Proteopedia:Table of Contents

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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)
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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.
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'''When you create a new page in Proteopedia, please add it to corresponding topic subpages.'''
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'''When you create a new page in Proteopedia, please add it to both the "Index by Topic" and the "Alphabetical Index".'''
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==Topics Pages Organized by Category==
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{{#tree:id=OrganizedByTopic|openlevels=0|
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==Index by Topic==
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{{#tree:id=IndexByTopic|openlevels=1|close=top|open=top|
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* Introduction to Structural Biology
+
-
** See [[About Macromolecular Structure]]
+
-
** Water
+
-
 
+
-
*** [[Water in macromolecular models|Water in Macromolecular Models]]
+
-
** Key Chemical Concepts for Structural Biology
+
 +
* [[Introduction to protein structure]] - A introductory overview of protein structure.
 +
* [[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]]
*** [[Amino Acids]]
-
*** [[Cation-pi interactions]]
+
*** [[Backbone_representations]]
-
*** [[Hydrogen bond]]
+
*** [[Peptide]]
-
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
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**** [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
-
*** [[Isoelectric point]]
+
**** [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
-
*** [[Salt bridges]]
+
-
* Biomolecules
+
** Conformational flexibility of a polypeptide chain
-
** [[About Macromolecular Structure]]
+
*** [[Phi and Psi Angles]]
 +
*** [[Ramachandran Plots]]
 +
*** [[Tutorial:Ramachandran principle and phi psi angles]]
 +
** [[Secondary structure]]
 +
*** [[Helices in Proteins]]
 +
**** [[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
 +
*** [[Sheets in Proteins]]
 +
**** [[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]
 +
** [[Structural_templates]]
 +
*** [[Globular_Proteins]]
 +
**** [[Turns in Proteins]]
 +
*** [[Fibrous Proteins]]
 +
**** [[Coiled_coil]]
 +
**** [[Collagen]] - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen.
 +
**** [[Fibroins]]
-
** Nucleotides, Nucleic Acids and Genetic Information
 
-
*** DNA
 
-
**** [[DNA]]
 
-
**** B-DNA [[1bna]]
 
-
**** [[Z-DNA]]
 
-
*** RNA
 
-
**** [[RNA]]
 
-
**** RNA motifs
 
-
***** [[RNA motifs]]
 
-
***** [[User:Wayne Decatur/kink-turn motif|Kink-turn motif]]
 
 +
** [[Unusual Motifs in Proteins]]
 +
*** [[Cation-pi_interactions]]
 +
*** [[Thermal_motion_of_peptide]]
-
** Amino Acids
+
** [[Intrinsically Disordered Protein]]
-
*** [[Amino Acids]]
+
-
*** [[Selenocysteine]]
+
-
** Proteins, Primary Structure
+
-
*** [[Conservation, Evolutionary]]
+
-
*** [[Isoelectric point]]
+
-
** Proteins, Three-Dimensional Structure
+
* Carbohydrates
-
*** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
+
**[[Carbohydrates]]
-
*** [[S347/The four tiers of protein structure]]
+
**[[Carbohydrates II]]
-
*** [[Secondary structure]]
+
* Cytoskeletal Proteins
-
*** Protein structural motifs
+
** [[Actin]]
-
**** [[User:James D Watson/Structural Templates]]
+
** [[Keratins]]
 +
** [[Tropomyosin]]
 +
** [[Tubulin]]
-
*** Protein Misfolding
+
* Lipids
-
**** [[Prion protein]]
+
**[[Lipids: structure and classification]]
-
**** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]
+
-
** Colored Proteins & those that Change Color
+
* Diseases & Related Topics
-
*** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
+
** [[Alzheimer's Disease]]
-
*** [[Dronpa]]
+
** [[Antibody]]
-
*** [[Factor IX]]
+
** [[Bacterial Infections]]
-
*** [[Luciferase]]
+
** [[Cancer]]
-
*** [[Dinoflagellate luciferase]]
+
** [[Coronavirus Disease 2019 (COVID-19)]]
-
 
+
** [[Diabetes & Hypoglycemia]]
-
** DNA Binding Proteins
+
** [[Hemophilia]]
-
*** [[Helix-turn-helix motif]]
+
** [[HIV]]
-
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]
+
** [[Hypertension & Congestive Heart Failure]]
-
 
+
** [[Immune Response]]
-
** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
+
** [[Inflammation & Rheumatoid Arthritis]]
-
*** Antibodies
+
** [[Influenza]]
-
**** [[Antibody]]
+
** [[Metabolic Disorders]]
-
**** [[IgA]]
+
** [[Neurodevelopmental Disorders]]
-
**** [[Epitopes]]
+
** [[Oncogenes]]
-
**** [[Major Histocompatibility Complex Class I]]
+
** [[Pharmaceutical Drugs]]
-
**** [[Monoclonal Antibody]]
+
** [[Pharmaceutical Drug Targets]]
-
*** [[Calmodulin in motion]]
+
** [[Toxins]]
-
*** [[Myoglobin]]
+
** [[Viral Infections]]
-
*** [[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]]
+
-
***[[Glutamate receptor (GluA2)|Glutamate Receptor]]
+
-
*** [[Lactose Permease]]
+
-
*** [[Proton Channels]]
+
-
*** [[Ion Channels]]
+
-
**** [[M2 Proton Channel]]
+
-
**** [[Voltage-gated calcium channels]]
+
-
****[[Glutamate receptor (GluA2)|Glutamate Receptor]]
+
-
*** [[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
+
-
*** [[Suppression of RNA Silencing by Viruses]]
+
-
*** Filamentous bacteriophage
+
-
**** [[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]]
+
-
 
+
-
 
+
-
* 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]]
+
* Enzymes
* Enzymes
-
** Enzymatic Catalysis
+
** [[Hydrolases]]
-
*** Acid-beta-glucosidase
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** [[Isomerases]]
-
**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
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** [[Ligases]]
-
**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
+
** [[Lyases]]
-
**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
+
** [[Oxidoreductases]]
-
**** Velaglucerase Alfa [[2wkl]]
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** [[Transferases]]
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*** Acid Proteases
+
-
**** [[HIV-1 protease]]
+
-
**** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
+
* Gene Expression & Replication
-
*** [[Aconitase]]
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** [[DNA Replication]]
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*** Cysteine Proteases
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** [[Nucleic Acids]]
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*** [[Hen Egg-White (HEW) Lysozyme]]
+
** [[Regulation of Gene Expression]]
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*** [[Choline Oxidase]]
+
** [[RNAi]]
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*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
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** [[Transcription & RNA Processing]]
-
*** [[Metalloproteases]]
+
** [[Translation]]
-
**** [[Matrix metalloproteinases]]
+
-
*** Oxidoreductases
+
-
**** [[NADH quinone oxidoreductase ]]
+
-
*** [[Phosphofructokinase %28PFK%29]]
+
-
*** [[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
+
* Large Macromolecular Assemblies
-
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
+
** [[Group:MUZIC|Muscle sarcomere: Z-Disk]]
-
*** [[Pyruvate phosphate dikinase]]
+
** [[Ribosome]]
-
 
+
** [[Ribosoma 70S]]
-
* Fibrous Proteins
+
** [[Nucleosomes]]
-
** [[Coiled coil]]
+
** [[Nucleosome structure]]
-
** [[Collagen]]
+
-
 
+
-
* Membrane Transport Proteins
+
-
** [[A Physical Model of the β2-Adrenergic Receptor]]
+
-
** [[Glutamate receptor (GluA2)|Glutamate 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]]
+
-
** [[Pore forming toxin, α-hemolsyin|The pore forming toxin, α-hemolsyin]]
+
-
 
+
-
 
+
-
* Myoglobin & Hemoglobin
+
-
** [[Myoglobin]]
+
-
** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
+
-
 
+
-
* Nervous System Proteins
+
-
 
+
-
** [[Acetylcholinesterase]] (AChE)
+
-
*** [[Acetylcholine]]
+
-
*** [[Flexibility of aromatic residues in acetylcholinesterase]]
+
-
 
+
-
*** AChE inhibitors (In Different Languages)
+
-
**** [[1eve]] AChE-Aricept complex, [[1eve (Arabic)]], [[1eve (Chinese)]], [[1eve (Italian)]], [[1eve (Russian)]], [[1eve (Spanish)]], [[1eve (Turkish)]]
+
-
**** [[1vot]] AChE-Huperzine A complex, [[1vot (Chinese)]]
+
-
 
+
-
 
+
-
*** Acetylcholinesterase - AChE native
+
-
**** [[3lii]] – hAChE - recombinant human
+
-
**** [[1ea5]], [[2ace]] – ''Tc''AChE – trigonal – ''Torpedo californica''
+
-
**** [[2j3d]] – ''Tc''AChE – monoclinic
+
-
**** [[1w75]] – ''Tc''AChE – orthorhombic
+
-
**** [[1eea]] – ''Tc''AChE – cubic
+
-
**** [[2vt6]], [[2vt7]] – ''Tc''AChE – different dosage
+
-
**** [[1qid]] to [[1qim]] - ''Tc''AChE synchrotron radiation damage
+
-
**** [[1j06]], [[1maa]] – mAChE - mouse
+
-
**** [[1qo9]] – ''Dm''AChE - ''Drosophila''
+
-
**** [[1c2o]], [[1c2b]] – electrophorus AChE – Electric eel
+
-
 
+
-
*** AChE active site inhibitors conjugating at the bottom of the active site gorge
+
-
**** [[2w9i]] – ''Tc''AChE + methylene blue
+
-
**** [[2wls]] – MosAChE + AMTS13
+
-
**** [[2vq6]] – ''Tc''AChE + 2-PAM
+
-
**** [[2j3q]] – ''Tc''AChE + Thioflavin T
+
-
**** [[2ha0]] – mAChE + ketoamyltrimethylammonium
+
-
**** [[2h9y]] – mAChE + TMTFA
+
-
**** [[1gpk]], [[1gpn]], [[1vot]] – ''Tc''AChE + huperzine
+
-
**** [[1gqr]] – ''Tc''AChE + rivastigmine
+
-
**** [[1gqs]] – ''Tc''AChE + NAP
+
-
**** [[1e66]] – ''Tc''AChE + huprine
+
-
**** [[1dx4]], [[1qon]] – ''Dm''AChE + tacrine derivative
+
-
**** [[1oce]] – ''Tc''AChE + MF268
+
-
**** [[1ax9]], [[1ack]] – ''Tc''AChE + edrophonium
+
-
**** [[1amn]] – ''Tc''AChE + TMTFA
+
-
**** [[1acj]] – ''Tc''AChE + tacrine
+
-
 
+
-
*** AChE peripheral site inhibitors conjugating at the surface of the protein
+
-
**** [[1ku6]] - mAChE + fasciculin 2
+
-
**** [[1ku6]], [[1mah]] - mAChE + fasciculin 2
+
-
**** [[1j07]] - mAChE + decidium
+
-
**** [[1n5m]] - mAChE + gallamine
+
-
**** [[1n5r]] - mAChE + propidium
+
-
**** [[1b41]], [[1f8u]] - hAChE + fasciculin 2
+
-
**** [[1fss]] - TcAChE + fasciculin 2
+
-
 
+
-
*** AChE bis inhibitors spanning the active site gorge
+
-
**** [[AChE bivalent inhibitors]]
+
-
**** [[3i6m]] – ''Tc''AChE + N-piperidinopropyl galanthamine
+
-
**** [[3i6z]] - ''Tc''AChE + saccharinohexyl galanthamine
+
-
**** [[1zgb]], [[1zgc]] – ''Tc''AChE + tacrine (10) hupyridone
+
-
**** [[2w6c]] – ''Tc''AChE + bis-(-)-nor-meptazinol
+
-
**** [[2ckm]], [[2cmf]] – ''Tc''AChE + bis-tacrine
+
-
**** [[2cek]] – ''Tc''AChE + N-[8-(1,2,3,4-tetrahydroacridin-9-ylthio)octyl]-1,2,3,4-tetrahydroacridin-9-amine
+
-
**** [[1ut6]] - ''Tc''AChE + N-9-(1,2,3,4-tetrahydroacridinyl)-1,8-diaminooctane
+
-
**** [[1odc]] - ''Tc''AChE + N-4-quinolyl-N-9-(1,2,3,4-tetrahydroacridinyl)-1,8-diaminooctane
+
-
**** [[1w4l]], [[1w6r]], [[1w76]], [[1dx6]], [[1qti]] - TcAChE + galanthamine and derivative
+
-
**** [[1q83]], [[1q84]] - mAChE + TZ2PA6
+
-
**** [[1h22]], [[1h23]] – ''Tc''AChE + bis-hupyridone
+
-
**** [[1hbj]] – ''Tc''AChE + quinoline derivativev
+
-
**** [[1e3q]] – ''Tc''AChE + bw284c51
+
-
**** [[1eve]] – ''Tc''AChE + e2020
+
-
**** [[1acl]] – ''Tc''AChE + decamethonium
+
-
 
+
-
 
+
-
*** AChE organophosphate inhibitors causing irreversible inhibition
+
-
**** [[2wu3]] – mAChE + fenamiphos and HI-6
+
-
**** [[2wu4]] – mAChE + fenamiphos and ortho-7
+
-
**** [[2jgf]] - mAChE + fenamiphos
+
-
**** [[2wfz]], [[2wg0]], [[1som]] - ''Tc''AChE + soman
+
-
**** [[2wg1]] - ''Tc''AChE + soman + 2-PAM
+
-
**** [[2whp]], [[2whq]], [[2whr]] – mAChE + sarin and HI-6
+
-
**** [[2jgg]] - mAChE + sarin
+
-
**** [[2jgl]] - mAChE + VX and sarin
+
-
**** [[1cfj]] - ''Tc''AChE + sarin, GB
+
-
**** [[3dl4]], [[3dl7]] – mAChE + tabun
+
-
**** [[2jey]] – mAChE + HLO-7
+
-
**** [[2c0p]], [[2c0q]] - mAChE + tabun
+
-
**** [[2jez]] - mAChE + tabun + HLO-7
+
-
**** [[2jf0]] - mAChE + tabun + Ortho-7
+
-
**** [[2jgh]] - mAChE + VX
+
-
**** [[1vxo]], [[1vxr]] - ''Tc''AChE + VX
+
-
**** [[2jgi]], [[2jgm]] - mAChE + DFP
+
-
**** [[1dfp]] - ''Tc''AChE + DFP
+
-
**** [[2jgj]], [[2jgk]], [[2jge]] - mAChE + methamidophos
+
-
**** [[2gyu]] - mAChE + HI-6
+
-
**** [[2gyv]] - mAChE + Ortho-7
+
-
**** [[2gyw]] - mAChE + obidoxime
+
-
 
+
-
*** AChE substrate analogues mimicking the binding of the substrate acetylcholine
+
-
**** [[2ha4]] – mAChE (mutant) + acetylcholine
+
-
**** [[2vja]], [[2vjb]], [[2vjc]], [[2vjd]], [[2cf5]] – ''Tc''AChE + 4-oxo-N,N,N-trimethylpentanaminium
+
-
**** [[2v96]], [[2v97]], [[2v98]], [[2v99]] – ''Tc''AChE + 1-(2-nitrophenyl)-2,2,2-trifluoroethyl-arsenocholine
+
-
**** [[2ha2]] – mAChE + succinylcholine
+
-
**** [[2ha3]] - mAChE + choline
+
-
**** [[2ha5]] – mAChE (mutant) + acetylthiocholine
+
-
**** [[2ha6]] – mAChE (mutant) + succinylthiocholine
+
-
**** [[2ha7]] – mAChE (mutant) + butyrylthiocholine
+
-
**** [[2ch4]], [[2c58]] – ''Tc''AChE + acetylthiocholine
+
-
**** [[2c5g]] – ''Tc''AChE + thiocholine
+
-
 
+
-
*** Others…
+
-
**** [[2j4f]] – ''Tc''AChE + Hg
+
-
**** [[1vzj]] – ''Tc''AChE tetramerization domain
+
-
**** [[1jjb]] – ''Tc''AChE + PEG
+
-
 
+
-
** [[Acetylcholine binding protein]] (AChBP)
+
-
** [[Butyrylcholinesterase]] (BChE)
+
-
** [[Glutamate receptor (GluA2)|Glutamate Receptor]]
+
-
 
+
-
 
+
-
* Prions and Intrinsically Disordered Proteins
+
-
** [[Prion protein]]
+
-
** [[Doppel]]
+
-
** [[Intrinsically Disordered Protein]]
+
-
 
+
-
* Small Iron Sulfur Proteins
+
-
** [[Ferredoxin]] (Fd)
+
-
*** 2Fe-2S containing ferredoxins
+
-
**** [[3hui]] – Fd – ''Rhodopseudomonas palustris''
+
-
**** [[2kaj]], [[1dox]], [[1doy]] – SyFd +Ga – Synechocystis – NMR
+
-
**** [[1off]] – SyFd
+
-
**** [[3gce]] – Fd – Nocardioides aromaticivorans
+
-
**** [[2e4p]], [[2e4q]] - Fd – ''Pseudomonas sp.''
+
-
**** [[2q3w]], [[1vm9]] - PmFd (mutant) – ''Pseudomonas mendocina''
+
-
**** [[2i7f]] - Fd – ''Rhodobacter capsulatus''
+
-
**** [[1rfk]] - Fd – Cyanobacterium ''masticogladus laminosus''
+
-
**** [[1vck]] - Fd – ''Pseudomonas resinovorans''
+
-
**** [[1wri]], [[1frr]] - Fd – Equisetum arvense
+
-
**** [[1sjg]] - PmFd– NMR
+
-
**** [[1iue]] - Fd– Plasmodium falciparum
+
-
**** [[1m2a]] –AeFd – Aquifex aeolicus
+
-
**** [[1m2b]], [[1m2d]], [[1f37]], [[1f5b]], [[1f5c]] – AeFd (mutant)
+
-
**** [[1l5p]] – Fd – Trichomonas vaginalis
+
-
**** [[1i7h]] - Fd – Escherichia coli
+
-
**** [[1czp]], [[1qt9]], [[1frd]], [[1fxa]] - aFd– anabaena
+
-
**** [[1j7a]], [[1j7b]], [[1j7c]] , [[1qoa]], [[1qob]], [[1qof]], [[1qog]]- aFd (mutant)
+
-
**** [[1e0z]] – Fd – Halobacterium salinarium
+
-
**** [[1pfd]] – Fd – Petroselinum crispum – NMR
+
-
**** [[1a70]] - Fd (mutant) – Spinacia oleracea
+
-
**** [[1awd]] - Fd – Chlorella fusca
+
-
**** [[2cjn]], [[2cjo]], [[1roe]] – SyFd – NMR
+
-
**** [[1rof]] – SyFd – Synechococcus elongates
+
-
**** [[1doi]] - Fd – Haloarcula marismortui
+
-
**** [[4fxc]] – Fd – Spirulina platensis
+
-
**** [[1fxi]] – Fd – Aphanothece sacrum
+
-
**** [[3dqy]], [[2qpz]] - Fd – Pseudomonas putida
+
-
 
+
-
*** 4Fe-4S containing ferredoxins
+
-
 
+
-
**** [[3eun]] – AvFd – Allochromatium vinosum
+
-
**** [[3exy]] - AvFd (mutant)
+
-
**** [[2vkr]] - Fd+Zn – Acidianus ambivalens
+
-
**** [[2z8q]] - PfFd (mutant) – Pyrococcus furiosus
+
-
**** [[2fgo]] - Fd– Pseudomonas aeruginosa
+
-
**** [[1iqz]], [[1ir0]] - BtFd – Bacillus thermoproteolyticus
+
-
**** [[1rgv]] - Fd – Thauera aromatica
+
-
**** [[1dax]], [[1dfd]] – DaFd – Desulfovibrio africanus – NMR
+
-
**** [[1fxr]] - DaFd
+
-
**** [[1vjw]] – Fd – Thermotoga maritima
+
-
 
+
-
*** 3Fe-4S containing ferredoxins
+
-
 
+
-
**** [[2v2k]] – Fd – Mycobacterium smegmatis
+
-
**** [[1wtf]] - BtFd (mutant)
+
-
**** [[1sj1]] - PfFd
+
-
**** [[1fxd]] - DgFd – Desulfovibrio gigas
+
-
**** [[1f2g]] – DgFd – NMR
+
-
**** [[1xer]] - Fd – Sulfolobus tokodaii
+
-
 
+
-
*** 4Fe-4S+3Fe-4S containing ferredoxins
+
-
 
+
-
**** [[1gao]], [[6fdr]], [[7fd1]], [[7fdr]], [[1axq]], [[6fd1]], [[1frh]], **** [[1fri]],[[1frj]], [[1frk]], [[1frl]], [[1frm]], [[1fda]], [[1fdb]], **** [[1fdd]], [[5fd1]], [[1fer]] – AvFd – Azotobacter vinelandii
+
-
**** [[1pc4]], [[1pc5]], [[1g6b]], [[1g3o]], [[1ff2]], [[1b0v]], [[1d3w]], **** [[1b0t]], [[1a6l]], [[1ftc]], [[1frx]], [[2fd2]], [[1fd2]] - AvFd (mutant)
+
-
**** [[1h98]] – Fd – Thermus thermophilus
+
-
**** [[1a8p]], [[1bd6]] - BsFd – Bacillus schlegelii – NMR
+
-
 
+
-
*** 4Fe-4S+4Fe-4S containing ferredoxins
+
-
 
+
-
**** [[1dur]] – Fd – Peptoniphilus asaccarolyticus
+
-
**** [[1bwe]], [[1bqx]] - BsFd (mutant) – NMR
+
-
**** [[2fdn]], [[1fca]] , [[1fdn]]- Fd – Clostridium acidi-urici
+
-
**** [[1blu]] - Fd – Chromatium vinosum
+
-
**** [[1clf ]]– Fd – Clostridium pasteurianum – NMR
+
-
 
+
-
*** Adrenoredoxin
+
-
 
+
-
**** [[2jqr]] – ADR Fd domain (mutant)+cytochrome c (mutant) – yeast – NMR
+
-
**** [[2bt6]] – cADR1 modified – cow
+
-
**** [[1l6u]], [[1l6v]] – cADR1 – NMR
+
-
**** [[1e6e]] – cADR (mutant)+ADR reductase
+
-
**** [[1cje]], [[1ayf]] - cADR
+
-
 
+
-
*** Putidaredoxin
+
-
 
+
-
**** [[1yji]], [[1yjj]], [[1pdx]] – PpPUT – Pseudomonas putida – NMR
+
-
**** [[3lb8]] – PpPUT (mutant)+PUT reductase
+
-
**** [[1xln]], [[1xlo]], [[1xlp]], [[1xlq]], [[1r7s]], [[1oqq]], [[1oqr]] - PpPUT (mutant)
+
-
**** [[1gpx]], [[1put]]- PpPUT (mutant) - NMR
+
-
 
+
-
*** Terpredoxin
+
-
 
+
-
**** [[1b9r]] – TER – Pseudomonas - NMR
+
-
 
+
-
 
+
-
* Toxins
+
-
** [[Pore forming toxin, α-hemolsyin|The pore forming toxin, α-hemolsyin]]
+
-
** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
+
-
 
+
-
 
+
-
* Diseases
+
-
** Cancer
+
-
*** [[SRC]]
+
-
*** [[Proteins involved in cancer]]
+
-
 
+
-
* Evolution
+
-
** [[Conservation, Evolutionary]]
+
-
** [[Extremophiles]]
+
-
 
+
-
* 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
+
-
*** T-box family
+
-
**** [[T-box proteins]]
+
-
**** [[Brachyury]]
+
-
**** [[TBX1]]
+
-
**** [[TBX3]]
+
-
**** [[TBX5]]
+
-
**** [[TBX15]]
+
-
*** [[C-Myc]]
+
-
*** [[Lac repressor]]
+
-
*** [[Reverse transcriptase]]
+
-
*** [[TATA-Binding Protein]]
+
-
*** [[RSP1275]]
+
-
*** [[Transcription Termination Factor Rho]]
+
-
 
+
-
** Protein Synthesis
+
-
*** [[1fnm|Ef-G]]
+
-
*** [[Ribosome]]
+
-
*** [[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit]]
+
-
*** [[Ribosomal back translocase|ribosomal back translocase, Escherichia coli LepA]]
+
-
*** [[SelB Recognition]]
+
-
*** [[1ehz|tRNA]]
+
-
 
+
-
** Regulation of Gene Expression
+
-
*** [[Lac repressor]]
+
-
*** [[Irr]] (Iron Response Regulator )
+
-
*** Oncogenes
+
-
**** [[P53]]
+
-
**** [[SRC]]
+
-
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]
+
-
 
+
-
* Immune System
+
-
** Antibodies
+
-
*** [[IgA]]
+
-
*** [[Epitopes]]
+
-
** [[Major Histocompatibility Complex Class I]]
+
-
*** [[Human beta two microglobulin]]
+
* Metabolism
* Metabolism
-
** Introduction to Metabolism
+
** [[Amino Acid Synthesis & Metabolism]]
-
 
+
** [[Carbohydrate Metabolism]]
-
** Glucose Catabolism
+
** [[Photosynthesis]]
-
*** [[Triose Phosphate Isomerase]]
+
** [[Regulation of Gene Expression]]
-
***[[Phosphofructokinase %28PFK%29]]
+
** [[Drug Metabolism by CYP450 Enzymes]]
-
 
+
-
 
+
-
** 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]]
+
-
 
+
-
 
+
-
 
+
-
* 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
+
-
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
+
-
**** [[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
+
-
*** [[User:Wayne Decatur/Sequence analysis tools|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
* Miscellaneous
-
** [[Molecular Playground]]
+
** [[Colored & Bioluminescent Proteins]]
-
** [[Research Groups]]
+
** [[Coronavirus Disease 2019 (COVID-19)]]
-
}}
+
** [[Enzimas: complejo enzima-sustrato]]
-
 
+
** [[3D Molecular Models]]
-
{{Clear}}
+
-
 
+
-
==Alphabetical Index==
+
-
(incomplete -- still in development as of Sept 18 2010. Missing many pages from the above Index by Topic and from [[Proteopedia:Interesting_Pages]])
+
* Signaling & Transport
 +
** [[Hormone]]
 +
** [[Membrane Channels & Pumps]]
-
[[Image: Picture_15.png|520px|right|thumb]]
 
-
{{#tree:id=alphabeticalIndex|openlevels=1|close=top|open=top|
 
-
** A
 
-
*** [[Acetylcholinesterase#Selected_3D_Structures_of_AChE|Acetylcholinesterase]]
 
-
*** [[Aconitase]]
 
-
*** [[Actin]]
 
-
*** [[ABC transporter]]
 
-
*** [[Actinin]]
 
-
*** [[Adenylyl cyclase]]
 
-
*** [[ADP-ribosyl cyclase]]
 
-
*** [[Adrenodoxin]]
 
-
*** [[Agrin]]
 
-
*** [[Angiotensin-Converting_Enzyme#Additional_3D_Structures_of_ACE|Angiotensin-Converting Enzyme]]
 
-
*** [[Annexin]]
 
-
*** [[Antibody#Additional_3D_Structures_of_the_Immunoglobulin|Antibody]] or [[Monoclonal_Antibody#Additional_3D_Structures_of_Selected_Therapeutic_Monoclonal_Antibodies|Monoclonal Antibody]]
 
-
*** [[Aquaporin]]
 
-
*** [[ATPase]]
 
-
*** [[Avidin]]
 
-
** B
 
-
*** [[Bungarotoxin]]
 
-
*** [[Butyrylcholinesterase]]
 
-
*** [[BPTI]] (Basic Pancreatic Trypsin Inhibitor)
 
-
** C
 
-
*** [[Cadherin]]
 
-
*** [[Calmodulin]]
 
-
*** [[Ca2+/Calmodulin dependent protein kinase]]
 
-
*** [[Catenin]]
 
-
*** [[Cathepsin]]
 
-
*** [[Cluster of Differentiation 38]]
 
-
*** [[Cystic Fibrosis Transmembrane regulator]]
 
-
*** [[Chymotrypsin]]
 
-
*** [[Chymotrypsin inhibitor 2]]
 
-
*** [[Cyclophilin]]
 
-
*** [[Cytochrome P450]]
 
-
** D
 
-
*** [[Dihydrofolate reductase]]
 
-
** E
 
-
*** [[Epidermal Growth Factor Receptor]]
 
-
*** [[Eglin]]
 
-
*** [[Elastase]]
 
-
*** [[Endoplasmin]]
 
-
** F
 
-
*** [[Fasciculin]]
 
-
*** [[Ferredoxin]]
 
-
*** [[Ferritin]]
 
-
*** [[Fibrin]]
 
-
*** [[Fibrinogen]]
 
-
*** [[Fibronectin]]
 
-
*** [[Filamin]]
 
-
*** [[Flavodoxin]]
 
-
*** [[Filamenting Temperature-Sensitive Mutant Z]]
 
-
** G
 
-
*** [[Gelsolin]]
 
-
*** [[Green Fluorescent Protein]]
 
-
*** [[Gyrase]]
 
-
** H
 
-
*** [[Heat shock protein]]
 
-
*** [[Hirudin]]
 
-
*** [[HMGR#Additional_3D_Structures_of_HMG-CoA_Reductase|HMG-CoA Reductase]]
 
-
** I
 
-
*** [[Ion_channels#Available_structures|Ion Channels]]
 
-
*** [[Isocitrate dehydrogenase]]
 
-
*** [[Isocitrate dehydrogenase kinase/phosphatase]]
 
-
** J
 
-
** K
 
-
*** [[Kinesin]]
 
-
** L
 
-
*** [[Lipase]]
 
-
** M
 
-
*** [[Malate Dehydrogenase]]
 
-
*** [[Monoclonal Antibody]]
 
-
*** [[Myoglobin]]
 
-
*** [[Myosin]]
 
-
** N
 
-
*** [[NEDD8]]
 
-
*** [[Nucleoporin]]
 
-
*** [[Neuroligin]]
 
-
** O
 
-
** P
 
-
*** [[PPAR#Additional_3D_Structures_of_PPAR|Peroxisome Proliferator-Activated Receptors]]
 
-
*** [[Phenylethanolamine N-methyltransferase]]
 
-
*** [[Potassium, Calcium Channel]]
 
-
*** [[Porin]]
 
-
*** [[Proteasome]]
 
-
** Q
 
-
** R
 
-
*** [[Recombinase A]]
 
-
*** [[Resolvase]]
 
-
*** [[Reverse_Transcriptase#3D_Structures_of_Reverse_transcriptase|Reverse Transcriptase]]
 
-
*** Ribosome & Ribosomal Proteins
 
-
**** [[Ribosome#Additional_Ribosome_Structures|Ribosome]]
 
-
**** [[Ribosomal protein S1|Ribosomal protein S1 (bacterial)]]
 
-
**** [[Ribosomal protein S2|Ribosomal protein S2 (bacterial)]]
 
-
**** [[Ribosomal protein S3|Ribosomal protein S3 (bacterial)]]
 
-
**** [[Ribosomal protein S4|Ribosomal protein S4 (bacterial)]]
 
-
**** [[Ribosomal protein S10|Ribosomal protein S10 (bacterial)]]
 
-
**** [[Ribosomal protein S11|Ribosomal protein S11 (bacterial)]]
 
-
**** [[Ribosomal protein S12|Ribosomal protein S12 (bacterial)]]
 
-
**** [[Ribosomal protein S13|Ribosomal protein S13 (bacterial)]]
 
-
**** [[Ribosomal protein S15|Ribosomal protein S15 (bacterial)]]
 
-
**** [[Ribosomal protein S17|Ribosomal protein S17 (bacterial)]]
 
-
**** [[Ribosomal protein THX|Ribosomal protein THX (bacterial)]]
 
-
**** [[Ribosomal protein S28|Ribosomal protein S28 (eukaryotes/archaea)]]
 
-
** S
 
-
*** [[Severin]]
 
-
*** [[SGAP#Structures_Available|Streptomyces griseus Aminopeptidase (SGAP)]]
 
-
*** [[Spectrin]]
 
-
*** [[Strepavidin]]
 
-
*** [[Subtilisin]]
 
-
*** [[SUMO]]
 
-
*** [[Superoxide Dismutase]]
 
-
*** [[Superoxide Reductase]]
 
-
** T
 
-
*** [[Talin]]
 
-
*** [[TATA-Binding Protein]]
 
-
*** [[Telethonin]]
 
-
*** [[Telomerase]]
 
-
*** [[Thermolysin]]
 
-
*** [[Thioredoxin]]
 
-
*** [[Titin]]
 
-
*** [[Topoisomerase]]
 
-
*** [[Tropomyosin]]
 
-
*** [[Troponin]]
 
-
*** [[Tubulin]]
 
-
** U
 
-
*** [[Ubiquitin]]
 
-
** V
 
-
*** [[VEGF#Additional_3D_Structures_of_VEGF|Vascular Endothelial Growth Factor]]
 
-
*** [[VEGFR#Additional_3D_Structures_of_VEGFR|Vascular Endothelial Growth Factor Receptor]]
 
-
*** [[Villin]]
 
-
*** [[Vinculin]]
 
-
** W
 
-
** X
 
-
** Y
 
-
** Z
 
}}
}}
 +
__NOTOC__
 +
__NOEDITSECTION__

Current revision

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the search slots at the left if you don't find what you are looking for below. Updated: 30-12-2021 (DD-MM-YYYY)

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