Proteins in Solution and at Interfaces : Methods and Applications in Biotechnology and Materials Science.
Title:
Proteins in Solution and at Interfaces : Methods and Applications in Biotechnology and Materials Science.
Author:
Ruso, Juan M.
ISBN:
9781118523186
Personal Author:
Edition:
1st ed.
Physical Description:
1 online resource (518 pages)
Series:
Wiley Series on Surface and Interfacial Chemistry ; v.8
Wiley Series on Surface and Interfacial Chemistry
Contents:
PROTEINS IN SOLUTION AND AT INTERFACES -- CONTENTS -- PREFACE -- CONTRIBUTORS -- PART I -- 1 X-RAY CRYSTALLOGRAPHY OF BIOLOGICAL MACROMOLECULES: FUNDAMENTALS AND APPLICATIONS -- 1.1 INTRODUCTION -- 1.2 FUNDAMENTALS OF X-RAY DIFFRACTION -- 1.2.1 X-Ray Radiation and Interaction with Matter -- 1.2.2 Crystals and Symmetry -- 1.2.3 Diffraction by Crystals -- 1.2.4 Real and Reciprocal Space -- 1.2.5 Structure Factors -- 1.2.6 Fourier Synthesis and Transform -- 1.2.7 The Phase Problem -- 1.3 THE STRUCTURE DETERMINATION PROCESS -- 1.3.1 Sample Production and Conditioning -- 1.3.2 Crystallization -- 1.3.3 Data Collection and Processing -- 1.3.4 Structure Determination -- 1.3.5 Electron Density Map Interpretation: Model Construction -- 1.3.6 Model Refinement -- 1.3.7 Validation -- 1.4 STRUCTURAL ANALYSIS AND BIOLOGICAL IMPLICATIONS -- 1.4.1 Structural Analysis -- 1.4.2 Biological Implications -- 1.5 FUTURE PROSPECTS -- ACKNOWLEDGMENTS -- REFERENCES -- 2 NUCLEAR MAGNETIC RESONANCE METHODS FOR STUDYING SOLUBLE, FIBROUS, AND MEMBRANE-EMBEDDED PROTEINS -- 2.1 INTRODUCTION AND BACKGROUND -- 2.1.1 Nuclear Angular Momentum -- 2.1.2 Chemical Shifts -- 2.1.3 Nuclear Spin Interactions -- 2.1.4 Relaxation -- 2.1.5 Isotopic Labeling -- 2.1.6 Samples -- 2.2 STRUCTURAL DATA -- 2.2.1 Resonance Assignment -- 2.2.2 Distance Measurements -- 2.2.3 Angular Information -- 2.2.4 Residual Dipolar Couplings -- 2.2.5 Use of Paramagnetic Agents -- 2.2.6 Oriented Samples -- 2.2.7 Structure Calculations -- 2.3 DYNAMICS -- 2.3.1 Fast (ps-ns) Motions -- 2.3.2 Slow (μs-ms) Motions -- 2.3.3 Motions in Solids -- 2.4 INTERMOLECULAR INTERACTIONS -- 2.4.1 Identification of Interaction Surfaces -- 2.4.2 Structural Restraints -- 2.5 DISCUSSION -- 2.5.1 Large Protein Systems -- 2.5.2 Advantages and Disadvantages of Solution and Solid-State MAS NMR -- 2.5.3 Complementary Techniques.
2.6 CONCLUSION -- REFERENCES -- 3 SMALL-ANGLE X-RAY SCATTERING APPLIED TO PROTEINS IN SOLUTION -- 3.1 INTRODUCTION -- 3.2 SAXS THEORY -- 3.2.1 General Equations -- 3.2.2 Isotropy -- 3.2.3 Homogeneous Scattering Particles (Two-Phase Model) -- 3.2.4 Model-Independent Shape Analysis: Kratky's Representation, Guinier's Law, and Porod's Invariant -- 3.2.5 Methods to Calculate P(q) -- 3.2.6 Protein-Protein Interaction: S(q) Evaluation -- 3.3 EXAMPLES -- 3.3.1 Rg, p(r), Kratky's Representation and Shape Reconstruction: Analysis of Protein TcOYE -- 3.3.2 Guinier's Analysis and Multipole Expansion Shape Reconstruction: The Replication Factor C Case -- 3.3.3 Partial Folded and Unfolded Protein: Analysis of the Protein Bovine Serum Albumin, BSA, Under the Influence of Denaturing Agents -- 3.4 PROTEIN INTERACTION: BSA CASE -- 3.5 PROTEIN AGGREGATION -- 3.6 CONCLUSION -- ACKNOWLEDGMENTS -- REFERENCES -- 4 ANALYZING THE SOLUTION STATE OF PROTEIN STRUCTURE, INTERACTIONS, AND LIGANDS BY SPECTROSCOPIC METHODS -- 4.1 INTRODUCTION -- 4.1.1 Overview -- 4.1.2 Protein Secondary Structures and Motifs -- 4.1.3 Structure Determination: Spectroscopic Methods -- 4.2 ULTRAVIOLET-VISIBLE ABSORPTION SPECTROSCOPY -- 4.2.1 Background -- 4.2.2 Lambert-Beer Law: Determination of Protein Concentration -- 4.2.3 Protein Absorbance: The Molecular Origin -- 4.2.4 Protein Absorbance Dependence on the Environment. Protein Unfolded -- 4.2.5 Protein-Ligand Interactions -- 4.2.6 Summary -- 4.3 CIRCULAR DICHROISM SPECTROSCOPY -- 4.3.1 Background -- 4.3.2 General Aspects of Protein CD Measurements -- 4.3.3 Structural Information on Peptides and Proteins Available from CD -- 4.3.4 Summary -- 4.4 FLUORESCENCE SPECTROSCOPY -- 4.4.1 Background -- 4.4.2 Trp/Tyr Fluorescence -- 4.4.3 Protein Folding -- 4.4.4 Extrinsic Fluorescent Dyes.
4.4.5 Applications of Fluorescent Dyes in Protein Characterization -- 4.4.6 Summary -- 4.5 FOURIER TRANSFORM INFRARED (FT-IR) AND RAMAN SPECTROSCOPY -- 4.5.1 Background -- 4.5.2 Protein Amide Bands -- 4.5.3 Application of FT-IR to Protein Secondary Structure -- 4.5.4 Analyzing the Solution State of Protein Structure -- 4.5.5 Protein Stability -- 4.5.6 Protein Aggregation -- 4.5.7 Time-Resolved FT-IR Spectroscopy -- 4.5.8 Summary -- 4.6 PHOTON CORRELATION SPECTROSCOPY: DYNAMIC LIGHT SCATTERING -- 4.6.1 Background -- 4.6.2 Protein Characteristics Determined by Means of DLS -- 4.6.3 Protein Aggregation and Interaction with Other Compounds -- 4.6.4 Summary -- 4.7 OUTLOOK AND CONCLUSION -- REFERENCES -- 5 RESOLVING MEMBRANE-BOUND PROTEIN ORIENTATION AND CONFORMATION BY NEUTRON REFLECTIVITY -- 5.1 INTRODUCTION -- 5.2 SPECULAR REFLECTIVITY -- 5.3 TETHERED BILAYERS -- 5.4 MODELING DATA -- 5.4.1 Modeling Tethered Bilayers -- 5.4.2 Uncertainty Analysis -- 5.4.3 Composition Space Model -- 5.5 DETERMINING THE ORIENTATION AND INSERTION OF MEMBRANE-BOUND PROTEINS -- 5.5.1 Example from the HIV-1 Gag Matrix (MA) Domain -- 5.5.2 Determining Protein Orientation -- 5.6 CONFORMATIONAL CHANGES OF PROTEINS ON THE MEMBRANE -- 5.7 CONCLUSION -- REFERENCES -- 6 INVESTIGATING PROTEIN INTERACTIONS AT SOLID SURFACES-IN SITU, NONLABELING TECHNIQUES -- 6.1 INTRODUCTION -- 6.2 SURFACE ANALYTICAL TECHNIQUES -- 6.2.1 Ellipsometry -- 6.2.2 Dual Polarization Interferometry -- 6.2.3 Surface Plasmon Resonance -- 6.2.4 Quartz Crystal Microbalance -- 6.2.5 Atomic Force Microscopy -- 6.3 COMPARISON OF THE TECHNIQUES -- 6.3.1 The Adsorbed Amount -- 6.3.2 Detection Limits with Respect to the Adsorbed Amount -- 6.3.3 Layer Thickness -- 6.3.4 Monitoring Binding Kinetics and Determination of Affinity Constants -- 6.4 COMBINING THE TECHNIQUES.
6.4.1 Combining QCM with Ellipsometry, DPI, and SPR -- 6.4.2 Combining AFM with Other Surface Analytical Techniques -- 6.5 CONCLUDING REMARKS -- REFERENCES -- 7 CALORIMETRIC METHODS TO CHARACTERIZE THE FORCES DRIVING MACROMOLECULAR ASSOCIATION AND FOLDING PROCESSES -- 7.1 INTRODUCTION -- 7.1.1 Relevance of Studying Macromolecular Energetics -- 7.1.2 A Brief History of Calorimetry -- 7.1.3 Scope of the Chapter -- 7.1.4 Basic Thermodynamic Functions -- 7.1.5 Explicit Consideration of Heat Capacity Changes -- 7.2 ISOTHERMAL TITRATION CALORIMETRY -- 7.2.1 Instrument Design and Principle of Operation -- 7.2.2 Optimizing Experimental Design Strategies -- 7.2.3 Analysis of ITC Binding Isotherms -- 7.2.4 Heat Capacity Changes of Macromolecular Association Processes -- 7.2.5 Parsing the Binding Energetics in Terms of Electrostatic/Non-electrostatic Interactions -- 7.2.6 Resolving Macromolecular Binding Energetics from Linked Processes -- 7.2.7 Resolving Binding Energetics Accompanied by Changes in the Reactant Folding States -- 7.2.8 Structural-Energetic Correlations: Interpretation of Calorimetric Data in Terms of Molecular Interactions -- 7.2.9 Applications of ITC to Characterize Biological Systems -- 7.2.10 Applications of ITC in Drug Design/Discovery -- 7.2.11 Web-Based Tools and Programs to Assist in Experimental Design, Data Analysis, and Evaluation of Database Depositories -- 7.3 DIFFERENTIAL SCANNING CALORIMETRY -- 7.3.1 Instrument Design and Principle of Operation -- 7.3.2 Analysis of DSC Endotherms -- 7.3.3 Resolving the Energetics of Macromolecular Folding in Terms of Linked Processes -- 7.3.4 Applications of DSC to Characterize the Thermodynamic Forces Driving Macromolecular Folding and Stability -- 7.3.5 Ligand-Binding Studies Characterized via DSC.
7.3.6 Combined Use of ITC and DSC to Derive a Complete Thermodynamic Characterization of Macromolecular Association and Folding -- 7.3.7 Reversibility of Temperature-Induced Unfolding Transitions: Methods to Circumvent Irreversible Folding/Unfolding Processes -- 7.3.8 Recent Applications of DSC in Drug Discovery Initiatives -- 7.3.9 Web-Based Tools and Programs to Evaluate and Predict Protein Folding and Stability -- 7.4 CURRENT AND FUTURE DIRECTIONS -- REFERENCES -- 8 VIRTUAL LIGAND SCREENING AGAINST COMPARATIVE MODELS OF PROTEINS -- 8.1 INTRODUCTION -- 8.2 PROGRAMS AND DATABASES -- 8.2.1 Software for Comparative Modeling -- 8.2.2 Database for Comparative Modeling -- 8.2.3 Software for Virtual Screening -- 8.2.4 Docking Database of Small Molecules -- 8.3 METHOD -- 8.3.1 General Remarks -- 8.3.2 Comparative Modeling of Protein Structures -- 8.3.3 Virtual Screening against Comparative Models -- 8.4 CONCLUSION -- REFERENCES -- 9 ATOMISTIC AND COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS OF MEMBRANE PROTEINS -- 9.1 INTRODUCTION TO MOLECULAR DYNAMICS SIMULATION -- 9.1.1 The Molecular Dynamics Approach -- 9.1.2 The Force Field -- 9.1.3 Additional Methodological Considerations -- 9.1.4 Simulation Scope -- 9.2 ATOMISTIC MEMBRANE PROTEIN SIMULATIONS -- 9.2.1 Initial Considerations -- 9.2.2 System Setup -- 9.2.3 Simulations and Analysis -- 9.3 APPROACHES TO MEMBRANE PROTEIN SELF-ASSEMBLY -- 9.3.1 Atomistic Self-Assembly Simulations -- 9.3.2 Coarse-Grained Models -- 9.3.3 Coarse-Grained Self-Assembly Simulations -- 9.3.4 Reverse-Mapping and Multiscale Approaches -- REFERENCES -- PART II -- 10 PREPARATION OF NANOMATERIALS BASED ON PEPTIDES AND PROTEINS -- 10.1 INTRODUCTION -- 10.2 PEPTIDE- AND PROTEIN-BASED NANOMATERIALS -- 10.2.1 Peptide-Based Nanomaterials -- 10.2.2 Protein-Based Nanomaterials -- 10.3 APPLICATIONS AND PROSPECTS -- REFERENCES.
11 NATURAL FIBROUS PROTEINS: STRUCTURAL ANALYSIS, ASSEMBLY, AND APPLICATIONS.
Abstract:
Explores new applications emerging from our latest understanding of proteins in solution and at interfaces Proteins in solution and at interfaces increasingly serve as the starting point for exciting new applications, from biomimetic materials to nanoparticle patterning. This book surveys the state of the science in the field, offering investigators a current understanding of the characteristics of proteins in solution and at interfaces as well as the techniques used to study these characteristics. Moreover, the authors explore many of the new and emerging applications that have resulted from the most recent studies. Topics include protein and protein aggregate structure; computational and experimental techniques to study protein structure, aggregation, and adsorption; proteins in non-standard conditions; and applications in biotechnology. Proteins in Solution and at Interfaces is divided into two parts: Part One introduces concepts as well as theoretical and experimental techniques that are used to study protein systems, including X-ray crystallography, nuclear magnetic resonance, small angle scattering, and spectroscopic methods Part Two examines current and emerging applications, including nanomaterials, natural fibrous proteins, and biomolecular thermodynamics The book's twenty-three chapters have been contributed by leading experts in the field. These contributions are based on a thorough review of the latest peer-reviewed findings as well as the authors' own research experience. Chapters begin with a discussion of core concepts and then gradually build in complexity, concluding with a forecast of future developments. Readers will not only gain a current understanding of proteins in solution and at interfaces, but also will discover how theoretical and technical developments in the field can be translated into new applications in
material design, genetic engineering, personalized medicine, drug delivery, biosensors, and biotechnology.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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