Proteopedia:Table of Contents

From Proteopedia

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• INTRODUCTION
  • Introduction to the Chemistry of Life
  • Water
    • Water in Macromolecular Models
  • Key chemical concepts for Structural Biology
    • Cation-pi interactions
    • Hydrogen bond
    • Hydrogen in Macromolecular Models

• BIOMOLECULES
  • Nucleotides, Nucleic Acids, and Genetic Information
    • DNA
      • Z-DNA
  • Amino_Acids
    • Selenocysteine
  • Proteins: Primary Structure
  • Proteins: Three-Dimensional Structure
    • S347/The four tiers of protein structure
    • [[Secondary_structure]
    • Protein Misfolding
      • [Prion_protein]
  • Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
    • Antibodies
      • IgA
      • Epitopes
    • Calmodulin_in_motion
    • Collagen
    • Hemoglobin; Hemoglobin_(Hebrew)
  • COLORED PROTEINS & THOSE THAT CHANGE COLOR
    • Green Fluorescent Protein; GFP_(Hebrew)
    • Dronpa
    • Factor IX
  • DNA BINDING PROTEINS
    • Helix-turn-helix motif
    • DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1
  • Lipids and Biological Membranes
  • Membrane Transport
    • A Physical Model of the β2-Adrenergic Receptor
    • [Proton_Channels]
    • [Mechanosensitive_channels:_opening_and_closing]
  • Prions & Intrinsically Disordered Proteins
    • Doppel
    • Intrinsically Disordered Protein
  • Toxins
    • Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis
  • Viruses
    • Filamentous bacteriphage
      • G3p - minor coat protein found on the surface of filamentous bacteriophage
    • HIV
      • HIV-1 protease
      • HIV-1 Gag
      • HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process
    • Herpes Simplex Virus
      • Herpes_Simplex_Virus_Thymidine_Kinase
    • Influenzan
      • Influenza_hemagglutinin
• ENZYMES
  • Enzymatic Catalysis
    • Aconitase
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
    • Serine Hydrolases
      • Serine_Protease
      • Acetylcholinesterase (AChE)
        • Acetylcholine
        • Flexibility_of_aromatic_residues_in_acetylcholinesterase
        • AChE inhibitors and substrates
          • 1eve AChE-Aricept complex; 1eve (Chinese); 1eve (Russian); 1eve (Spanish); 1eve (Turkish)
          • AChE_bivalent_inhibitors
    • Triose_Phosphate_Isomerase
    • [Pyruvate_phosphate_dikinase]
    • Cysteine Proteases
      • Tobacco_Etch_Virus_(TEV)_Protease
      • Streptomyces_griseus_Aminopeptidase_(SGAP)
    • Acid Proteases
      • HIV-1 protease
      • [Pepsin]
    • Metaloproteases
      • [Metalloproteases]
      • [Matrix_metalloproteinases]
    • Oxidoreductases
      • [NADH quinone oxidoreductase ]
  • Enzyme Kinetics, Inhibition, and Control
  • Biochemical Signaling
    • [Nitric_oxide_synthase]
    • [Recoverin,_a_calcium-activated_myristoyl_switch]

• METABOLISM
  • Introduction to Metabolism
  • Glucose Catabolism
    • Triose_Phosphate_Isomerase
  • Glycogen Metabolism and Gluconeogenesis
    • [Phosphoglucose_isomerase]
  • Citric Acid Cycle
  • Electron Transport and Oxidative Phosphorylation
    • [NADH quinone oxidoreductase ]
  • Photosynthesis
    • [Photosystem_II]
    • Ribulose-1,5-bisphosphate_carboxylase/oxygenase
    • [PrrA_in_Rhodobacter_sphaeroides]
    • [Pyruvate_phosphate_dikinase]
  • Lipid Metabolism
  • Amino Acid Metabolism
    • [Phenylalanine_hydroxylase]
  • Mammalian Fuel Metabolism: Integration and Regulation

• GENE EXPRESSION AND REPLICATION
  • Nucleotide Metabolism
  • Nucleic Acid Structure
    • Z-DNA
    • [Nucleosomes]
  • DNA Replication, Repair, and Recombination
    • DNA Replication,Transcription and Translation
    • [PcrA_helicase]
    • Fpg_Nei_Protein_Superfamily - DNA Repair and Base Excision DNA Repair
    • Human RecQ-Like protein 1 - RecQ family of DNA helicases are conserved in from bacteria to man
    • Structure_of_E._coli_DnaC_helicase_loader
    • Rop_protein
  • Transcription and RNA Processing
    • TATA-Binding_Protein
    • RSP1275
    • Transcription_Termination_Factor_Rho
  • Protein Synthesis
    • Ribosome
    • SelB_Recognition
  • Regulation of Gene Expression
    • Tangible_Models_of_Cdc42_Interacting_With_Intersectin

• EVOLUTION
  • Conservation, Evolutionary
  • Extremophiles

• IMMUNE SYSTEM
  • [Major_Histocompatibility_Complex_Class_I]

• METHODS OF STRUCTURE DETERMINATION
  • X-ray
    • X-ray_crystallography
      • Asymmetric_Unit
      • Biological_Unit
      • Electron_density_maps
    • SAXS
  • NMR
    • [NMR_Ensembles_of_Models]
  • Electron Microscopy

• METHODS OF STRUCTURE & SEQUENCE ANALYSIS
  • STRUCTURAL ANALYSIS & VISUALIZATION
    • Chime
    • Jmol
      • Visualising Protein Structure - Introduction to Jmol
      • FirstGlance_in_Jmol
    • Teaching Proteopedia
    • Generate Unfolded Structures
    • Homology Model
      • Homology Modeling
      • TRIM5a Homology Models - Differences in models as a function of their templates
    • DRuMS - set of standard color schemes for macromolecular visualization
  • SEQUENCE ANALYSIS
    • Sequence Analysis Tools

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