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{{#tree:id=siteTree|openlevels=1|root='''Chemistry of Life'''|close=top|open=top|
This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below. Updated:  {{REVISIONDAY2}}-{{REVISIONMONTH}}-{{REVISIONYEAR}} (DD-MM-YYYY)


* INTRODUCTION
'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
** Introduction to the Chemistry of Life


** WATER
==Topics Pages Organized by Category==
{{#tree:id=OrganizedByTopic|openlevels=0|


*** [[Water_in_macromolecular_models|Water in Macromolecular Models]]
* [[Introduction to protein structure]] - A introductory overview of protein structure.
** KEY CHEMICAL CONCEPTS FOR STRUCTURAL BIOLOGY
* [[About Macromolecular Structure]] - List of pages about macromolecular structure terms and concepts.
* [[Proteopedia:Topic Pages|Topic pages]] - List of pages about specific proteins or protein families.
* [[Index pages]] - List of pages that list other pages within Proteopedia.
* Basics of Protein Structure
**[[Introduction to protein structure]] - A introductory overview of protein structure
**[[Proteins: primary and secondary structure]]
**[[Myoglobin of Physeter catodon: structure]]
** The Building Blocks
*** [[Amino Acids]]
*** [[Backbone_representations]]
*** [[Peptide]]
**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]


*** [[Cation-pi interactions]]
** Conformational flexibility of a polypeptide chain
*** [[Hydrogen bond]]
*** [[Phi and Psi Angles]]
*** [[Hydrogen_in_macromolecular_models|Hydrogen in Macromolecular Models]]
*** [[Ramachandran Plots]]
*** [[Isoelectric_point]]
*** [[Tutorial:Ramachandran principle and phi psi angles]]
 
** [[Secondary structure]]
* BIOMOLECULES
*** [[Helices in Proteins]]
**[[About_Macromolecular_Structure]]
**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
 
*** [[Sheets in Proteins]]
** NUCLEOTIDES, NUCLEIC ACIDS AND GENETIC INFORMATION
**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
*** DNA
** [[Structural_templates]]
**** [[DNA]]
*** [[Globular_Proteins]]
**** B-DNA [[1bna]]
**** [[Turns in Proteins]]
**** [[Z-DNA]]
*** [[Fibrous Proteins]]
 
** 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]]
**** [[Coiled_coil]]
**** [[Collagen]]
**** [[Collagen]] - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen.
*** Protein Misfolding
**** [[Fibroins]]
**** [[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
 
** MEMBRANE TRANSPORT PROTEINS
*** [[A Physical Model of the β2-Adrenergic Receptor]]
*** [[Lactose_Permease]]
*** [[Proton_Channels]]
*** [[Ion_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, MEOSIS, 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
***[[Hen_Egg-White_%28HEW%29_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_%28PFK%29]]
 
** Enzyme Kinetics, Inhibition, and Control
***[[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]]
 
** BIOCHEMICAL SIGNALING
*** [[Nitric_oxide_synthase]]
*** [[Recoverin,_a_calcium-activated_myristoyl_switch]]
*** [[Bcl-2]]
*** [[C-Myc]]
 
* METABOLISM
** Introduction to Metabolism
 
** Glucose Catabolism
*** [[Triose_Phosphate_Isomerase]]
***[[Phosphofructokinase_%28PFK%29]]
 
 
** 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
** [[Unusual Motifs in Proteins]]
*** [[DNA]]
*** [[Cation-pi_interactions]]
**** B-DNA [[1bna]]
*** [[Thermal_motion_of_peptide]]
**** [[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]]
***[[1x9n#Crystal_Structure_of_Human_DNA_Ligase_I_bound_to_5.27-adenylated.2C_nicked_DNA]]
*** [[Rop_protein]]


** Transcription and RNA Processing
** [[Intrinsically Disordered Protein]]
*** [[C-Myc]]
*** [[Lac_repressor]]
*** [[TATA-Binding_Protein]]
*** [[RSP1275]]
*** [[Transcription_Termination_Factor_Rho]]


** Protein Synthesis
* Carbohydrates
*** [[Ribosome]]
**[[Carbohydrates]]  
*** [[SelB_Recognition]]
**[[Carbohydrates II]]
** Regulation of Gene Expression
* Cytoskeletal Proteins
*** [[Lac_repressor]]
** [[Actin]]
*** [[Irr]]
** [[Keratins]]
*** [[P53]]
** [[Tropomyosin]]
*** [[Tangible_Models_of_Cdc42_Interacting_With_Intersectin]]
** [[Tubulin]]


* EVOLUTION
* Lipids
** [[Conservation, Evolutionary]]
**[[Lipids: structure and classification]]


** [[Extremophiles]]
* Diseases & Related Topics
** [[Alzheimer's Disease]]
** [[Antibody]]
** [[Bacterial Infections]]
** [[Cancer]]
** [[Coronavirus Disease 2019 (COVID-19)]]
** [[Diabetes & Hypoglycemia]]
** [[Hemophilia]]
** [[HIV]]
** [[Hypertension & Congestive Heart Failure]]
** [[Immune Response]]
** [[Inflammation & Rheumatoid Arthritis]]
** [[Influenza]]
** [[Metabolic Disorders]]
** [[Neurodevelopmental Disorders]]
** [[Oncogenes]]
** [[Pharmaceutical Drugs]]
** [[Pharmaceutical Drug Targets]]
** [[Toxins]]
** [[Viral Infections]]


* IMMUNE SYSTEM
* Enzymes
** Antibodies
** [[Hydrolases]]
*** [[IgA]]
** [[Isomerases]]
*** [[Epitopes]]
** [[Ligases]]
** [[Major_Histocompatibility_Complex_Class_I]]
** [[Lyases]]
** [[Oxidoreductases]]
** [[Transferases]]


* Gene Expression & Replication
** [[DNA Replication]]
** [[Nucleic Acids]]
** [[Regulation of Gene Expression]]
** [[RNAi]]
** [[Transcription & RNA Processing]]
** [[Translation]]


* Large Macromolecular Assemblies
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
** [[Ribosome]]
** [[Ribosoma 70S]]
** [[Nucleosomes]]
** [[Nucleosome structure]]


* METHODS OF STRUCTURE DETERMINATION
* Metabolism
** X-ray
** [[Amino Acid Synthesis & Metabolism]]
*** [[X-ray_crystallography]]
** [[Carbohydrate Metabolism]]
**** [[Asymmetric_Unit]]
** [[Photosynthesis]]
**** [[Biological_Unit]]
** [[Regulation of Gene Expression]]
**** [[Electron_density_maps]]
** [[Drug Metabolism by CYP450 Enzymes]]
*** SAXS
**  NMR
*** [[NMR_Ensembles_of_Models]]
** Electron Microscopy


* METHODS OF STRUCTURE & SEQUENCE ANALYSIS 
* Miscellaneous
** STRUCTURAL ANALYSIS & VISUALIZATION
** [[Colored & Bioluminescent Proteins]]
*** [[Chime]]
** [[Coronavirus Disease 2019 (COVID-19)]]
*** Jmol
** [[Enzimas: complejo enzima-sustrato]]
**** [[S347/Visualising_protein_structure|Visualising Protein Structure]] - Introduction to Jmol
** [[3D Molecular Models]]
**** [[FirstGlance_in_Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization


** SEQUENCE ANALYSIS
* Signaling & Transport
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]
** [[Hormone]]
** [[Membrane Channels & Pumps]]


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