Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods. The book opens with an extensive section on protein production, including new methodologies for membrane and metal-binding proteins, as well as high-throughput protein production and screening. It continues with sections on structural analyses and data management, as well as modeling, simulation, and visualization. Overall, the spectrum of topics reflects the trend towards tackling more diverse challenges of studying macromolecular machineries and complexes. Written for the highly successful
Methods in Molecular Biology series, chapters include the type of detail and key implementation advice to ensure successful results.
Authoritative and up-to-date, Structural Genomics: General Applications, Second Edition serves as a vital guide to structural biologists in small to medium-sized laboratories seeking to better utilize this powerful area of study.
Chapter 11 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. For further details see license information in the chapter.
Part I: Protein Production
1. High-Throughput Protein Engineering by Massively Parallel Combinatorial Mutagenesis
Yuk Kei Wan, Gigi C.G. Choi, and Alan S.L. Wong
2. Rational Design and Construction of Active-Site Labeled Enzymes
Man-Wah Tsang, Yun-Chung Leung, and Kwok-Yin Wong
3. Screening and Production of Recombinant Human Proteins: Ligation Independent Cloning
Claire Strain-Damerell, Pravin Mahajan, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola Burgess-Brown
4. Screening and Production of Recombinant Human Proteins: Protein Production in E. coli
Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Alejandra Fernandez-Cid, Opher Gileadi, and Susanne Gräslund
5. Screening and Production of Recombinant Human Proteins: Protein Production in Insect Cells
Pravin Mahajan, Claire Strain-Damerell, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola A. Burgess-Brown
6. Expression Screening of Human Integral Membrane Proteins Using BacMam
Pravin Mahajan, Katherine Ellis, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Gamma Chi, Henry Man, Katharina L. Dürr, and Nicola A. Burgess-Brown
7. High-Throughput Expression Screening in Mammalian Suspension Cells
Susan D. Chapple and Michael R. Dyson
8. In Vitro Production of Perdeuterated Proteins in H2O for Biomolecular NMR Studies
Lionel Imbert, Rachel Lenoir-Capello, Elodie Crublet, Alicia Vallet, Rida Awad, Isabel Ayala, Celine Juillan-Binard, Hubert Mayerhofer, Rime Kerfah, Pierre Gans, Emeric Miclet, and Jerome Boisbouvier
9. Minimizing Heterogeneity of Protein Samples for Metal Transporter Proteins Using SAXS and Metal Radioisotopes
Shah Kamranur Rahman
Part II: Structural Analyses and Data Management
10. Hydrogen/Deuterium Exchange-Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins
Pui-Kin So
11. BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy András Micsonai, Éva Bulyáki, and József Kardos
12. Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb
Andrei L. Turinsky, Sam Dupont, Alexander Botzki, Sabry Razick, Brian Turner,
Ian M. Donaldson, and Shoshana J. Wodak
13. State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and In Vitro Biochemical Experiments
David Cooper, Marek Grabowski, Matthew D. Zimmerman, Przemyslaw J. Porebski, Ivan G. Shabalin, Magdalena Woinska, Marcin J. Domagalski, Heping Zheng, Piotr Sroka, Marcin Cymborowski, Mateusz P. Czub, Ewa Niedzialkowska, Barat S. Venkataramany, Tomasz Osinski, Zbigniew Fratczak, Jacek Bajor, Juliusz Gonera, Elizabeth MacLean, Kamila Wojciechowska, Wojciech Wajerowicz, Maksymilian Chruszcz, and Wladek Minor
Part III: Modeling, Simulation, and Visualization
14. Protein Structure Modeling with MODELLER Benjamin Webb and Andrej Sali
15. Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program
Pengfei Li and Kenneth M. Merz Jr.
16. Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen
Yu Wai Chen, Yong Wang, Yun-Chung Leung, and Kwok-Yin Wong
17. Simulation of Proteins Modified with a Fluorescent Label
Zoe Chan and Yun-Chung Leung
18. Protocol for Simulations of PEGylated Proteins with Martini 3
Fabian Grünewald, Peter C. Kroon, Paulo C.T. Souza, and Siewert J. Marrink
19. Molecular Data Visualization on Mobile Devices: A Quick Starter´s Guide
Chin-Pang Bennu Yiu and Yu Wai Chen
20. Molecular Data Visualization with Augmented Reality (AR) on Mobile Devices
Chin-Pang Bennu Yiu and Yu Wai Chen
This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods. The book opens with an extensive section on protein production, including new methodologies for membrane and metal-binding proteins, as well as high-throughput protein production and screening. It continues with sections on structural analyses and data management, as well as modeling, simulation, and visualization. Overall, the spectrum of topics reflects the trend towards tackling more diverse challenges of studying macromolecular machineries and complexes. Written for the highly successful
Methods in Molecular Biology series, chapters include the type of detail and key implementation advice to ensure successful results.
Authoritative and up-to-date,
Structural Genomics: General Applications, Second Edition serves as a vital guide to structural biologists in small to medium-sized laboratories seeking to better utilize this powerful area of study.
Chapter 11 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. For further details see license information in the chapter.
High-Throughput Protein Engineering by Massively Parallel Combinatorial Mutagenesis.- Rational Design and Construction of Active-Site Labeled Enzymes.- Screening and Production of Recombinant Human Proteins: Ligation Independent Cloning.- Screening and Production of Recombinant Human Proteins: Protein Production in E. coli.- Screening and Production of Recombinant Human Proteins: Protein Production in Insect Cells.- Expression Screening of Human Integral Membrane Proteins Using BacMam.- High-Throughput Expression Screening in Mammalian Suspension Cells.- In Vitro Production of Perdeuterated Proteins in H2O for Biomolecular NMR Studies.- Minimizing Heterogeneity of Protein Samples for Metal Transporter Proteins Using SAXS and Metal Radioisotopes.- Hydrogen/Deuterium Exchange-Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins.- BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy.- Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb.- State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and In Vitro Biochemical Experiments.- Protein Structure Modeling with MODELLER.- Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program.- Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen.- Simulation of Proteins Modified with a Fluorescent Label.- Protocol for Simulations of PEGylated Proteins with Martini 3.- Molecular Data Visualization on Mobile Devices: A Quick Starter's Guide.- Molecular Data Visualization with Augmented Reality (AR) on Mobile Devices.
Inhaltsverzeichnis
Part I: Protein Production
1. High-Throughput Protein Engineering by Massively Parallel Combinatorial Mutagenesis
Yuk Kei Wan, Gigi C.G. Choi, and Alan S.L. Wong
2. Rational Design and Construction of Active-Site Labeled Enzymes
Man-Wah Tsang, Yun-Chung Leung, and Kwok-Yin Wong
3. Screening and Production of Recombinant Human Proteins: Ligation Independent Cloning
Claire Strain-Damerell, Pravin Mahajan, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola Burgess-Brown
4. Screening and Production of Recombinant Human Proteins: Protein Production in E. coli
Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Alejandra Fernandez-Cid, Opher Gileadi, and Susanne Gräslund
5. Screening and Production of Recombinant Human Proteins: Protein Production in Insect Cells
Pravin Mahajan, Claire Strain-Damerell, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola A. Burgess-Brown
6. Expression Screening of Human Integral Membrane Proteins Using BacMam
Pravin Mahajan, Katherine Ellis, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Gamma Chi, Henry Man, Katharina L. Dürr, and Nicola A. Burgess-Brown
7. High-Throughput Expression Screening in Mammalian Suspension Cells
Susan D. Chapple and Michael R. Dyson
8. In Vitro Production of Perdeuterated Proteins in H2O for Biomolecular NMR Studies
Lionel Imbert, Rachel Lenoir-Capello, Elodie Crublet, Alicia Vallet, Rida Awad, Isabel Ayala, Celine Juillan-Binard, Hubert Mayerhofer, Rime Kerfah, Pierre Gans, Emeric Miclet, and Jerome Boisbouvier
9. Minimizing Heterogeneity of Protein Samples for Metal Transporter Proteins Using SAXS and Metal Radioisotopes
Shah Kamranur Rahman
Part II: Structural Analyses and Data Management
10. Hydrogen/Deuterium Exchange-Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins
Pui-Kin So
11. BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy
András Micsonai, Éva Bulyáki, and József Kardos
12. Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb
Andrei L. Turinsky, Sam Dupont, Alexander Botzki, Sabry Razick, Brian Turner,
Ian M. Donaldson, and Shoshana J. Wodak
13. State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and In Vitro Biochemical Experiments
David Cooper, Marek Grabowski, Matthew D. Zimmerman, Przemyslaw J. Porebski, Ivan G. Shabalin, Magdalena Woinska, Marcin J. Domagalski, Heping Zheng, Piotr Sroka, Marcin Cymborowski, Mateusz P. Czub, Ewa Niedzialkowska, Barat S. Venkataramany, Tomasz Osinski, Zbigniew Fratczak, Jacek Bajor, Juliusz Gonera, Elizabeth MacLean, Kamila Wojciechowska, Wojciech Wajerowicz, Maksymilian Chruszcz, and Wladek Minor
Part III: Modeling, Simulation, and Visualization
14. Protein Structure Modeling with MODELLER
Benjamin Webb and Andrej Sali
15. Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program
Pengfei Li and Kenneth M. Merz Jr.
16. Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen
Yu Wai Chen, Yong Wang, Yun-Chung Leung, and Kwok-Yin Wong
17. Simulation of Proteins Modified with a Fluorescent Label
Zoe Chan and Yun-Chung Leung
18. Protocol for Simulations of PEGylated Proteins with Martini 3
Fabian Grünewald, Peter C. Kroon, Paulo C.T. Souza, and Siewert J. Marrink
19. Molecular Data Visualization on Mobile Devices: A Quick Starter's Guide
Chin-Pang Bennu Yiu and Yu Wai Chen
20. Molecular Data Visualization with Augmented Reality (AR) on Mobile Devices
Chin-Pang Bennu Yiu and Yu Wai Chen
Klappentext
This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods. The book opens with an extensive section on protein production, including new methodologies for membrane and metal-binding proteins, as well as high-throughput protein production and screening. It continues with sections on structural analyses and data management, as well as modeling, simulation, and visualization. Overall, the spectrum of topics reflects the trend towards tackling more diverse challenges of studying macromolecular machineries and complexes. Written for the highly successful Methods in Molecular Biology series, chapters include the type of detail and key implementation advice to ensure successful results.
n
Authoritative and up-to-date, Structural Genomics: General Applications, Second Edition serves as a vital guide to structural biologists in small to medium-sized laboratories seeking to better utilize this powerful area of study.
n
n
Chapter 11 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. For further details see license information in the chapter.n
Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
