edited by Mark Chance
Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics presents a wide variety of mass spectrometry methods used to explore structural mechanisms, protein dynamics and interactions between proteins.
Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics includes footprinting and plistex specifically, setting this book apart from the competition.
Contents
1. Overview of Mass Spectrometry Technologies for Examining Protein Structure: Current and Future Directions
- Hydrogen/Deuterium Exchange Mass Spectrometry
- Hydroxyl-Radical-Mediated Protein Footprinting
- Chemical Cross-linking
2. Hydrogen Exchange Mass Spectrometry: Principles and Capabilities
- The Chemistry of Hydrogen Exchange
- HX Mechanisms in Proteins
- Deuterium Incorporation into Proteins
- Measuring HX with Mass Spectrometry
- Capabilities of HX MS in Structural Biology
3. Covalent Labeling Methods for Examining Protein Structure and Protein Interactions
- Chemistry of Hydroxyl Radical Footprinting
- Mass Spectrometry Approaches for Quantitative Protein Footprinting
- Examples of Various Methods that Generate Hydroxyl Radicals in Solution to Examine Protein Structure
- The Future: Hybrid Approaches that Combine Experimental and Computational Data
4. Complementary Methods for Structure Determination: Hydroxyl-Radical-Mediated Footprinting and Deuterium Exchange Mass Spectrometry as Applied to Serpin Structure
- Technical Comparison of Hydroxyl-Radical-Mediated Footprinting and H/D Exchange Methodologies
- Structural Mass Spectrometry Data
- Solvent Accessibility
- Dynamics
- Significance for Serpin Structure and Function
5. Deuterium Exchange Approaches for Examining Protein Interactions: Case Studies of Complex Formation
- Interactions of Regulatory and Catalytic Subunits of Protein Kinase A
- Allostery in Protein-Protein Interactions Revealed by H/D Exchange
- Interactions of the Inhibitor IkBα with the Transcription Factor NF-kB
6. Hydrogen/Deuterium Exchange Studies of Viruses
- Overview of Virus Lifecycles
- Structural Investigations of Viral Capsids
- Dynamics of Viral Capsids
- Hydrogen/Deuterium Exchange Studies of Virus Capsid Structure
- Hydrogen/Deuterium Exchange Studies of Viral Protein Dyanmics
- Technical Aspects of Performing Hydrogen/Deuterium Exchange Experiments on Viruses
7. Use of Enhanced Peptide Amide Hydrogen/Deuterium Exchange-Mass Spectrometry (DXMS) in the Examination of Protein-Protein Interactions
- Theory of H/D Exchange
- Overview of DXMS Technology for Protein-Protein Interactions
- DXMS of Human Growth Hormone and Its Binding Protein
- DXMS of PKA Regulatory Subunits
- DXMS of PKA R-Submit D/D Domains and D-AKAP2 AKB Domain
- Epitope Mapping by DXMS
8. Cross-linking as a Tool to Examine Protein Complexes: Examples of Cross-linking Strategies and Computational Modeling
- Cross-linking Strategies
- Cross-linking Methodology
- challenges Associated with Combining Cross-linking with Mass Spectrometry
- Advances in Mass Spectrometry Instrumentation and Capabilities
- Novel Cross-linking Reagents for Mass Spectrometry
- Analytical Software
- Using Cross-linking Distance Constraints to Build Experimental Models of Protein Complexes
9. Complex Formation in the Actin Cytoskeleton: Cross-linking Tools to Define Actin Protein Structure and Interactions
- Mapping Cross-linking with Methods Other than Mass Spectrometry
- Actin-Actin Cross-linking
- Intrastrand Cross-linked Actin between GLN41 and CYS374
- Regulation of Cytoskeleton by ABPs and Mapping their Interfaces with Actin by Cross-linking
- Cross-linking of Actin and Muscle Proteins—Examples of Experimental Approaches
- Conclusing Remarks
10. Computational Approaches to Examining Protein-Protein Interactions: Combining Experimental and Computational Data in the Era of Structural Genomics
- Interactome in Structural Genomics
- Importance of Computational Methods in Structural Genomics
- Combining Computational Method with Experimental Data in Modeling the Structure of Protein Binary Complex
11. Studies of Intact Proteins and Protein Complexes: ESI MS Approaches
- Tertiary Structure Integrity and Conformational Heterogeneity (Charge State Distributions).
- Quaternary Structure Integrity and Composition of Non-Covalent Complexes
- Functional Competence
- Flexibility Maps and Binding Interfaces
- Gas Phase Ion Chemistry and Its Influence of the Measurement of Protein Properties in Solution
- Challenges and Future Outlook
12. Two Approaches to Mass Spectrometric Protein Footprinting: PLIMSTEX and FPOP
- Introduction: Protein-Ligand Interactions by Mass Spectrometry, Titration, and Hydrogen/Deuterium Amide Exchange and Fast Photochemical Oxidation of Proteins
- Protein-Ligand Interactions by Mass Spectrometry, Titration, and H/D Amide Exchange (PLIMSTEX)
- Applications of PLMSTEX
- Self-Association of Insulin: A Protein/Protein Interaction
- Features of PLMSTEX
- Fast Photochemical Oxidation of Proteins: An Example of Fast Protein Footprinting
- Features of FPOP
Index
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