Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics

1st Edition - September 28, 2022
Imprint: Academic Press
Editors: Prakash Saudagar, Timir Tripathi
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 1 2 7 - 8
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 3 6 6 - 1

Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics presents the latest emerging technologies in spectroscopy and advances in established spectrosc… Read more

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Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics presents the latest emerging technologies in spectroscopy and advances in established spectroscopic methods. The book presents a guide to research methods in biomolecular spectroscopy, providing comprehensive coverage of developments in the spectroscopic techniques used to study protein structure and dynamics. Seventeen chapters from leading researchers cover key aspects of spectroscopic methods, with each chapter covering structure, folding, and dynamics. This title will help researchers keep up-to-date on the latest novel methods and advances in established methods.

Cover
Title page
Table of Contents
Copyright
Dedication
Contributors
Editors biography
Foreword
Preface
Chapter 1: Fundamentals of spectroscopy for biomolecular structure and dynamics
Abstract
1: Introduction to spectroscopy
2: General design of a spectrometer instrumentation
3: Various spectroscopic methods
4: Conclusions
References
Chapter 2: Fluorescence-based techniques to assess biomolecular structure and dynamics
Abstract
1: Introduction
2: Environmental effects used in fluorescence structural studies
3: Förster resonance energy transfer
4: Fluorescence quenching
5: Fluorescence anisotropy
6: Diffusion-based estimation of biomolecular size and shape
7: Biomolecules in situ
8: Conclusions
References
Chapter 3: Structural analysis of biomacromolecules using circular dichroism spectroscopy
Abstract
1: Introduction
2: Applications of CD in protein studies
3: Applications of CD in studying polysaccharides
4: Applications of CD in nucleic acid measurements
5: Conclusions and outlook
References
Chapter 4: Nuclear magnetic resonance spectroscopy for protein structure, folding, and dynamics
Abstract
1: Introduction
2: NMR spectroscopy approaches to study protein folding and dynamics
3: Conclusion and future prospects
References
Chapter 5: Advanced NMR spectroscopy methods to study protein structure and dynamics
Abstract
Acknowledgments
1: Introduction
2: Traditional NMR spectroscopy approaches for small-medium-sized proteins
3: Protein backbone dynamics
4: NMR spectroscopy for large proteins
5: Methods for probing protein dynamics of large proteins
6: Methods for simultaneous study of the structure and dynamics of proteins
7: Conclusions
References
Chapter 6: Applications of infrared spectroscopy to study proteins
Abstract
1: Introduction
2: Infrared spectrum
3: Infrared spectrum for the structural characterization of proteins
4: Infrared spectrophotometers
5: Types of IR measurements
6: IR absorption and detection of amino acid side chains
7: IR absorption and detection of the protein backbone
8: IR spectroscopy for studying proteins
9: Studying proteins with IR spectroscopy: Case studies
10: Conclusion and future perspectives
References
Chapter 7: Raman spectroscopy to study biomolecules, their structure, and dynamics
Abstract
Acknowledgments
1: Introduction
2: Applications of Raman spectroscopy
3: Conclusions
References
Chapter 8: Spectroscopic investigation of biomolecular dynamics using light scattering methods
Abstract
1: Introduction
2: Basics of light scattering
3: Applications of light scattering methods
4: Conclusion and future perspectives
References
Chapter 9: Protein footprinting by mass spectrometry: H/D exchange, specific amino acid labeling, and fast photochemical oxidation of proteins
Abstract
Acknowledgments
1: Introduction
2: Hydrogen-deuterium exchange mass spectrometry
3: Specific amino acid labeling
4: FPOP for protein structural studies
5: Conclusions
References
Chapter 10: Small-angle scattering techniques for biomolecular structure and dynamics
Abstract
Acknowledgments
1: Introduction to small-angle scattering experiments
2: Structural studies
3: Dynamics analysis
4: Models
5: Conclusions
References
Chapter 11: Advances in X-ray crystallography methods to study structural dynamics of macromolecules
Abstract
1: Introduction
2: Protein extraction and purification
3: Increasing the solubility and stability of proteins
4: Assessing the homogeneity and purity of protein samples
5: New crystallization methods
6: New crystallization additives
7: Advances in instrument and data-processing software
8: Conclusions and future perspectives
References
Chapter 12: Spectroscopic methods to study protein folding kinetics: Methodology, data analysis, and interpretation of the results
Abstract
1: Introduction
2: Kinetics of protein folding
3: Applications in protein engineering
4: Conclusions
References
Chapter 13: Spectroscopic methods to study the thermodynamics of biomolecular interactions
Abstract
Acknowledgments
1: Introduction
2: Overview of biomolecular forces
3: Thermodynamics overview
4: Methods for binding constant and thermodynamics study
5: Conclusions
References
Chapter 14: Spectroscopic methods to detect and analyze protein oligomerization, aggregation, and fibrillation
Abstract
Acknowledgments
1: Introduction
2: UV-visible spectroscopy
3: Circular dichroism spectroscopy
4: Fluorescence spectroscopy
5: Infrared spectroscopy
6: Dynamic light scattering spectroscopy
7: Raman spectroscopy
8: NMR spectroscopy
9: Conclusion
References
Chapter 15: Multimodal spectroscopic methods for the analysis of carbohydrates
Abstract
1: Introduction
2: Sample preparation for the spectroscopic analysis of carbohydrates
3: Advanced analysis of carbohydrates
4: Conclusions
References
Chapter 16: Integration of spectroscopic and computational data to analyze protein structure, function, folding, and dynamics
Abstract
1: Protein structures: A race with time
2: Spectroscopic tools to study protein structure and dynamics
3: Computational tools to study protein structure and dynamics
4: Integrating spectroscopic data with computational data
5: Case studies
6: Conclusion and future perspectives
References
Chapter 17: Advance data handling tools for easy, fast, and accurate interpretation of spectroscopic data
Abstract
1: Introduction
2: Spectroscopic data handling tools
3: Conclusions
References
Index

Prakash Saudagar

Dr. Prakash Saudagar is an active researcher and a sterling classroom teacher, currently working as an Assistant Professor at the Department of Biochemistry, National Institute of Technology Warangal, India. He obtained his Ph.D. degree from the Indian Institute of Technology, Guwahati, India, in 2013. His research has immensely contributed to exploring potential drug target proteins and inhibitors. His research interests include molecular and biochemical parasitology, infectious disease, and protein biochemistry. He has a strong command over computational techniques and in-vitro techniques used to study proteins. He has published more than 40 research articles in reputed journals like the International Journal of Biological Molecules, FEBS, FEBS OpenBio, PLOS one, Scientific Reports, Biological Chemistry, Parasitology International, Molecular Simulation, etc., and book chapters in Elsevier and Springer to his name. He has been PI/Co-PI in research grants from SERB and DST. He has been awarded the B.S. Narasinga Rao award SBC, India (2011), Best presentation award, ICIDN, Nepal (2015), Young Faculty Award, VIF India (2016), and Young Scientist Award, Telangana Academy of Science (2018). He is an associate fellow of the Telangana Academy of Science (2018) and a life member of the Indian Science Congress and Society of Biological Chemists. He has guided several Ph.D. and M.Tech. students, postdoctoral fellows, project fellows, and trainees. He has many interdisciplinary collaborating partners in prestigious institutions in India and abroad.

Affiliations and expertise

Assistant Professor at the Department of Biochemistry, National Institute of Technology Warangal, India

Timir Tripathi

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

Affiliations and expertise

Professor of Molecular Biology, School of Life Sciences, North-Eastern Hill University, Shillong, India

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