VISUALISATION TRIDIMENSIONNELLE DES MOLECULES A L'AIDE DE RasTop

ENSEIGNEMENT DE BIOCHIMIE RELATIF A LA PARTIE ENZYMOLOGIE APPROFONDIE (Professeur M. BAAZIZ)
FACULTE DES SCIENCES -SEMLALIA, UNIVERSITE CADI AYYAD, MARRAKECH, MAROC.
Site Web: http://www.takween.com, E.mail: baaziz@ucam.ac.ma

EXEMPLES DE STRUCTURES MOLECULAIRES

 Le site web Protein Data Bank (http://www.rcsb.org/pdb/) peut être utilisé pour télécharger des structures de protéines. Faire une recherche par mots clés ou introduire le code de la protéine directement (ex. 1kpb for acid phosphatase). Des exemples de protéines sont donnés dans le tableau (liste inspirée de celle du Dr.LEE, Department of Biology SUNY- Fredonia, Fredonia, NY 14063 )

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Protéines (Références) Description
Acid Phosphatase (1kbp)
 Strater et al., Science 268: 1489-1492 (1995)		 From kidney beans, for those who want more acid phosphatase data.
Actin (1j6z)
Otterbein et al., Science 293: 708-711 (2001)		 Component of muscle cell filaments.
Adenylyl Cyclase complex with Gsa-GTPgS (1cjk)
    Tesmer et al., Science 278: 1907-1916 (1997)		 Adenylyl cyclase converts ATP to the second messenger cyclic AMP (cAMP)
Anthrax Toxin Protective Antigen (1acc)
     Petosa et al., Nature 385: 833 (1997)		 Component of the anthrax toxin.
APE1 Endonuclease (1de9)
     Mol et al., Nature 403: 451-456 (2000)		 AP Endonuclease repairs DNA damage.
Bacteriorhodopsin (1c8s)
     Leucke et al., Science 286: 255-260 (1999)		 A light driven proton pump.
Bam HI Endonuclease (1bhm)
    Newman et al., Science 269: 656-663		 Bam HI cleaves DNA at the sequence 5' -GGATCC- 3'
Catabolite Activator Protein (CAP)-DNA Complex (2cgp)
     Schultz et al., Science 253: 1001- 1007 (1991)		 Regulatory protein of the lac operon
Cholera toxin-related heat-labile Enterotoxin of E. coli  (1lts)
    Sixma et al., Nature 351: 371-377 (1991)		 Enterotoxins are produced by some intestinal bacteria and cause diarrheal diseases.
See also- Sixma et al., Nature 355: 561-564 (1992)
Cyclin-dependent Kinase 2 (1hck)
     De Bondt et al., Nature 363: 595-602 (1993)		 Cyclin-dependent protein kinases are important regulators of the cell cycle. 
Cytochrome bc1 complex (1bgy)
     Iwata et al., Science 281: 64-71 (1998)		 Complex is one component of electron transport chain.
DNA Polymerase III- b Subunit (1pol)
     Kong et al., Cell 69: 425-437 (1992)		 Subunit provides clamp that can slide along DNA.
DNA Gyrase (1ab4)
     Morais Cabral et al., Nature 388: 903-906 (1997)		 Supercoils DNA in bacteria
Elongation Factor Tu with Phe-tRNAPhe (1ttt)
     Nissen et al., Science 270: 1464-1472 (1995)		 Recommended choice.
F1-ATPase (1h8e)
     Abrahams et al., Nature 370: 621-628 (1994)		 Protein synthesizes ATP on mitochondrial membrane.
Fructose-1,6-bisphosphatase (4fbp)
     Ke et al., Proc. Natl. Acad. Sci. USA 88: 2989-2993 (1991)		 Key regulatory enzyme in gluconeogenesis
GCN4 Leucine Zipper (2zta)
     O-Shea et al., Science 254: 539-544 (1991)		 Eukaryotic transcription factor.
Glyphosate Herbicide with EPSP Synthase (1G6S)
     Schonbrunn et al., Proc. Natl. Acad. Sci. USA 98:1376 (2001)		 Glyphosate is active ingredient in Roundup.
Green Fluorescent Protein (1emb)
     Ormo et al., Science 273: 1392-1395 (1996)		 Fluorscent protein from jellyfish.
GroEL (1aon)
     Xu et al., Nature 388: 741-750 (1997)		 Molecular Chaperone Complex
Histone Acetyltransferase of GCN5 (1qst)
     Rojas et al., Nature 401: 93-98 (1999)		 Important in the regulation of gene expression.
Histone Deacetylase (1c3r)
     Finnin et al., Nature 401: 188-193 (1999)		 Important in the regulation of gene expression.
HIV Protease (1hvp)
     Navia et al., Nature 337: 615-620 (1989)		 An aspartyl protease.
Human Serum Albumin (1bmo)
     He & Carter, Nature 358: 209-215(1992)		 An abundant protein found in the circulatory system that aids in the transport of many ligands.
Interleukin-1 Receptor (1ira)
     Schreuder et al., Nature 386: 194-200 (1997)		 Receptor for activating of macrophages.
Lac repressor protein (1efa)
    Friedman et al., Science 268: 1721-1727 (1995)		 also see Lewis et al., Science 271: 1247-1254 (1996)
Lambda Integrase (1ae9)
     Kwon et al., Science 276: 126-131		 Integrase catalyzes rearrangements between DNA sequences.
MAP Kinase (2erk)
     Canagarajah et al., Cell 90: 859-869 (1997)		 Signal transduction pahtways
Nitrogenase Iron Protein (1nip)
     Georgiadis et al., Science 257: 1653-1659 (1992)		 Reduces nitrogen during nitrogen fixation.
Nucleosome (1aoi)
     Luger et al., Nature 389: 251-260 (1997)		 Histone proteins and DNA in core packaging particle.
Phosphofructokinase (1pfk)
     Evans & Hudson Nature 279: 500-504 (1979)		 Controls rate of glycolysis.

Purine Nucleoside Phosphorylase (PNP):
PNP humain native (1ula).
PNP humain complexée avec Ganine (1ulb).

Purine nucleoside + Pi <----> alpha-D-ribose 1-phhosphate + Purine
Le déficit en PNP empêche le catabolisme de l'inosine en hypoxanthine ainsi que de la guanosine en guanine, ce qui aboutit à l'accumulation de guanosine et d'inosine et leurs déoxydérivés, et à l'effondrement des taux de guanine, ainsi que d'hypoxanthine, xanthine et acide urique. Synthèse d'inhibiteur compétitif de PNP (texte en arabe).
Potassium Channel (1bl8)
     Doyle et al., Science 280: 69-77 (1998)		 A selective membrane channel protein.
Ras-RasGAP complex (1wq1)
     Scheffzek et al., Science 277: 333-338 (1997)		 Ras proteins are critical regulators of signal transduction pathways.
Rhodopsin (1f88)
    Palczewski et al., Science 289: 739-745 (2000)		 Rhodopsin is activated by light and initiates the vision signalling pathway.
Ribulose-bisphosphate carboxylase/oxygenase (Rubisco) (1rus)
     Andersson et al., Nature 337: 229-234 (1989)		 Catalyzes the fixation of CO2 during the Calvin cycle.
RNA polymerase domain of primase (1dde)
    Keck et al., Science 287: 2482-2486 (2000)		 Primases are DNA replication priming RNA polymerases required for the initiation of DNA synthesis.
Seryl-tRNA synthetase with seryl adenylate (1ser)
     Belrhali et al., Science 263: 1432-1436 (1994)		 As discussed in lecture; also see Biou et al., Science 263: 1404-1410 (1994)
Signal Recognition Particle- ribonucleoprotein core (1dul)
    Batey et al., Science 287: 1232-1239 (2000)		 SRPs bind to signal sequences and mediate the docking of the translating ribosome to the endoplasmic reticulum.
Single Stranded Binding Protein RPA (1jmc)
     Bochkarev et al., Nature 385: 176-181 (1997)		 Bind to DNA during replication.
Taq DNA Polymerase (1taq)
     Kim et al., Nature 376: 612-616 (1995)		 The thermostable DNA polymerase used for PCR.
TATA-box Binding Polypeptide (1tgh)
     Kim et al., Nature 365: 520-527 (1993)		 Critical protein in eukaryotic transcription.
Topoisomerase I (1a35)
     Redinbo et al., Science 279: 1504-1513 (1998)		 Topoisomerase I break one strand of a DNA duplex.  This is an important step in DNA replication, transcription, and translation.
Topoisomerase II (1bjt)
     Berger et al., Nature 379: 225 (1996)		 Different class of topoisomerases.
Transcription Regulatory protein GA-binding protein (GABP) (1awc)
    Batchelor et al., Science 279: 1037-1041 (1998)		 Regulation of eukaryotic gene expression.
trp Repressor/Operator Complex (1tro)
     Otwinowski et al., Nature 335: 321 (1988)		 Regulation of prokaryotic gene expression.
Ubiquitin cascade proteins E6AP-UbcH7 (1d5f)
    Huang et al., Science 286: 1321-1326 (1999)		 Proteolysis of cellular proteins by ubiquitin is an important regulatory process for many cellular activities.
VP40 Ebola Virus Matrix Protein (1ES6)
     Dessen et al., EMBO J. 19: 4228-4236 (2000)		 Role in virus assembly and budding.
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