Structural Proteomics: High-Throughput Methods

ISBN-13: 9781617377891 / Angielski / Miękka / 2010 / 602 str.

Bostjan Kobe; Mitchell Guss; Thomas Huber

Opis

The objective of this volume is to provide readers with a current view of all aspects of the 'pipeline' that takes protein targets to structures and how these have been optimised. This volume includes chapters describing, in-depth, the individual steps in the Structural Genomics pipeline, as well as less detailed overviews of individual Structural Genomics initiatives. It is the first book of protocols to cover techniques in a new and emerging field.

Recenzje

From the reviews:

"This book compiles an impressive array of contributions from a variety of contributors ... usually in a format that is accessible to any jobbing structural biologist, or those other molecular biologists with an linking to press their molecular targets into crystal screens or NMR tubes. ... In sum, this is a book it is useful to have to hand ... ." (Paul C. Driscoll, ChemBioChem, Issue 9, August, 2008)

"This book ... details some of the `tricks of the trade' involved in the field of structural genomics. ... This will be a useful text for laboratories already involved in fields covered in the book who want to increase the number of projects in the lab or for those who want to expand into neighbouring fields." (Darren Thompson, Microbiology Today, November, 2008)

Spis treści

Section 1: Protein target selection, bioinformatic approaches and data management Target selection for structural genomics: An Overview. Russell L. Marsden and Christine A. Orengo A General target selection method for crystallographic proteomics. Gautier Robin, Nathan P. Cowieson, Gregor Guncar, Jade Forwood, Pawel Listwan, David A. Hume, Bostjan Kobe, Jennifer L. Martin, Thomas Huber Target Selection: Triage in the Structural Genomics Battlefield. James Raftery. Data Management in Structural Genomics: An Overview. S. Haquin, E. Oeuillet, A. Pajon, M. Harris, A.T. Jones, H. van Tilbeurgh, J.L. Markley, Z. Zolnai, and A. Poupon Data deposition and annotation at the Worldwide Protein Data Bank. Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M. Berman Prediction of protein disorder. Zsuzsanna Dosztányi and Peter Tompa Protein domain prediction. Helgi Ingolfsson and Golan Yona Protein Structure Modeling With MODELLER. Narayanan Eswar, David Eramian, Ben Webb, Min-Yi Shen and Andrej Sali Section 2: Protein production High throughput cloning with restriction enzymes. Volker Sievert, Asgar Ergin and Konrad Büssow Automated recombinant protein expression screening in Escherichia coli. Didier Busso, Matthieu Stierlé, Jean-Claude Thierry and Dino Moras From no expression to high-level soluble expression in Escherichia coli by screening a library of the target protein with randomized N-terminus. Kyoung Hoon Kim, Jin Kuk Yang, Geoffrey S. Waldo, Thomas C. Terwilliger, and Se Won Suh Application of High-Throughput Methodologies to the Expression of Recombinant Proteins in E. coli. YoavPeleg and Tamar Unger A high-throughput platform for eukaryotic genes. Yunjia Chen, Shihong Qiu, Chi-Hao Luan and 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, Peter Loppnau, Catrine Johansson, Eidarus Salah, Nadia H. Pantic Assembly of protein complexes by co-expression in prokaryotic and eukaryotic hosts. Anastassis Perrakis and Christophe Romier Cell-free protein synthesis for analysis by NMR spectroscopy. Margit A. Apponyi, Kiyoshi Ozawa, Nicholas E. Dixon and Gottfried Otting A medium or high-throughput protein refolding assay. Nathan P. Cowieson, Beth Wensley, Gautier Robin, Gregor Guncar, Jade Forwood, David A. Hume, Bostjan Kobe and Jennifer L. Martin Structural Proteomics of Membrane Proteins: A Survey of Published Techniques and Design of a Rational High-Throughput Strategy. Melissa Swope Willis and Christopher M. Koth Section 3: Biophysical and functional chatacterization of proteins Methods for protein characterization by mass spectrometry, thermal shift (ThermoFluor) assay, and multi-angle or static light scattering. Joanne E. Nettleship, James Brown, Matthew R. Groves and Arie Geerlof High-Throughput Methods for Analyzing Transition Metals in Proteins on a Microgram Scale. Anelia Atanassova, Martin Högbom and 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, Cheryl H. Arrowsmith, Alexander F. Yakunin Section 4: Structural characterization of

O autorze

The objective of this volume of Methods in Molecular Biology on Structural Proteomics: High-throughput methods is to provide readers with a current view of all aspects of the 'pipeline' that takes protein targets to structures and how these have been optimised. This is the first book of protocols to cover techniques in a new and emerging field. The volume includes chapters describing, in-depth, the individual steps in the Structural Genomics pipeline, as well as less detailed overviews of individual Structural Genomics initiatives. The readers are encouraged to access further details on the methodologies in on-line resources and in the cited literature. We emphasize that most methods are as amenable to small laboratories as to large consortia, and do not require major investments in facilities. It is hoped that this volume will help smaller laboratories establish some of the high-throughput techniques.

Blurb

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.