Biophysical Chemistry

  1. Macromolecular Structure
    1. Protein Structure Analysis
      1. Primary Structure
        1. Amino Acid Sequence
          1. Post-translational Modifications
            1. Sequence-Structure Relationships
            2. Secondary Structure
              1. Alpha Helices
                1. Geometry and Hydrogen Bonding
                  1. Helix Dipole
                    1. Stability Factors
                    2. Beta Sheets
                      1. Parallel and Antiparallel
                        1. Hydrogen Bonding Patterns
                          1. Twist and Curvature
                          2. Turns and Loops
                            1. Beta Turns
                              1. Gamma Turns
                                1. Random Coil
                                2. Ramachandran Analysis
                                  1. Allowed Conformations
                                    1. Glycine and Proline Effects
                                  2. Tertiary Structure
                                    1. Folding Patterns
                                      1. Domain Organization
                                        1. Active Sites
                                          1. Binding Sites
                                          2. Quaternary Structure
                                            1. Subunit Assembly
                                              1. Symmetry Operations
                                                1. Interface Analysis
                                              2. Protein Folding
                                                1. Folding Pathways
                                                  1. Nucleation-Condensation
                                                    1. Framework Model
                                                      1. Hydrophobic Collapse
                                                      2. Folding Intermediates
                                                        1. Molten Globule State
                                                          1. Folding Intermediates
                                                            1. Kinetic Traps
                                                            2. Energy Landscapes
                                                              1. Funnel Model
                                                                1. Roughness
                                                                  1. Folding Barriers
                                                                  2. Molecular Chaperones
                                                                    1. Heat Shock Proteins
                                                                      1. Chaperonins
                                                                        1. Folding Mechanisms
                                                                        2. Protein Misfolding
                                                                          1. Aggregation Mechanisms
                                                                            1. Amyloid Formation
                                                                              1. Disease Relevance
                                                                            2. Nucleic Acid Structure
                                                                              1. DNA Structure
                                                                                1. B-Form DNA
                                                                                  1. A-Form DNA
                                                                                    1. Z-Form DNA
                                                                                      1. Base Stacking
                                                                                        1. Groove Dimensions
                                                                                        2. RNA Structure
                                                                                          1. Secondary Structure Prediction
                                                                                            1. Stem-Loop Structures
                                                                                              1. Pseudoknots
                                                                                                1. Ribozyme Structure
                                                                                                2. DNA Topology
                                                                                                  1. Supercoiling
                                                                                                    1. Linking Number
                                                                                                      1. Topoisomerase Action
                                                                                                      2. Nucleic Acid Flexibility
                                                                                                        1. Persistence Length
                                                                                                          1. Bending and Twisting
                                                                                                            1. Sequence-Dependent Flexibility

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                                                                                                        6. Chemical Kinetics and Dynamics

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                                                                                                        8. Spectroscopic Methods