Advances in Protein Molecular and Structural Biology Methods
Editat de Timir Tripathi, Vikash Kumar Dubeyen Limba Engleză Paperback – 19 ian 2022
It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application.
- Presents a thorough overview of the latest and emerging methods and technologies for protein study
- Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy
- Includes computational and machine learning methods
- Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
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Specificații
ISBN-13: 9780323902649
ISBN-10: 0323902642
Pagini: 714
Ilustrații: 160 illustrations (40 in full color)
Dimensiuni: 216 x 276 mm
Editura: ELSEVIER SCIENCE
ISBN-10: 0323902642
Pagini: 714
Ilustrații: 160 illustrations (40 in full color)
Dimensiuni: 216 x 276 mm
Editura: ELSEVIER SCIENCE
Cuprins
Section I: Techniques to optimize recombinant protein expression in bacteria, yeast, insect, and mammalian cells
1. Strategies to Improve the Expression and Solubility of Recombinant Proteins in Bacteria
Niharika Nag, Heena Khan, and Timir Tripathi
2. Advances in Heterologous Protein Expression Strategies in Yeast and Insect Systems
Meenakshi Singh, Smita Gupta, Arun Kumar Rawat, Sudhir Kumar Singh
3. Methods for Transient Expression and Purification of Monoclonal Antibodies in Mammalian Cells
Suchitra Kamle, Dawei Li, Chun Geun Lee, Jack A. Elias
4. Methods for Recombinant Production and Purification of Intrinsically Disordered Proteins
Steffen P. Graether
Section 2: Biophysical techniques including, NMR, X-ray crystallography, cryo-EM, etc.
5. Methods to Determine the Oligomeric Structure of Proteins
Purna Bahadur Chetri, Heena Khan, and Timir Tripathi
6. Multimodal Methods to Study Protein Aggregation and Fibrillation
Maria Georgina Herrera, Marco Giampà, Nicolo Tonali and Veronica Isabel Dodero
7. Experimental Methods to Study the Thermodynamics of Protein-Protein Interactions
Santanu Sasidharan, Niharika Nag, Timir Tripathi, and Prakash Saudagar
8. Experimental Methods to Study the Kinetics of Protein-Protein Interactions
Abhay Narayan Singh, Kristijan Ramadan, Shalini Singh
9. Computational Techniques to Study Protein-Protein Interactions
Khattab Al-Khafaji, Tugba Taskin-Tok
10. Experimental Methods to Study Protein-Nucleic Acid Interactions
Roberto Giambruno, Jakob Rupert, and Elsa Zacco
11. Advanced Computational Tools for Quantitative Analysis of Protein-nucleic acid Interfaces
Sunandan Mukherjee and Chandran Nithin
12. Experimental Techniques to Study Protein Dynamics and Conformations
Akshita Gupta, Anamika Singh, Nabeel Ahmad, Tej P. Singh, Sujata Sharma, Pradeep Sharma
13. Computational Techniques to Study Protein Dynamics and Conformations
Laura Orellana, Anil Mhashal, and Agusti Emperador
14. Application of Circular Dichroism Spectroscopy in Studying Protein Folding, Stability, and Interaction
Md. Anzarul Haque, Punit Kaur, Asimul Islam, and Md. Imtaiyaz Hassan
15. Studying Protein Folding Dynamics using Single Molecule Fluorescence Methods
Narattam Mandal, Krishnananda Chattopadhyay, Achinta Sannigrahi
16. Advances in Liquid-state NMR Spectroscopy to Study the Structure, Function, and Dynamics of Biomacromolecules
Priyanka Aggarwal, Pooja Kumari and Neel Sarovar Bhavesh
17. In-Cell NMR Spectroscopy: A Tool for Cellular Structure Biology
Vijay Kumar
18. Current Trends in Membrane Protein Crystallography
Koomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, Appu K. Singh
19. Advances in Sample Preparation and Data Processing for Single-particle Cryo-Electron Microscopy
Anshul Assaiya, Suparna Bhar and Janesh Kumar
20. Advanced Mass Spectrometry-Based Approaches for Molecular-Structural Biologists
Joanna Bons, Jacob Rose, Amy O’Broin, and Birgit Schilling
21. Developments, Advancements, and Contributions of Mass Spectrometry in Omics Technologies
Saravanan Kumar
22. Role of Structural Biology Methods in Drug Discovery
Fouzia Nasim and Insaf Ahmed Qureshi
Section 3: Computational methods including MD simulation, coupling MD and deep machine learning, etc
23. Prediction, Validation, and Analysis of Protein Structures: A Beginner’s Guide
Santanu Sasidharan and Prakash Saudagar
24. Advances in Structure-Based Virtual Screening for Drug Discovery
Olujide O. Olubiyi, Suman Samantray and Alexander-Maurice Illig
25. Methods and Applications of Machine Learning in Structure-Based Drug Discovery
Madhumathi Sanjeevi, Prajna N Hebbar, Natarajan Aiswarya, Rashmi S., Chandrasekar Narayanan Rahul, Ajitha Mohan, Jeyaraman Jeyakanthan and Kanagaraj Sekar
26. Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics
Aditya K. Padhi, Matej Janezic, Kam Y. J. Zhang
27. Applications of Molecular Dynamics Simulations in Drug Discovery
Xubo Lin
28. Envisaging the Conformational Space of Proteins by Coupling Machine Learning and Molecular Dynamics
Murali Aarthy, Sanjeev Kumar Singh
29. Immunoinformatics and Reverse Vaccinology Methods to Design Peptide-based Vaccines
Vinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, Vijay Kumar Prajapati
Section 4: Tools and techniques to study IDPs
30. Computational Methods to Study Intrinsically Disordered Proteins
Prateek Kumar, Aparna Bhardwaj, Vladimir N. Uversky, Timir Tripathi, and Rajanish Giri
31. Experimental Methods to Study Intrinsically Disordered Proteins
Niharika Nag, Purna B Chetri, Vladimir N. Uversky, Rajanish Giri, and Timir Tripathi
32. Analysis of Structure and Dynamics of Intrinsically Disordered Regions in Proteins using Solution NMR Methods
Nikita V Saibo, Snigdha Maiti, Bidisha Acharya, and Soumya De
33. Methods to Study the Effect of Solution Variables on the Conformational Dynamics of IDPs
Hakan Alıcı, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber
34. Molecular Simulations to Study IDP-IDP Interactions and Their Complexes
Kota Kasahara
Section 5: Protein interaction networks, signaling, engineering, and function, etc.
35. Exploring Large-Scale Protein Function using Systematic Mutant Analysis
Amrita Arpita Padhy, Subhashree Sahoo, Shivani Kumari, Varsha Kumari, Parul Mishra
36. Approaches and Methods to Study Cell Signaling: Linguistics of Cellular Communication
Siddharth Neog and Vishal Trivedi
37. Methods to Study Systems Biology of Signaling Networks: A Case Study of NSCLC
Nikhil H. Samarth and Shailza Singh
38. Advancements in the Analysis of Protein Post-Translational Modifications
Sandip Mukherjee, Ritesh Kumar, Arianne L. Theiss, and K. Venuprasad
39. Protein Engineering: Methods and Applications
Saurabh Bansal and Bishwajit Kundu
40. Designer 3D-DNA Nanodevices: Structures, Functions and Cellular Applications
Kahkashan Bansal, Anjali Rajwar, and Dhiraj Bhatia
1. Strategies to Improve the Expression and Solubility of Recombinant Proteins in Bacteria
Niharika Nag, Heena Khan, and Timir Tripathi
2. Advances in Heterologous Protein Expression Strategies in Yeast and Insect Systems
Meenakshi Singh, Smita Gupta, Arun Kumar Rawat, Sudhir Kumar Singh
3. Methods for Transient Expression and Purification of Monoclonal Antibodies in Mammalian Cells
Suchitra Kamle, Dawei Li, Chun Geun Lee, Jack A. Elias
4. Methods for Recombinant Production and Purification of Intrinsically Disordered Proteins
Steffen P. Graether
Section 2: Biophysical techniques including, NMR, X-ray crystallography, cryo-EM, etc.
5. Methods to Determine the Oligomeric Structure of Proteins
Purna Bahadur Chetri, Heena Khan, and Timir Tripathi
6. Multimodal Methods to Study Protein Aggregation and Fibrillation
Maria Georgina Herrera, Marco Giampà, Nicolo Tonali and Veronica Isabel Dodero
7. Experimental Methods to Study the Thermodynamics of Protein-Protein Interactions
Santanu Sasidharan, Niharika Nag, Timir Tripathi, and Prakash Saudagar
8. Experimental Methods to Study the Kinetics of Protein-Protein Interactions
Abhay Narayan Singh, Kristijan Ramadan, Shalini Singh
9. Computational Techniques to Study Protein-Protein Interactions
Khattab Al-Khafaji, Tugba Taskin-Tok
10. Experimental Methods to Study Protein-Nucleic Acid Interactions
Roberto Giambruno, Jakob Rupert, and Elsa Zacco
11. Advanced Computational Tools for Quantitative Analysis of Protein-nucleic acid Interfaces
Sunandan Mukherjee and Chandran Nithin
12. Experimental Techniques to Study Protein Dynamics and Conformations
Akshita Gupta, Anamika Singh, Nabeel Ahmad, Tej P. Singh, Sujata Sharma, Pradeep Sharma
13. Computational Techniques to Study Protein Dynamics and Conformations
Laura Orellana, Anil Mhashal, and Agusti Emperador
14. Application of Circular Dichroism Spectroscopy in Studying Protein Folding, Stability, and Interaction
Md. Anzarul Haque, Punit Kaur, Asimul Islam, and Md. Imtaiyaz Hassan
15. Studying Protein Folding Dynamics using Single Molecule Fluorescence Methods
Narattam Mandal, Krishnananda Chattopadhyay, Achinta Sannigrahi
16. Advances in Liquid-state NMR Spectroscopy to Study the Structure, Function, and Dynamics of Biomacromolecules
Priyanka Aggarwal, Pooja Kumari and Neel Sarovar Bhavesh
17. In-Cell NMR Spectroscopy: A Tool for Cellular Structure Biology
Vijay Kumar
18. Current Trends in Membrane Protein Crystallography
Koomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, Appu K. Singh
19. Advances in Sample Preparation and Data Processing for Single-particle Cryo-Electron Microscopy
Anshul Assaiya, Suparna Bhar and Janesh Kumar
20. Advanced Mass Spectrometry-Based Approaches for Molecular-Structural Biologists
Joanna Bons, Jacob Rose, Amy O’Broin, and Birgit Schilling
21. Developments, Advancements, and Contributions of Mass Spectrometry in Omics Technologies
Saravanan Kumar
22. Role of Structural Biology Methods in Drug Discovery
Fouzia Nasim and Insaf Ahmed Qureshi
Section 3: Computational methods including MD simulation, coupling MD and deep machine learning, etc
23. Prediction, Validation, and Analysis of Protein Structures: A Beginner’s Guide
Santanu Sasidharan and Prakash Saudagar
24. Advances in Structure-Based Virtual Screening for Drug Discovery
Olujide O. Olubiyi, Suman Samantray and Alexander-Maurice Illig
25. Methods and Applications of Machine Learning in Structure-Based Drug Discovery
Madhumathi Sanjeevi, Prajna N Hebbar, Natarajan Aiswarya, Rashmi S., Chandrasekar Narayanan Rahul, Ajitha Mohan, Jeyaraman Jeyakanthan and Kanagaraj Sekar
26. Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics
Aditya K. Padhi, Matej Janezic, Kam Y. J. Zhang
27. Applications of Molecular Dynamics Simulations in Drug Discovery
Xubo Lin
28. Envisaging the Conformational Space of Proteins by Coupling Machine Learning and Molecular Dynamics
Murali Aarthy, Sanjeev Kumar Singh
29. Immunoinformatics and Reverse Vaccinology Methods to Design Peptide-based Vaccines
Vinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, Vijay Kumar Prajapati
Section 4: Tools and techniques to study IDPs
30. Computational Methods to Study Intrinsically Disordered Proteins
Prateek Kumar, Aparna Bhardwaj, Vladimir N. Uversky, Timir Tripathi, and Rajanish Giri
31. Experimental Methods to Study Intrinsically Disordered Proteins
Niharika Nag, Purna B Chetri, Vladimir N. Uversky, Rajanish Giri, and Timir Tripathi
32. Analysis of Structure and Dynamics of Intrinsically Disordered Regions in Proteins using Solution NMR Methods
Nikita V Saibo, Snigdha Maiti, Bidisha Acharya, and Soumya De
33. Methods to Study the Effect of Solution Variables on the Conformational Dynamics of IDPs
Hakan Alıcı, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber
34. Molecular Simulations to Study IDP-IDP Interactions and Their Complexes
Kota Kasahara
Section 5: Protein interaction networks, signaling, engineering, and function, etc.
35. Exploring Large-Scale Protein Function using Systematic Mutant Analysis
Amrita Arpita Padhy, Subhashree Sahoo, Shivani Kumari, Varsha Kumari, Parul Mishra
36. Approaches and Methods to Study Cell Signaling: Linguistics of Cellular Communication
Siddharth Neog and Vishal Trivedi
37. Methods to Study Systems Biology of Signaling Networks: A Case Study of NSCLC
Nikhil H. Samarth and Shailza Singh
38. Advancements in the Analysis of Protein Post-Translational Modifications
Sandip Mukherjee, Ritesh Kumar, Arianne L. Theiss, and K. Venuprasad
39. Protein Engineering: Methods and Applications
Saurabh Bansal and Bishwajit Kundu
40. Designer 3D-DNA Nanodevices: Structures, Functions and Cellular Applications
Kahkashan Bansal, Anjali Rajwar, and Dhiraj Bhatia