1 General Overview of Basic Concepts in Molecular Biophysics.

1.1. Covalent Structure of Biopolymers.

1.2. Noncovalent Interactions and Higher-order Structure.

1.3. The Protein Folding Problem.

1.4. Protein Energy Landscapes and the Folding Problem.

1.5. Protein Dynamics and Function.

References.

2 Overview of “Traditional” Experimental Arsenal to Study Biomolecular Structure and Dynamics.

2.1. X-Ray Crystallography.

2.2. Solution Scattering Techniques.

2.3. NMR Spectroscopy.

2.4. Other Spectroscopic Techniques.

2.5. Other Biophysical Methods to Study Macromolecular Interactions and Dynamics.

References.

3 Overview of Biological Mass Spectrometry.

3.1. Basic Principles of Mass Spectrometry.

3.2. Methods of Producing Biomolecular Ions.

3.3. Mass Analysis.

3.4. Tandem Mass Spectrometry.

3.5. Brief Overview of Common Mass Analyzers.

References.

4 Mass Spectrometry-Based Approaches to Study Biomolecular Higher-Order Structure.

4.1. Biomolecular Topography: Contact and Proximity Maps via Chemical Cross-Linking.

4.2. Mapping Solvent-Exposed Regions: Footprinting Methods.

4.3. Emerging Low-Resolution Methods: Zero-Interference Approaches.

References.

5 Mass Spectrometry-based Approaches to Study Biomolecular Dynamics: Equilibrium Intermediates.

5.1. Monitoring Equilibrium Intermediates: Protein Ion Charge State Distributions (ESI MS).

5.2. Chemical Labeling and Trapping Equilibrium States in Unfolding Experiments.

5.3. Structure and Dynamics of Intermediate Equilibrium States: Use of Hydrogen Exchange.

5.4. Measurements of Local Patterns of Hydrogen Exchange.

References.

6 Kinetic Studies by Mass Spectrometry.

6.1. Kinetics of Protein Folding.

6.2. Kinetics by Mass Spectrometry.

6.3. Kinetics of Enzyme Catalysis.

References.

7 Protein Interaction: A Closer Look at the “Structure–Dynamics–Function” Triad.

7.1. Protein–Ligand Interactions: Characterization of Noncovalent Complexes Using Direct ESI MS Measurements.

7.2. Indirect Characterization of Noncovalent Interactions: Measurements Under Native Conditions.

7.3. Indirect Characterization of Noncovalent Interactions: Exploiting Protein Dynamics Under Denaturing Conditions.

7.4. Understanding Protein Action: Mechanistic Insights from the Analysis of Structure and Dynamics Under Native Conditions.

7.5. Understanding Protein Action: Mechanistic Insights from the Analysis of Structure and Dynamics Under Denaturing Conditions.

References.

8 Synergism Between Biophysical Techniques.

8.1. Hen Egg White Lysozyme.

8.2. Molecular Chaperones.

References.

9 Other Biopolymers and Synthetic Polymers of Biological Interest.

9.1. DNA.

9.2. RNA.

9.3. Oligosaccharides.

9.4. “Passive” Polymers of Biotic and Abiotic Origin.

References.

10 Biomolecular Ions in a Solvent-Free Environment.

10.1. General Considerations: Role of Solvent in Maintaining Biomolecular Structure and Modulating its Dynamics.

10.2. Experimental Methods to Study Biomolecular Structure in Vacuo.

10.3. Protein and Peptide Ion Behavior in a Solvent-Free Environment.

10.4. Protein Hydration in the Gas Phase: Bridging “Micro” and “Macro”.

References.

11 Mass Spectrometry on the March: Where Next? From Molecular Biophysics to Structural Biology, Perspectives and Challenges.

11.1. Assembly and Function of Large Macromolecular Complexes: From Oligomers to Subcellular Structures to . . . Organisms?

11.2. Structure and Dynamics of Membrane Proteins.

11.3. Macromolecular Trafficking and Cellular Signaling.

11.4. In Vivo versus in Vitro Behavior of Biopolymers.

References.

Appendix: Physics of Electrospray.

Index.