Advances in Protein Molecular and Structural Biology Methods

Timir Tripathi, Vikash Kumar Dubey, Timir Tripathi, Vikash Kumar Dubey

• Publisher: Academic Press
• Year: 2022
• Print ISBN: 9780323902649
• eBook ISBN: 9780323902656
• Topic: Biological Sciences
• Subtopic: Molecular Biology
• Index: Biological Sciences

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

Table of contents

• Title of Book
• Cover image
• Title page
• Table of Contents
• Copyright
• Dedicated to
• Contributors
• About the Editors
• Foreword
• Preface
• Chapter 1 Strategies to improve the expression and solubility of recombinant proteins in E. coli
• Chapter 2 Advances in heterologous protein expression strategies in yeast and insect systems
• Chapter 3 Methods for transient expression and purification of monoclonal antibodies in mammalian cells
• Chapter 4 Methods for recombinant production and purification of intrinsically disordered proteins
• Chapter 5 Methods to determine the oligomeric structure of proteins
• Chapter 6 Multimodal methods to study protein aggregation and fibrillation
• Chapter 7 Experimental methods to study the thermodynamics of protein–protein interactions
• Chapter 8 Experimental methods to study the kinetics of protein–protein interactions
• Chapter 9 Computational techniques for studying protein-protein interactions
• Chapter 10 Experimental methods to study protein–nucleic acid interactions
• Chapter 11 Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces
• Chapter 12 Experimental techniques to study protein dynamics and conformations
• Chapter 13 Computational techniques to study protein dynamics and conformations
• Chapter 14 Application of circular dichroism spectroscopy in studying protein folding, stability, and interaction
• Chapter 15 Studying protein-folding dynamics using single-molecule fluorescence methods
• Chapter 16 Advances in liquid-state NMR spectroscopy to study the structure, function, and dynamics of biomacromolecules
• Chapter 17 In-cell NMR spectroscopy: A tool to study cellular structure biology
• Chapter 18 Current trends in membrane protein crystallography
• Chapter 19 Advances in sample preparation and data processing for single-particle cryo-electron microscopy
• Chapter 20 Advanced mass spectrometry-based methods for protein molecular-structural biologists
• Chapter 21 Developments, advancements, and contributions of mass spectrometry in omics technologies
• Chapter 22 Role of structural biology methods in drug discovery
• Chapter 23 Prediction, validation, and analysis of protein structures: A beginner’s guide
• Chapter 24 Advances in structure-based virtual screening for drug discovery
• Chapter 25 Methods and applications of machine learning in structure-based drug discovery
• Chapter 26 Molecular dynamics simulations: Principles, methods, and applications in protein conformational dynamics
• Chapter 27 Applications of molecular dynamics simulations in drug discovery
• Chapter 28 Envisaging the conformational space of proteins by coupling machine learning and molecular dynamics
• Chapter 29 Immunoinformatics and reverse vaccinology methods to design peptide-based vaccines
• Chapter 30 Computational methods to study intrinsically disordered proteins
• Chapter 31 Experimental methods to study intrinsically disordered proteins
• Chapter 32 Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods
• Chapter 33 Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins
• Chapter 34 Molecular simulations to study IDP-IDP interactions and their complexes
• Chapter 35 Exploring large-scale protein function using systematic mutant analysis
• Chapter 36 Approaches and methods to study cell signaling: Linguistics of cellular communication
• Chapter 37 Methods to study systems biology of signaling networks: A case study of NSCLC
• Chapter 38 Advancements in the analysis of protein post-translational modifications
• Chapter 39 Protein engineering: Methods and applications
• Chapter 40 Designer 3D-DNA nanodevices: Structures, functions, and cellular applications
• Index