Proteins and Proteomics

  1. Protein Structure Determination Methods
    1. X-ray Crystallography
      1. Principles of X-ray Diffraction
        1. Crystal Formation and Quality
          1. Data Collection and Processing
            1. Phase Problem and Solutions
              1. Structure Refinement
                1. Resolution and Quality Assessment
                  1. Limitations and Artifacts
                  2. Nuclear Magnetic Resonance (NMR) Spectroscopy
                    1. Principles of NMR
                      1. Protein NMR Techniques
                        1. Structure Determination Process
                          1. Dynamic Information from NMR
                            1. Size Limitations
                              1. Solution vs Solid-State NMR
                              2. Cryo-Electron Microscopy (Cryo-EM)
                                1. Single Particle Analysis
                                  1. Sample Preparation
                                    1. Image Processing
                                      1. Resolution Revolution
                                        1. Advantages for Large Complexes
                                          1. Membrane Protein Applications
                                          2. Small-Angle X-ray Scattering (SAXS)
                                            1. Solution Structure Information
                                              1. Shape and Size Determination
                                                1. Flexibility and Dynamics
                                                  1. Complementary to High-Resolution Methods
                                                  2. Computational Structure Prediction
                                                    1. Homology Modeling
                                                      1. Ab Initio Prediction
                                                        1. Fold Recognition
                                                          1. AlphaFold and AI Methods
                                                            1. Model Quality Assessment
                                                            2. Hybrid and Integrative Approaches
                                                              1. Combining Multiple Techniques
                                                                1. Cross-linking Mass Spectrometry
                                                                  1. Hydrogen-Deuterium Exchange
                                                                    1. Integrative Modeling Platforms

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                                                                  2. Protein Structure Hierarchy

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                                                                  4. Protein Folding, Misfolding, and Denaturation