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 North-Eastern Hill University.Professor Timir Tripathi is a Professor of Molecular Biology, School of Life Sciences, North-Eastern Hill University, Shillong, India. Earlier, he served as the Regional Director of Indira Gandhi National Open University. His previous role was Senior Assistant Professor and Principal Investigator at the Department of Biochemistry, NEHU, Shillong. He holds a Ph.D. from Jawaharlal Nehru University, New Delhi. His primary research 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. Professor Tripathi 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
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.
