Advances in Protein Molecular and Structural Biology Methods

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 Dedication Contents Contributors About the Editors Foreword • Amit Sharma Preface 1. Strategies to improve the expression and solubility of recombinant proteins in E. coli • 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, and Sudhir Kumar Singh 3. Methods for transient expression and purification of monoclonal antibodies in mammalian cells • Suchitra Kamle, Dawei Li, Chun Geun Lee, and Jack A. Elias 4. Methods for recombinant production and purification of intrinsically disordered proteins • Steffen P. Graether 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 studythe kinetics of protein–protein interactions • Abhay Narayan Singh, Kristijan Ramadan, and Shalini Singh 9. Computational techniques for studying protein-protein interactions • Khattab Al-Khafaji and 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–nucleicacid 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, and Pradeep Sharma 13. Computational techniques to study protein dynamics and conformations • Anil Mhashal, Agusti Emperador, and Laura Orellana 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, and 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 to study cellular structure biology • Vijay Kumar 18. Current trends in membrane protein crystallography • Koomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, and 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 methods for protein 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 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, S. Rashmi, Chandrashekar 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 Janežic, and 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 and Sanjeev Kumar Singh 29. Immunoinformatics and reverse vaccinology methods to design peptide-based vaccines • Vinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, and Vijay Kumar Prajapati 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 Bahadur 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 intrinsically disordered proteins • Hakan Alici, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber 34. Molecular simulations to study IDP-IDP interactions and their complexes • Kota Kasahara 35. Exploring large-scale protein function using systematic mutant analysis • Amrita Arpita Padhy, Subhashree Sahoo, Kummari Shivani, Varsha Kumari, and 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 • Anjali Rajwar, Payal Vaswani, A. Hema Naveena, and Dhiraj Bhatia Index Intro -- Advances in Protein Molecular and Structural Biology Methods -- Copyright -- Dedication -- Contents -- Contributors -- About the Editors -- Foreword -- Preface -- Chapter 1 Strategies to improve the expression and solubility of recombinant proteins in E. coli -- 1 Introduction -- 2 Before starting with protein expression -- 3 Materials required -- 4 Standard protocol for recombinant protein expression in E. coli -- 4.1 For protein solubilization -- 4.2 For protein purification -- 5 Troubleshooting strategies -- 5.1 Handling protein expression and solubility issues -- 5.1.1 DNA sequence and codon bias issues -- 5.1.2 Varying host strain -- 5.1.3 Isopropyl β-d-1-thiogalactopyranoside (IPTG) -- 5.1.4 Temperature -- 5.1.5 Culture media -- 5.1.6 Buffer additives -- 5.1.7 Glycerol -- 5.1.8 Detergents -- 5.1.9 Ethanol -- 5.1.10 Co-expression of chaperones -- 5.1.11 Folding modulators or fusion partner proteins -- 5.2 Handling of inclusion bodies -- 5.3 Handling protein leakage -- 5.4 Handling of toxic proteins -- 5.5 Handling of unstable proteins -- 5.6 Posttranslational modifications -- 6 Conclusion and future perspectives -- References -- Chapter 2 Advances in heterologous protein expression strategies in yeast and insect systems -- 1 Introduction -- 2 Heterologous protein expression strategies in yeast systems -- 2.1 Introduction -- 2.2 Synthetic gene optimization -- 2.3 Expression optimization by controlling gene copy number -- 2.4 Optimization of promoters -- 2.5 Engineering yeast secretion pathway -- 2.5.1 Polypeptide targeting and translocation -- 2.5.2 ER engineering by modulating UPR and ERAD activity -- 2.5.3 Intracellular protein trafficking engineering -- 2.5.4 Modification vacuolar sorting pathway and protease disruption -- 2.5.5 Glycoengineering strategies in yeast expression systems