Structural Proteomics High Throughput Methods 1st Edition by Bostjan Kobe, Mitchell Guss, Thomas Huber ISBN 978-1588298096 1588298096

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ISBN 10:  1588298096

ISBN 13: 978-1588298096

Author: Bostjan Kobe, Mitchell Guss, Thomas Huber

Structural genomics is a newly emerging field that has arisen following the successful footsteps of the major sequencing efforts generally bundled under the heading “genomics”. In Structural Proteomics: High Throughput Methods, readers are provided with a current view of all aspects of the ‘pipeline’ that takes protein targets to structures and how these have been optimized. This volume includes chapters describing in-depth the individual steps in the Structural Genomics pipeline, as well as overviews of individual Structural Genomics initiatives. Topics include Target Selection for structural genomics, Protein structure modeling, High-throughput cloning, Mass Spectrometry modeling. Structural Proteomics: High Throughput Methods, encourages its readers to access further details on the methodologies in on-line resources as well as in cited literature making it an invaluable resource. Most methods in this important book are as amenable to small laboratories as to large consortia, and do not require major investments in facilities. This essential volume provides insight into the diversity of approaches adopted by different laboratories and proves that ‘high throughput’ is really the defining characteristic of structural genomics.

 

Table of contents: 

Protein Target Selection, Bioinformatic Approaches, and Data Management
Target Selection for Structural Genomics: An Overview
Russell L. Marsden, Christine A. Orengo

A General Target Selection Method for Crystallographic Proteomics
Gautier Robin, Nathan P. Cowieson, Gregor Guncar, Jade K. Forwood, Pawel Listwan, David A. Hume et al.

Target Selection: Triage in the Structural Genomics Battlefield
James Raftery

Data Management in Structural Genomics: An Overview
Sabrina Haquin, Eric Oeuillet, Anne Pajon, Mark Harris, Alwyn T. Jones, Herman van Tilbeurgh et al.

Data Deposition and Annotation at the Worldwide Protein Data Bank
Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura et al.

Prediction of Protein Disorder
Zsuzsanna Dosztányi, Peter Tompa

Protein Domain Prediction
Helgi Ingolfsson, Golan Yona

Protein Structure Modeling with MODELLER
Narayanan Eswar, David Eramian, Ben Webb, Min-Yi Shen, Andrej Sali

Protein Production
High Throughput Cloning with Restriction Enzymes
Volker Sievert, Asgar Ergin, Konrad Büssow

Automated Recombinant Protein Expression Screening in Escherichia coli
Didier Busso, Matthieu Stierlé, Jean-Claude Thierry, Dino Moras

From No Expression to High-Level Soluble Expression in Escherichia coli by Screening a Library of the Target Proteins with Randomized N-Termini
Kyoung Hoon Kim, Jin Kuk Yang, Geoffrey S. Waldo, Thomas C. Terwilliger, Se Won Suh

Application of High-Throughput Methodologies to the Expression of Recombinant Proteins in E. coli
Yoav Peleg, Tamar Unger

A High Throughput Platform for Eukaryotic Genes
Yunjia Chen, Shihong Qiu, Chi-Hao Luan, Ming Luo

High Throughput Production of Recombinant Human Proteins for Crystallography
Opher Gileadi, Nicola A. Burgess-Brown, Steve M. Colebrook, Georgina Berridge, Pavel Savitsky, Carol E. A. Smee et al.

Assembly of Protein Complexes by Coexpression in Prokaryotic and Eukaryotic Hosts: an Overview
Anastassis Perrakis, Christophe Romier

Cell-Free Protein Synthesis for Analysis by NMR Spectroscopy
Margit A. Apponyi, Kiyoshi Ozawa, Nicholas E. Dixon, Gottfried Otting

A Medium or High Throughput Protein Refolding Assay
Nathan P. Cowieson, Beth Wensley, Gautier Robin, Gregor Guncar, Jade Forwood, David A. Hume et al.

Structural Proteomics of Membrane Proteins: a Survey of Published Techniques and Design of a Rational High Throughput Strategy
Melissa Swope Willis, Christopher M. Koth

Biophysical and Functional Characterization of Proteins
High Throughput Methods for Analyzing Transition Metals in Proteins on a Microgram Scale
Anelia Atanassova, Martin Högbom, Deborah B. Zamble

High Throughput Screening of Purified Proteins for Enzymatic Activity
Michael Proudfoot, Ekaterina Kuznetsova, Stephen A. Sanders, Claudio F. Gonzalez, Greg Brown, Aled M. Edwards et al.

Structural Characterization of Proteins
Strategies for Improving Crystallization Success Rates
Rebecca Page

Protein Crystallization in Restricted Geometry: Advancing Old Ideas for Modern Times in Structural Proteomics
Joseph D. Ng, Raymond C. Stevens, Peter Kuhn

Fluorescence Approaches to Growing Macromolecule Crystals
Marc Pusey, Elizabeth Forsythe, Aniruddha Achari

Efficient Macromolecular Crystallization Using Microfluidics and Randomized Design of Screening Reagents
Andrew P. May, Brent W. Segelke

Increasing Protein Crystallization Screening Success with Heterogeneous Nucleating Agents
Anil S. Thakur, Janet Newman, Jennifer L. Martin, Bostjan Kobe

High Throughput pH Optimization of Protein Crystallization
Ran Meged, Orly Dym, Joel L. Sussman

Automated Structure Solution with the PHENIX Suite
Peter H. Zwart, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Li-Wei Hung, Thomas R. Ioerger, Airlie J. McCoy et al.

NMR Screening for Rapid Protein Characterization in Structural Proteomics
Justine M. Hill

Microcoil NMR Spectroscopy: a Novel Tool for Biological High Throughput NMR Spectroscopy
Russell E. Hopson, Wolfgang Peti

Protein Structure Determination Using a Combination of Cross-linking, Mass Spectrometry, and Molecular Modeling
Dmitri Mouradov, Gordon King, Ian L. Ross, Jade K. Forwood, David A. Hume, Andrea Sinz et al.

Structural Proteomics Initiatives Overviews
Structural Genomics of Minimal Organisms: Pipeline and Results
Sung-Hou Kim, Dong-Hae Shin, Rosalind Kim, Paul Adams, John-Marc Chandonia

Structural Genomics of Pathogenic Protozoa: an Overview
Erkang Fan, David Baker, Stanley Fields, Michael H. Gelb, Frederick S. Buckner, Wesley C. Van Voorhis et al.

High Throughput Crystallography at SGC Toronto: an Overview
Alexey Bochkarev, Wolfram Tempel

The Structural Biology and Genomics Platform in Strasbourg: an Overview
Didier Busso, Jean-Claude Thierry, Dino Moras

Bacterial Structural Genomics Initiative: Overview of Methods and Technologies Applied to the Process of Structure Determination
Miroslaw Cygler, Ming-ni Hung, John Wagner, Allan Matte

High Throughput Protein Production and Crystallization at NYSGXRC
Michael J. Sauder, Marc E. Rutter, Kevin Bain, Isabelle Rooney, Tarun Gheyi, Shane Atwell et al.

Overview of the Pipeline for Structural and Functional Characterization of Macrophage Proteins at the University of Queensland
Weining Meng, Jade K. Forwood, Gregor Guncar, Gautier Robin, Nathan P. Cowieson, Pawel Listwan et al.

*Structural Genomics of the Bacterial Mobile Metagenome: an Overview

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Tags: Bostjan Kobe, Mitchell Guss, Thomas Huber, Structural Proteomics, High Throughput Methods