....Pages 245-254
Docking and Virtual Screening in Drug Discovery (Maria Kontoyianni)....Pages 255-266
Bioinformatics Resources for Interpreting Proteomics Mass Spectrometry Data (Iulia M. Lazar)....Pages 267-295
Back Matter ....Pages 297-302

✦ Subjects

Drug development -- Laboratory manuals;Proteomics -- Laboratory manuals;Drug development;Proteomics;Drug Discovery -- methods