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Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also…mehr
Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering.
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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Inhaltsangabe
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 Al c , 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
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 Al c , 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
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