5 Genome sequencing. Growth of EMBL H. sapiens D. melanogaster by D. DevosGenome sequencing.Tamaños milesORFs MbasesMycoplasma 0.6BacteriasLevadura 6 16HumanoGrowth of EMBLH. sapiensE. coliS. cerevisiaeC. elegansD. melanogasterH. influenzae
11 Protein structure determination USANortheast Struct. Genomics Research Consor. Rutgers U.NY Struct. Genomics Research Rockefeller U.Southeast Collab. Struct. Genomics U. GeorgiaStruct. Genomics Center Lawrence Berkeley Natl. Lab.Joint Center for Struct. Genomics Scripps Research Inst.Tuberculosis Bact. Struct. Genomics Consort Los Alamos Natl. Lab.Midwest Center for Struct. Genomics Argonne Natl. Lab.OthersCNRS Orsay/Gif-sur-YvetteProtein Structure Factory BerlinNMR facility OxfordAstex Technology CambridgeRIKEN TokyoXray crystallographyNMRBy D. Devos
15 Folding@home: Simulations of the villin headpiece 3 Phe1 Trp1 PheThe folding time is on the order of 10 micro-seconds.CA(2+)-REGULATED ACTIN-BINDING PROTEIN.VILLIN CONSISTS OF A LARGE CORE FRAGMENT, THE AMINO-TERMINAL PORTION, AND A SMALL HEADPIECE, THE CARBOXYL-TERMINAL PORTION. THE HEADPIECE BINDS F-ACTIN STRONGLY IN BOTH THE PRESENCE AND ABSENCE OF CALCIUM.MAJOR COMPONENT OF MICROVILLI OF INTESTINAL EPITHELIAL CELLS.
16 Folding@home: Unfolding of HIV integrase (DNAb dom.) HIV uses proteins to insert its genetic code into our DNA. The DNA binding domain of HIV integrase is the protein which HIV uses to grab onto our DNA such that it can then connect its genetic code into ours. This movie shows a single trajectory of the unfolding of this protein under extreme denaturating conditions.
17 Physical principles: not in the next few years? Protein structure predictionInformatics (copying from known cases)- Homology modelingScore = 85.1 bits (208), Expect = 6e-19Identities = 27/56 (48%), Positives = 42/56 (74%), Gaps = 1/56 (1%)Query: 2 FIAIYDYKAETEEDLTIK KGEKLEIIEKEGD-WWKAKAIGSGEIGYIPANYIAAAE 56F+A+YDY+A TE+DL+ KGEK +I WW+A GE GYIP+NY+A +Sbjct: 8 FVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD 63- ThreadingMAKEFGIPAA VAGTVLNVVE AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIKKKGKRAVIAWPseudo-Energy level?PDBFoldrankingBy D. DevosMAKEFGIPAA VAGTVLNVVEAGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIKKKGKRAVIAW
24 Estrogen Receptor-DNA binding Estrogen Receptor-DNA binding. The estrogen receptor recognizes and binds specific sequences of DNA. Upon binding, the protein induces bending in the DNA axis.
25 High Density Lipoprotein Particle High Density Lipoprotein Particle. The model surrounded a circular disk of 160 lipids, forming a bilayer, with two apoA-I proteins and 6000 water molecules, altogether a 46,000 atom system.
26 Kinesin Motility http://www.proweb.org/~kinesin/ Kinesin is a force-generating enzyme, or motor protein, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. This work is used to power the transport of intracellular organelles along microtubules.Liz Greene, Steve Henikoff & Sharyn Endow
27 Kinesin Motility How does kinesin walk along a MT protofilament? Kinesin itself is an alpha2-beta2 heterotetramer of two heavy and two light chainsHow does kinesin walk along a MT protofilament?TwistingmodelFloppy logic modelAlternate-sides modelRob Cross & Minia Alonso
28 Kinesin Motility Song et al. (2001) Neurospora crassa kinesin Mandelkow lab
29 Kinesin MotilityModel of kinesin dimer walking along a microtubule protofilament. (Hoenger et al.2000).Mandelkow lab
30 Kinesin Motility http://www.scripps.edu/milligan/projects.html Animated Model for Processive Motility by KinesinAnimated Model for Muscle Myosin-Based MotilityRon Milligan Lab
31 Bioinformatics Lab.Eduardo López ViñasUgo BastollaPaulino Gómez-PuertasCentro de Astrobiología (CSIC-INTA)
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