Proteins and Proteomics

  1. Protein Structure Hierarchy
    1. Primary Structure
      1. Definition: The Linear Sequence of Amino Acids
        1. Naming Conventions and Notation
          1. Peptide Mapping and Sequencing
            1. Chemical Sequencing Methods
              1. Mass Spectrometry Sequencing
                1. Edman Degradation
                2. Importance of Sequence in Determining Function
                  1. Mutations and Sequence Variants
                    1. Point Mutations
                      1. Insertions and Deletions
                        1. Silent, Missense, and Nonsense Mutations
                        2. Sequence Alignment and Homology
                          1. Pairwise Alignment
                            1. Multiple Sequence Alignment
                              1. Evolutionary Relationships
                            2. Secondary Structure
                              1. Definition: Localized Folding Patterns
                                1. Stabilizing Forces
                                  1. Hydrogen Bonding
                                    1. Backbone Interactions
                                    2. Common Motifs
                                      1. The Alpha-Helix
                                        1. Structure and Geometry
                                          1. Stabilizing Interactions
                                            1. Helix Dipole
                                              1. Helix Parameters
                                                1. Proline and Glycine Effects
                                                2. The Beta-Pleated Sheet
                                                  1. Structure and Geometry
                                                    1. Parallel Sheets
                                                      1. Antiparallel Sheets
                                                        1. Hydrogen Bonding Patterns
                                                          1. Beta-Strand Characteristics
                                                          2. Beta-Turns and Loops
                                                            1. Types of Turns
                                                              1. Role in Protein Folding
                                                                1. Hairpin Loops
                                                                  1. Random Coil Regions
                                                                  2. Other Secondary Structures
                                                                    1. 3-10 Helix
                                                                      1. Pi-Helix
                                                                        1. Polyproline Helix
                                                                      2. The Ramachandran Plot
                                                                        1. Allowed and Disallowed Regions
                                                                          1. Interpretation and Applications
                                                                            1. Glycine and Proline Special Cases
                                                                            2. Secondary Structure Prediction
                                                                              1. Computational Methods
                                                                                1. Accuracy and Limitations
                                                                              2. Tertiary Structure
                                                                                1. Definition: Overall 3D Conformation of a Single Polypeptide
                                                                                  1. Stabilizing Forces and Interactions
                                                                                    1. Hydrophobic Interactions
                                                                                      1. Disulfide Bridges
                                                                                        1. Hydrogen Bonds
                                                                                          1. Ionic Bonds (Salt Bridges)
                                                                                            1. Van der Waals Forces
                                                                                              1. Aromatic Interactions
                                                                                              2. Structural and Functional Domains
                                                                                                1. Domain Definition
                                                                                                  1. Domain Organization
                                                                                                    1. Domain Shuffling and Evolution
                                                                                                      1. Interdomain Interactions
                                                                                                      2. Protein Motifs (Supersecondary Structures)
                                                                                                        1. Helix-Turn-Helix
                                                                                                          1. Beta-Alpha-Beta Motif
                                                                                                            1. Greek Key Motif
                                                                                                              1. Beta-Barrel Motifs
                                                                                                                1. Coiled-Coil Motifs
                                                                                                                2. Protein Folding Pathways
                                                                                                                  1. Nucleation Sites
                                                                                                                    1. Folding Intermediates
                                                                                                                      1. Kinetic vs Thermodynamic Control
                                                                                                                      2. Structural Classification Systems
                                                                                                                        1. SCOP Database
                                                                                                                          1. CATH Database
                                                                                                                            1. Protein Fold Families
                                                                                                                          2. Quaternary Structure
                                                                                                                            1. Definition: Arrangement of Multiple Polypeptide Subunits
                                                                                                                              1. Terminology
                                                                                                                                1. Oligomers
                                                                                                                                  1. Protomers
                                                                                                                                    1. Subunits
                                                                                                                                      1. Monomers
                                                                                                                                      2. Types of Quaternary Structures
                                                                                                                                        1. Homo-oligomers
                                                                                                                                          1. Hetero-oligomers
                                                                                                                                            1. Symmetry in Quaternary Structures
                                                                                                                                            2. Subunit Interactions
                                                                                                                                              1. Interface Contacts
                                                                                                                                                1. Cooperative Binding
                                                                                                                                                  1. Allosteric Regulation in Multimeric Proteins
                                                                                                                                                  2. Examples of Quaternary Structures
                                                                                                                                                    1. Hemoglobin
                                                                                                                                                      1. Immunoglobulins
                                                                                                                                                        1. Viral Capsids
                                                                                                                                                          1. Ribosomes

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                                                                                                                                                      1. Fundamentals of Proteins

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                                                                                                                                                      3. Protein Structure Determination Methods