Introduction to Biomolecular Structure and Biophysics: Basics of Biophysics

ISBN-13: 9789811352799 / Angielski / Miękka / 2018 / 274 str.

Misra, Gauri

Opis

This comprehensive book presents a modern concept in biophysics based on recently published research. It highlights various aspects of the biophysical fundamentals and techniques that are currently used to study different physical properties of biomolecules, and relates the biological phenomenon with the underlying physical concepts. The content is divided into nine chapters summarizing the structural details of proteins, including recently discovered novel folds, higher order structures of nucleic acids, as well as lipids and the physical forces governing the macromolecular interactions which are essential for the various biological processes. It also provides insights into the recent advances in biophysical techniques including Hydrogen Deuterium Exchange with Mass Spectrometry (HDX-MS), Small angle X-ray scattering (SAXS) and Cryo Electron Microscopy (cryo EM), supplemented with interesting experimental data.It is a valuable reference resource for anyone with a desire to gain a better understanding of the fundamentals of biophysical concepts and techniques of important biomolecules.

Spis treści

Detailed table of contents

Chapter 1. Principles of protein structure and function.- Chapter 1.1. Structure, classification & properties of amino acids.- Chapter 1.2. Principles of ionization equilibria.- Chapter 1.2.1 Titration of amino acids.- Chapter 1.2.2. Ionization of side chains.- Chapter 1.3. Structural levels of proteins.- Chapter 1.3.1. Primary structure.- Chapter 1.3.2. Secondary structure.- Chapter 1.3.3. Tertiary structure.- Chapter 1.3.4. Quaternary structure.- Chapter 1.3.5. Forces stabilizing protein structures.- Chapter 1.4. Conformation of globular proteins.- Chapter 1.4.1. Hemoglobin.- Chapter 1.4.2. Myoglobin.- Chapter 1.4.3. Lysozyme.- Chapter 1.4.4. Cytochromes.- Chapter 1.5. Membrane proteins.- Chapter 1.5.1. Integral proteins.- Chapter 1.5.2. Peripheral proteins.- Chapter 2. Protein folding.- Chapter 2.1. Introduction.- Chapter 2.2.1. Driving forces in protein folding.- Chapter 2.2.1. Hydrogen bond and electrostatic interactions.- Chapter 2.2.2. Hydrophobic bonds.- Chapter 2.2.3. van der Waal’s forces.- Chapter 2.2.4. Disulphide bonds.- Chapter 2.2.5. Chaperons.- Chapter 2.3. Protein folding mechanism.- Chapter 2.3.1. Protein folding pathways in protein folding.- Chapter 2.3.2. Folding/unfolding, m-values.- Chapter 2.3.3. Models of protein folding.- Chapter 2.3.4. Principles of protein misfolding.- Chapter 2.4. Protein Structure and Stability.- Chapter 2.4.1 Effect of charged ions and chemical reagents.- Chapter 2.4.2. Effect of pH and temperature.- Chapter 2.4.3. Thermodynamic linkage between protein structure stability and function.- Chapter 2.4.4. Kinetics and equilibrium in folding intermediates.- Chapter 2.5. Computational Methods to Analyze Protein Folding.- Chapter 2.5. Computational folding.- Chapter 2.5.1.1. Lattice model.- Chapter 2.5.1.2. Off-lattice model.- Chapter 2.5.2. Structures of hypothetical folding intermediates and molecular dynamics simulation of protein folding.- Chapter 3. Nucleic acid structure and functions.- Chapter 3.1. Components of Nucleic acids.- Chapter 3.1.1. Purine and pyrimidine bases.- Chapter 3.1.2. Nucleosides and nucleotides.- Chapter 3.2. Structure of Nucleic acids.- Chapter 3.2.1. Double helical structure of DNA.- Chapter 3.2.2. Helix parameters.- Chapter 3.2.3. DNA Supercoiling & gyrase.- Chapter 3.2.4. Intercalation.- Chapter 3.3. Different forms of DNA.- Chapter 3.3.1. A-DNA.- Chapter 3.3.2. B-DNA.- Chapter 3.3.3. Z-DNA.- Chapter 3.3.4. Circular DNA.- Chapter 3.4. Different forms of RNA.- Chapter 3.4.1. tRNA.- Chapter 3.4.2. mRNA.- Chapter 3.4.3. rRNA.- Chapter 3.5. Conformational parameters of nucleic acids.- Chapter 3.6. Structural and biological significance of major and minor groove of DNA.- Chapter 3.7. Chargaff’s rule. Chapter 3.8. Nucleic acids geometries/Forces stabilizing Nucleic acid structures.- Chapter 3.8.1. Glycosidic bond, rotational isomers and sugar puckering.- Chapter 3.8.2. Base pairing.- Chapter 3.8.3. Base stacking.- Chapter 3.9. Wobble base-pairing and its correlation with genetic diseases. Chapter 3.9.1. Introduction.- Chapter 3.9.2. Wobble hypothesis.- Chapter 3.9.3. tRNA base pairing schemes.- Chapter 3.9.4. Biological importance.- Chapter 3.9.5. Correlation between the wobble base pairing with genetic disease.- Chapter 3.10. Properties of Nucleic acids.- Chapter 3.10.1. DNA polymorphism.- Chapter 3.10.2. Hyperchromicity.- Chapter 3.10.3. Cot curve.- Chapter 3.10.4. C value paradox. .- Chapter 3.11. Other functions of Nucleotides.- Chapter 3.11.1. Energy carrier.- Chapter 3.11.2. Chemical messengers.- Chapter 3.11.3. Enzyme cofactor components.- Chapter 3.12. Nucleic acid fractionation.- Chapter 3.12.1. Precipitation.- Chapter 3.12.2. Purification.- Chapter 3.12.3. Electrophoresis.- Chapter 3.12.4. Ultracentrifugation.- Chapter 4. Higher order nucleic acid structures.- Chapter 4.1. Triple stranded nucleic acid structures.- Chapter 4.1.1. DNA triplex.- Chapter 4.1.2. RNA triplex.- Chapter 4.1.3. Role of triplexes in therapeutics.- Chapter 4.2. Four stranded nucleic acid structures.- Chapter 4.2.1. G-quadruplex.- Chapter 4.2.2. i-motif.- Chapter 4.2.3. Role of G-quadraplex and i-motif in nanotechnology.- Chapter 4.2.4. Telomeric DNA.- Chapter 4.3. Coaxial stacking.- Chapter 4.4. Thermal melting of DNA thermodynamic parameters and analysis.- Chapter 4.4.1. Introduction.- Chapter 4.4.2. Hybridization.- Chapter 4.4.3. Denaturation.- Chapter 4.4.4. Annealing.- Chapter 4.4.5. Thermodynamics of the two-stage model.- Chapter 4.5. Keto-enol tautomerization.- Chapter 4.5.1. Introduction.- Chapter 4.5.2. Mechanism.- Chapter 4.5.3. Erlenmeyer rule.- Chapter 4.5.4. Stereochemistry of ketonization.- Chapter 4.5.5. Phenols.- Chapter 4.6. Tetra loop-receptor interactions.- Chapter 4.7 A-minor motif.- Chapter 4.8. Ribose Zipper.- Chapter 4.9.  DNA supercoiling in bacterial cell.- Chapter 4.9.1.1. Introduction.- Chapter 4.9.1.2. Methods to measure degree of supercoiling.- Chapter 4.10. DNA histone interactions in eukaryotic cell.- Chapter 5. Molecular Interactions.- Chapter 5.1 Macromolecular Interactions.- Chapter 5.1.1. Protein-protein interactions.- Chapter 5.1.2. Protein-nucleic acid interactions.- Chapter 5.2. Small molecular interactions.- Chapter 5.2.1. Ligand interactions at equilibrium.- Chapter 5.2.2. Binding of small molecules by polymers.- Chapter 5.2.3. Binding of two different ligands.- Chapter 5.3. Models for binding.- Chapter 5.3.1.  Identical and Independent site model.- Chapter 5.3.2. MWC and sequential models.- Chapter 5.3.3. Cooperative, non-cooperative, excluded site binding.- Chapter 5.4. Energetics and dynamics of binding.- Chapter 5.5. Structure of protein-ligand complexes.- Chapter 5.5.1. Relationship between protein conformations and binding.- Chapter 5.5.2. Binding of immunoglobulin and DNA binding protein.- Chapter 5.5.3. Affinity and specificity in intermolecular interactions.- Chapter 6. Lipid and membrane structures.- Chapter 6.1. Lipids: Shape and Structural parameters.- Chapter 6.1.1. Assemblies.-Chapter 6.1.2. Volume.- Chapter 6.1.3. Surface area.- Chapter 6.1.4. Length relationship.- Chapter 6.2. X-ray studies.- Chapter 6.2.1. Lipids.- Chapter 6.2.2. Membranes.- Chapter 6.3. Phase transitions.- Chapter 6.3.1. Anhydrous lipid bilayers.- Chapter 6.3.2. Hydrated lipid bilayers.- Membrane biophysics.- Chapter 7.1. Membrane structure & models.- Chapter 7.1.1. Physical properties of membrane.- Chapter 7.1.2. Biophysical properties of membrane.- Chapter 7.1.2.1. Surface tension.- Chapter 7.1.2.2. Adsorption.- Chapter 7.2. Structure and function of cell membrane.- Chapter 7.3. Membrane structure.- Chapter 7.3.1. Composition, function, membrane transport.- Chapter 7.3.1.1. Simple diffusion and Brownian motion.- Chapter 7.3.1.2. Osmolysis and dialysis.- Chapter 7.3.1.3. Passive and active transport.- Chapter 7.4. Transport of ions and molecules through cell membranes.- Chapter 7.4.1. Ion transport across energy conserving membranes.- Chapter 7.4.2. Measurement of driving forces, metabolite and ion transport.- Chapter 7.4.3. Membrane potentials and concept of redox potential. Chapter 7.4.5. Structure and function of Na⁺/K⁺ ATPase and Ca²⁺ ATPase pumps.- Chapter 7.4.6. Role of ion channels in cellular function.- Chapter 7.5. Physiological and metabolic implications of ion pumps and channels.- Chapter 8. Techniques in Biophysics.- Chapter 8.1. Structural analysis by UV-VIS spectroscopy.- Chapter 8.1.1. Principle of ultraviolet-visible absorption.- Chapter 8.1.2. Applications.- Chapter 8.2. Circular Dichroism.- Chapter 8.2.1. Principle.- Chapter 8.2.2. Applications.- Chapter 8.3. NMR.- Chapter 8.3.1. Theoretical principles of NMR.- Chapter 8.3.2. Application.- Chapter 8.4. X-ray crystallography.- Chapter 8.4.1. Early scientific history of Crystals and X-rays.- Chapter 8.4.2. X-ray Diffraction and scattering.- Chapter 8.4.3. Crystallization and data collection.- Chapter 8.4.4. Structure solution and refinement.- Chapter 8.4.5. Applications.- Chapter 8.5. Isothermal Calorimetry (ITC).- Chapter 8.5.1. Principle.- Chapter 8.5.2. Applications.- Chapter 8.6. Differential Scanning calorimetry (DSC).- Chapter 8.6.1. Principle.- Chapter 8.6.2. Applications in biology.- Chapter 8.7. Fluorescence Spectroscopy.- Chapter 8.7.1. Basic Principles of Fluorescence Spectroscopy.- Chapter 8.7.2. Various types of fluorescence based studies.- Chapter 8.7.2.1. Intrinsic fluorescence.- Chapter 8.7.2. Extrinsic fluorescence.- Chapter 8.7.3. Data analysis.- chapter 8.7.4. Applications.- Chapter 8.8. ORD and CD.- Chapter 8.8.1. Principles of ORD and CD.- Chapter 8.8.2. Cotton effect.- Chapter 8.8.3. Relation between ORD and CD.- Chapter 8.8.4. Application.- Chapter 9. Advance techniques in Biophysics.- Chapter 9.1. Hydrogen Deuterium Exchange with Mass Spectrometry.- Chapter 9.1.1. Introduction.- Chapter 9.1.2. Principles of hydrogen exchange.- Chapter 9.1.3. Use of mass spectrometry applied to hydrogen exchange.- Chapter 9.1.4. Applications in protein dynamics and interactions.- Chapter 9.2. Small angle X-ray scattering.- Chapter 9.2.1. Introduction.- Chapter 9.2.2. Principle.- Chapter 9.2.3. Applications.- Chapter 9.3. Cryo-electron Microscopy.- Chapter 9.3.1. Introduction.- Chapter 9.3.2. Principle.- Chapter 9.3.3. Applications. 

O autorze

Dr. Gauri Misra is currently working as Assistant Professor at Amity University, Noida (U.P.) India. Before joining Amity University, she has worked as Assistant Professor at HYGIA Institute of Pharmaceutical Education and Research, Lucknow (U.P.) India. From 2010 to 2011, she worked as a postdoctoral fellow at CHUL Research Centre, Quebec, Canada. As a postdoctoral fellow, she focused towards understanding the role of androgen receptor towards the growth and proliferation of breast cancer cells using structural biology approaches. She also contributed successfully in various collaborative projects. During her doctoral studies at Central Drug Research Institute, Lucknow (U.P.) India she made an innovative contribution towards understanding the structural and functional characterization of proteins that are involved in transit peptide-mediated pathway from Plasmodium falciparum. She has been the recipient of many awards including, Eli-Lilly Asia Outstanding Thesis Award (first prize) in 2009, and best oral presentation award at the “National seminar on Crystallography-37” Jadavpur University, Kolkata, 6-8th Feb. 2008. She has been an outstanding performer receiving gold medal and honors at various stages of her academic journey.  Previously, she had been selected as visiting scientist under INSA-Bilateral Exchange program to visit Israel Structural Proteomics Center situated at Weizmann Institute of Science, Rehovot, Israel in 2014.

She is serving as reviewer for various prestigious international journals. Furthermore, she is member of many scientific societies including, Indian Biophysical Society and Indian Science Congress Association. She has also delivered invited talks at various prestigious platforms. Till date, she has authored and co-authored 12 articles in peer-reviewed journals. During the past 6 years, she has been actively involved in both research and teaching graduate and postgraduate students from diversified background of biological sciences, engineering and pharma programs.

Blurb

This comprehensive book presents a modern concept in biophysics based on recently published research. It highlights various aspects of the biophysical fundamentals and techniques that are currently used to study different physical properties of biomolecules, and relates the biological phenomenon with the underlying physical concepts. The content is divided into nine chapters summarizing the structural details of proteins, including recently discovered novel folds, higher order structures of nucleic acids, as well as lipids and the physical forces governing the macromolecular interactions which are essential for the various biological processes. It also provides insights into recent advances in biophysical techniques including Hydrogen Deuterium Exchange with Mass Spectrometry (HDX-MS), Small Angle X-ray Scattering (SAXS) and cryo Electron Microscopy (cryo EM), supplemented with interesting experimental data.

It is a valuable reference resource for anyone with a desire to gain a better understanding of the fundamentals of biophysical concepts and techniques used to study important biomolecules.