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Advances in Protein Molecular and Structural Biology Methods

  • Book
  • January 2022
  • Elsevier Science and Technology
  • ID: 5446523

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.

Please Note: This is an On Demand product, delivery may take up to 11 working days after payment has been received.

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 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

Timir Tripathi Regional Director of Indira Gandhi National Open University (IGNOU), Regional Centre Kohima, Nagaland, India. Timir Tripathi is the Regional Director of Indira Gandhi National Open University (IGNOU), Regional Centre Kohima, Nagaland, India. Earlier, he served as Senior Assistant Professor and Principal Investigator at the Department of Biochemistry, North-Eastern Hill University, Shillong, India. He holds a Ph.D. from the Central Drug Research Institute, Lucknow, India. He was a visiting faculty at ICGEB, New Delhi, India (2011), and Khon Kaen University, Thailand (2015). He is known for his research in the fields of protein biophysics, biochemistry, structural biology, and drug discovery. He has over 16 years of experience in teaching and research on protein structure, function, and dynamics at the post-graduate and doctoral levels. He has developed and improved methods to investigate and analyze proteins. His research areas include protein interaction dynamics and understanding the roles of non-catalytic domains in regulating the catalytic activity of proteins. The common theme in his research is an interest in understanding biological phenomena involving proteins at the molecular, structural, and mechanistic levels. He has handled several research grants as a principal investigator from various national and international funding agencies, including DST-Russian Foundation for Basic Research, UGC-Israel Science Foundation, DBT, SERB, DHR, and ICMR. He has received several awards, including Prof. B.K. Bachhawat Memorial Young Scientist Lecture Award (2020) by the National Academy of Sciences, India, ISCB-Young Scientist Award (2019), ICMR-Shakuntala Amir Chand Prize (2018), BRSI-Malviya Memorial Award (2017), DST Fasttrack Young Scientist Award (2012), DBT Overseas Associateship Award (2012), Dr. D.M. Bose Award (2008), etc. He is an elected member of the National Academy of Sciences, India, and the Royal Society of Biology, UK. He has published more than 100 research papers, reviews, commentaries, viewpoints, and editorial articles in international journals, has edited three books, and published several book chapters. He currently serves on the editorial boards of several international journals, including International Journal of Biological Macromolecules, Acta Tropica, Scientific Reports, PLoS One, etc. 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.