BookDev Bukhsh Singh, Timir Tripathi, editors.
Summary: This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.
Contents:
Intro
Preface
Contents
About the Editors
1: Protein Purification, Estimation, Storage, and Effect on Structure-Function-Dynamics
1.1 Introduction
1.2 Protein Purification
1.2.1 Protein Precipitation/Salting Out
1.2.2 Buffer Exchange/Dialysis
1.2.3 Immuno-Affinity Chromatography
1.2.4 Affinity Chromatography
1.2.5 Ion-Exchange Chromatography
1.2.6 Size-Exclusion or Gel Filtration Chromatography (SEC/GFC)
1.2.7 High-Pressure/Performance Liquid Chromatography (HPLC)
1.2.8 Hydrophobic Interaction Chromatography
1.3 Resolving and Display of Protein 1.6.3 Cycles of Freeze-Thaw
1.6.4 Organic Solvents and pH
1.6.5 Proteases/Peptidases
1.6.6 Protein Concentration
1.6.7 Reducing Agents
1.6.8 Salt Conditions and Urea
1.6.9 Temperature
1.7 Factors Affecting the Stability of Proteins
1.8 Effect on the Dynamics of Protein
1.9 Conclusions
References
2: Experimental and Computational Methods to Determine Protein Structure and Stability
2.1 Protein Purification Techniques
2.1.1 General Aspects of Protein Purification
2.1.2 Stabilizing Proteins
2.1.3 Quantification of Proteins 2.1.4 Purification of Proteins Based on Solubility
2.1.5 Purification of Proteins Based on Size
2.1.5.1 Ultrafiltration
2.1.5.2 Gel Filtration or Molecular Sieve or Size Exclusion Chromatography
2.1.5.3 SDS-PAGE
2.1.6 Purification of Proteins Based on Charge
2.1.6.1 Ion-Exchange Chromatography
2.1.6.2 Isoelectric Focusing
2.1.6.3 Polyacrylamide Gel Electrophoresis
2.1.7 Purification of Proteins Based on Polarity (Hydrophobic Interaction Chromatography)
2.1.8 Purification of Proteins Based on theBinding Property (Affinity Chromatography) 2.2 Biophysical and Biochemical Characterization of Protein
2.2.1 Biophysical Characterization Methods
2.2.2 Dynamic Light Scattering (DLS)
2.2.2.1 Applications of DLS
2.2.3 Circular Dichroism (CD) Spectroscopy
2.2.3.1 Applications of CD
2.2.3.2 Advantages of CD
2.2.4 Differential Scanning Calorimetry (DSC)
2.2.4.1 Applications of DSC
2.2.5 Fourier-Transform Infrared (FTIR) Spectroscopy
2.2.5.1 Advantages of FTIR
2.2.6 Isothermal Titration Calorimetry (ITC)
2.2.6.1 Applications of ITC
2.2.7 Biochemical Characterization
2.2.8 Oxidation
2.2.9 Deamidation