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
  • Proteins: Primary Structure
  • Proteins: Three-Dimensional Structure
    • S347/The four tiers of protein structure
  • 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
  • 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_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
      • Acetylcholinesterase (AChE)
        • Acetylcholine
        • Flexibility_of_aromatic_residues_in_acetylcholinesterase
        • AChE inhibitors and substrates
          • 1eve AChE-Aricept complex; [[1eve (Turkish[]; 1eve (Chinese); 1eve (Spanish); 1eve (Russian),
          • AChE_bivalent_inhibitors
    • Triose_Phosphate_Isomerase
  • Enzyme Kinetics, Inhibition, and Control
  • Biochemical Signaling

• METABOLISM
  • Introduction to Metabolism
  • Glucose Catabolism
  • Glycogen Metabolism and Gluconeogenesis
  • Citric Acid Cycle
  • Electron Transport and Oxidative Phosphorylation
  • Photosynthesis
  • Lipid Metabolism
  • Amino Acid Metabolism
  • Mammalian Fuel Metabolism: Integration and Regulation

• GENE EXPRESSION AND REPLICATION
  • Nucleotide Metabolism
  • Nucleic Acid Structure
  • DNA Replication, Repair, and Recombination
    • DNA Replication,Transcription and Translation
    • 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
  • Transcription and RNA Processing
  • Protein Synthesis
  • Regulation of Gene Expression

• EVOLUTION
  • Conservation, Evolutionary
  • Extremophiles

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

• METHODS OF STRUCTURE & SEQUENCE ANALYSIS
  • STRUCTURAL ANALYSIS & VISUALIZATION
    • Chime
    • Jmol
      • S347/Visualising_protein_structure - Introduction to Jmol
      • FirstGlance_in_Jmol
    • User:Wayne Decatur/Teaching Proteopedia
    • User:Wayne Decatur/Generate Unfolded Structures
    • Homology Model
      • User:Wayne Decatur/Homology Modeling
      • User:Emi Nakayama/TRIM5a Homology Models - Differences in models as a function of their templates
    • DRuMS - set of standard color schemes for macromolecular visualization
  • SEQUENCE ANALYSIS
    • User:Wayne Decatur/Sequence analysis tools

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