Proteopedia:Table of Contents

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• Introduction to Structural Biology
  • See About Macromolecular Structure
  • Water
    • Water in Macromolecular Models
  • Key Chemical Concepts for Structural Biology
    • Amino Acids
    • Cation-pi interactions
    • Hydrogen bond
    • Hydrogen in Macromolecular Models
    • Isoelectric point
    • Salt bridges
• Biomolecules
  • About Macromolecular Structure
  • Nucleotides, Nucleic Acids and Genetic Information
    • DNA
      • DNA
      • B-DNA 1bna
      • Z-DNA
  • Amino Acids
    • Amino Acids
    • Selenocysteine
  • Proteins, Primary Structure
    • Conservation, Evolutionary
    • Isoelectric point
  • Proteins, Three-Dimensional Structure
    • User:Tommie_Hata/Protein_Structure_Tutorial
    • S347/The four tiers of protein structure
    • Secondary structure
    • Protein structural motifs
      • User:James D Watson/Structural Templates
    • Fibrous Proteins
      • Coiled coil
      • Collagen
    • Protein Misfolding
      • Prion protein
      • A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35
  • 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
  • Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
    • Antibodies
      • IgA
      • Epitopes
      • Major Histocompatibility Complex Class I
    • Calmodulin in motion
    • Myoglobin
    • Hemoglobin; Hemoglobin (Hebrew)
    • Kinesin-5
  • Lipids and Biological Membranes
  • Lipid Binding Proteins
    • CRABP I ( Cellular Retinoic Acid Binding Protein )
  • Membrane Transport Proteins
    • A Physical Model of the β2-Adrenergic Receptor
    • Lactose Permease
    • Proton Channels
    • Ion channels
      • M2 Proton Channel
      • Voltage-gated calcium channels
    • Mechanosensitive channels: opening and closing
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
  • Prions and Intrinsically Disordered Proteins
    • Prion protein
    • Doppel
    • Intrinsically Disordered Protein
  • Toxins
    • Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis
  • Mitosis, Meiosis and Cargo Transport Proteins
    • Kinesin-5
  • Viruses
    • User:Wayne Decatur/Suppression of RNA Silencing by 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
      • User:Eric Martz/Molecular Playground/HIVDrug
    • Herpes Simplex Virus
      • Herpes Simplex Virus Thymidine Kinase
    • Influenza
      • Influenza hemagglutinin
      • Avian Influenza Neuraminidase, Tamiflu and Relenza
• Enzymes
  • Enzymatic Catalysis
    • Acid-beta-glucosidase
      • reHuman Acid-beta-glucosidase made in CHO cells 1ogs
      • reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide 1y7v
      • reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin 2v3d
      • Velaglucerase Alfa 2wkl
    • Acid Proteases
      • HIV-1 protease
      • Streptomyces griseus Aminopeptidase (SGAP); Aminopeptidase
    • Aconitase
    • Cysteine Proteases
    • Hen Egg-White (HEW) Lysozyme
    • Choline Oxidase
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
    • Metalloproteases
      • Matrix metalloproteinases
    • Oxidoreductases
      • NADH quinone oxidoreductase
    • Phosphofructokinase (PFK)
    • Pyruvate phosphate dikinase
    • Serotonin N-acetyltransferase
    • Serine Hydrolases
      • Acetylcholinesterase (AChE)
        • Acetylcholine
        • Flexibility of aromatic residues in acetylcholinesterase
        • AChE inhibitors and substrates
          • 1eve AChE-Aricept complex; 1eve (Arabic); 1eve (Chinese); 1eve (Italian); 1eve (Russian); 1eve (Spanish); 1eve (Turkish)
          • AChE bivalent inhibitors
      • Tobacco Etch Virus (TEV) Protease
    • Serine Protease
      • Trypsin
    • Triose Phosphate Isomerase
  • Enzyme Inhibitors
    • Alpha-1-antitrypsin
  • Enzyme Kinetics, Inhibition, and Control
    • Avian Influenza Neuraminidase, Tamiflu and Relenza
  • Biochemical Signaling
    • Nitric oxide synthase, NOS structures
    • Recoverin, a calcium-activated myristoyl switch
    • Bcl-2
    • C-Myc
    • C-di-GMP signaling
  • Enzymes - Molecular Machines
    • Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
    • Pyruvate phosphate dikinase
• Metabolism
  • Introduction to Metabolism
  • Glucose Catabolism
    • Triose Phosphate Isomerase
    • Phosphofructokinase (PFK)
  • Glycogen Metabolism and Gluconeogenesis
    • Phosphoglucose isomerase
    • Calmodulin in motion
    • Biotin Protein Ligase
  • Citric Acid Cycle
    • Aconitase
  • 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
    • Acid-beta-glucosidase
  • Amino Acid Metabolism
    • Aromatic amino acid hydroxylases
    • Phenylalanine hydroxylase
    • Tyrosine hydroxylase
    • ATP Phosphoribosyl Transferase
    • Isochorismate pyruvate lyase
  • Mammalian Fuel Metabolism: Integration and Regulation
  • Nucleotide Metabolism
    • Dihydrofolate reductase
• Gene Expression and Replication
  • Nucleic Acid Structure
    • DNA
      • B-DNA 1bna
      • Z-DNA
    • Nucleosomes
  • DNA Replication, Repair, and Recombination
    • DNA Replication,Transcription and Translation
    • DNA Polymerase I
    • 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
    • 1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA
    • Rop protein
  • Transcription and RNA Processing
    • C-Myc
    • Lac repressor
    • Reverse transcriptase
    • TATA-Binding Protein
    • RSP1275
    • Transcription Termination Factor Rho
  • Protein Synthesis
    • Ribosome
    • SelB Recognition
  • Regulation of Gene Expression
    • Lac repressor
    • Irr (Iron Response Regulator )
    • Oncogenes
      • P53
      • SRC
    • Tangible Models of Cdc42 Interacting With Intersectin
• Evolution
  • Conservation, Evolutionary
  • Extremophiles
• Immune System
  • Antibodies
    • IgA
    • Epitopes
  • Major Histocompatibility Complex Class I
    • Human beta two microglobulin
• Diseases
  • Cancer
    • SRC
    • Proteins involved in cancer
• 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
    • CPK - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
    • 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
• Model Structures
  • See Theoretical models
  • African Malaria Mosquito Acetylcholinesterase
  • Structure of E. coli DnaC helicase loader
  • User:Yuan-Ping Pang/HAB•BoNTAe
• Miscellaneous
  • Molecular Playground
  • Research Groups