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.
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Table of Contents
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 Giamp�, 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 Alici, 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
Authors
Timir Tripathi Molecular and Structural Biophysics Laboratory, Department of Zoology, School of Life Sciences, North-Eastern Hill University, Shillong, Meghalaya, India.Prof. Timir Tripathi is a Professor of Molecular Biology in the Department of Zoology, School of Life Sciences, North-Eastern Hill University, Shillong, India. Earlier, he served as the Regional Director of Indira Gandhi National Open University, Kohima, Nagaland (2022-2023), where he contributed significantly to educational leadership, governance, and management. Before this, he was Senior Assistant Professor and Principal Investigator at the Department of Biochemistry, NEHU, Shillong (2009-2022). He holds a Ph.D. from Jawaharlal Nehru University, New Delhi, while working at the Central Drug Research Institute, Lucknow. He was a visiting faculty at ICGEB, New Delhi, India, and Khon Kaen University, Thailand. His research interests lie in the field of protein-substrate interaction and dynamics and understanding the roles of non-catalytic domains in regulating the catalytic activity of proteins. His primary focus is studying the conformational dynamics, interaction, and stabilization of the complexes formed by intrinsically disordered neuropathological protein aggregates, their properties of liquid-liquid phase separation, interaction, and roles in nucleocytoplasmic transport in neurodegenerative diseases. In addition, he is interested in analyzing the structural and functional characteristics of drug target proteins from the helminth liver fluke parasite Fasciola gigantica to identify new therapeutic strategies. He has received several national and international awards. He is an Associate Fellow of the Indian National Science Academy, New Delhi, and an elected member of the National Academy of Sciences, India, the Royal Society of Chemistry, and the Royal Society of Biology, UK. He has handled several research grants as a principal investigator from various national and international funding agencies. He has published over 100 research papers, reviews, commentaries, viewpoints, outlooks, and editorial articles in international journals, and has contributed several book chapters. He has edited six books and authored two textbooks for undergraduate and postgraduate students. Currently, he serves as the editor of the International Journal of Biological Macromolecules (Elsevier), senior editor of Critical Insights in Biophysics (Taylor & Francis), and is a member of the editorial boards of Scientific Reports and Acta Tropica.
Vikash Kumar Dubey Professor, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India. Vikash Kumar Dubey is a Professor at the School of Biochemical Engineering and Associate Dean for Academic Affairs at the Indian Institute of Technology (BHU), Varanasi, India. Prior to joining IIT (BHU), he was a postdoctoral fellow at Florida State University, USA before joining IIT Guwahati, India, where he served as Associate Professor and Professor. He has published over 130 articles in peer-reviewed journals and over 80 conference presentations/proceedings. He has seven awarded and licensed USA patents and many Indian patents. He has also written several book chapters and has guided a number of PhD students, MTech students, and postdoctoral fellows. He has received several awards and has been elected as a member of a number of scientific societies and academies; Among these, he is currently the Vice President of the Bioinformatics and Drug Discovery Society [BIDDS], India and a Fellow of the Royal Society of Biology, UK.
