Proteopedia:Table of Contents

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Introduction to Structural Biology
- Water

- - Water in Macromolecular Models
- Key Chemical Concepts for Structural Biology

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
  - 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

- 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

- Lipids and Biological Membranes

- Membrane Transport Proteins

- Prions and Intrinsically Disordered Proteins

- 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
  - Herpes Simplex Virus
    - Herpes_Simplex_Virus_Thymidine_Kinase
  - Influenza
    - Influenza_hemagglutinin
    - Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza

Enzymes
- Enzymatic Catalysis
  - Acid-beta-glucosidase [[1ogs]
  - Hen_Egg-White_(HEW)_Lysozyme
  - Serine Hydrolases
    - Serine_Protease
    - Trypsin
    - Alpha-1-antitrypsin
    - 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
  - Cysteine Proteases
    - Tobacco_Etch_Virus_(TEV)_Protease
    - Streptomyces_griseus_Aminopeptidase_(SGAP); Aminopeptidase
  - Acid Proteases
    - HIV-1 protease
    - Pepsin
  - Metaloproteases
    - Metalloproteases
    - Matrix_metalloproteinases
  - Oxidoreductases
    - NADH quinone oxidoreductase
  - Triose_Phosphate_Isomerase
  - Aconitase
  - Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System
  - Pyruvate_phosphate_dikinase
  - Phosphofructokinase_(PFK)

- Enzyme Kinetics, Inhibition, and Control
  - Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza

- Biochemical 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

- Citric Acid Cycle
  - Aconitase

- Electron Transport and Oxidative Phosphorylation
  - NADH quinone oxidoreductase

- Photosynthesis

- Lipid Metabolism
  - Acid-beta-glucosidase
- Amino Acid Metabolism
- 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

- Protein Synthesis
  - Ribosome
  - SelB_Recognition
- Regulation of Gene Expression

Evolution
- Conservation, Evolutionary

- Extremophiles

Immune System
- Antibodies
  - IgA
  - Epitopes
- Major_Histocompatibility_Complex_Class_I

Diseases
- Cancer
  - SRC
  - Proteins involved in cancer

Methods of Structure Determination
- X-ray
  - X-ray_crystallography
  - 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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Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman, Eran Hodis, Wayne Decatur, Alexander Berchansky, Judy Voet, Alejandro Porto, Helen Ginn, David Canner, Israel Hanukoglu, Karen L. Lee, Arthur Cox, Yuan-Ping Pang, Tilman Schirmer, Eric Martz, Tomas Klumpler, Karl Oberholser, Angel Herraez, Jaime Prilusky

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