Proteins and Proteomics

  1. Regulation of Protein Activity
    1. Allosteric Control
      1. Allosteric Sites
        1. Distinct from Active Sites
          1. Conformational Coupling
          2. Positive and Negative Modulation
            1. Activators and Inhibitors
              1. Heterotropic vs Homotropic Effects
              2. Cooperativity
                1. Hill Coefficient
                  1. Sigmoid Binding Curves
                  2. Models of Allostery
                    1. Concerted Model
                      1. Sequential Model
                        1. Ensemble Model
                      2. Post-Translational Modifications (PTMs)
                        1. Phosphorylation
                          1. Kinases and Phosphatases
                            1. Specificity Determinants
                              1. Regulatory Mechanisms
                              2. Functional Consequences
                                1. Activity Modulation
                                  1. Protein Interactions
                                    1. Subcellular Localization
                                    2. Phosphorylation Sites
                                      1. Serine/Threonine Phosphorylation
                                        1. Tyrosine Phosphorylation
                                          1. Histidine Phosphorylation
                                        2. Glycosylation
                                          1. N-linked Glycosylation
                                            1. Asparagine Modification
                                              1. ER and Golgi Processing
                                                1. Quality Control Functions
                                                2. O-linked Glycosylation
                                                  1. Serine/Threonine Modification
                                                    1. Mucin-Type Glycosylation
                                                    2. Functions of Glycosylation
                                                      1. Protein Folding
                                                        1. Stability and Protection
                                                          1. Cell Recognition
                                                        2. Ubiquitination
                                                          1. Ubiquitin Structure and Function
                                                            1. Ubiquitin-Proteasome Pathway
                                                              1. E1, E2, E3 Enzyme Cascade
                                                                1. Substrate Recognition
                                                                2. Types of Ubiquitination
                                                                  1. Monoubiquitination
                                                                    1. Polyubiquitination
                                                                      1. Ubiquitin Chain Linkages
                                                                      2. Deubiquitinating Enzymes
                                                                      3. Acetylation
                                                                        1. Histone Acetylation
                                                                          1. Non-Histone Protein Acetylation
                                                                            1. Acetyltransferases and Deacetylases
                                                                              1. Functional Consequences
                                                                              2. Methylation
                                                                                1. Histone Methylation
                                                                                  1. Non-Histone Methylation
                                                                                    1. Methyltransferases and Demethylases
                                                                                      1. Epigenetic Regulation
                                                                                      2. Lipidation
                                                                                        1. Prenylation
                                                                                          1. Farnesylation
                                                                                            1. Geranylgeranylation
                                                                                              1. Membrane Association
                                                                                              2. Myristoylation
                                                                                                1. N-Terminal Modification
                                                                                                  1. Membrane Targeting
                                                                                                  2. Palmitoylation
                                                                                                    1. S-Acylation
                                                                                                      1. Dynamic Modification
                                                                                                    2. Sumoylation
                                                                                                      1. Small Ubiquitin-like Modifier
                                                                                                        1. SUMO Conjugation Pathway
                                                                                                          1. Nuclear Functions
                                                                                                          2. Proteolytic Cleavage and Activation
                                                                                                            1. Zymogen Activation
                                                                                                              1. Digestive Enzymes
                                                                                                                1. Blood Coagulation
                                                                                                                2. Signal Peptide Removal
                                                                                                                  1. ER Targeting
                                                                                                                    1. Mitochondrial Import
                                                                                                                    2. Protein Processing
                                                                                                                      1. Propeptide Removal
                                                                                                                        1. Maturation Cleavage
                                                                                                                      2. Other Important PTMs
                                                                                                                        1. Nitrosylation
                                                                                                                          1. Citrullination
                                                                                                                            1. Neddylation
                                                                                                                              1. Hydroxylation
                                                                                                                            2. Protein Synthesis and Degradation
                                                                                                                              1. Regulation of Translation
                                                                                                                                1. Initiation Control
                                                                                                                                  1. Cap-Dependent Initiation
                                                                                                                                    1. IRES-Mediated Initiation
                                                                                                                                      1. eIF Regulation
                                                                                                                                      2. Elongation and Termination
                                                                                                                                        1. Ribosome Dynamics
                                                                                                                                          1. Translation Factors
                                                                                                                                          2. microRNA Regulation
                                                                                                                                            1. Ribosome Profiling
                                                                                                                                            2. Protein Turnover
                                                                                                                                              1. Half-life Determinants
                                                                                                                                                1. N-End Rule
                                                                                                                                                  1. PEST Sequences
                                                                                                                                                    1. Degrons
                                                                                                                                                    2. Measurement of Protein Turnover
                                                                                                                                                    3. The Ubiquitin-Proteasome System
                                                                                                                                                      1. 26S Proteasome Structure
                                                                                                                                                        1. 20S Catalytic Core
                                                                                                                                                          1. 19S Regulatory Particles
                                                                                                                                                          2. Substrate Recognition and Processing
                                                                                                                                                            1. Proteasome Inhibitors
                                                                                                                                                            2. Autophagy and Lysosomal Degradation
                                                                                                                                                              1. Macroautophagy
                                                                                                                                                                1. Chaperone-Mediated Autophagy
                                                                                                                                                                  1. Selective Autophagy
                                                                                                                                                                    1. Lysosomal Proteases

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                                                                                                                                                                5. Protein Function and Diversity

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                                                                                                                                                                7. Introduction to Proteomics