Predicción de estructura de proteínas .

1. Abril 2003 Predicción de estructura de proteínas. MASTER BIOINFORMÁTICA 2003. Paulino Gómez-Puertas. Centro de Astrobiología. CSIC-INTA

2. by: R. Guigó

3. ATP subunit Molecular chaperonin GroEL heptamer (Dr Jianpeng Ma, Harvard Univ.)

4. From DNA sec. to protein

5. Genome sequencing. Growth of EMBL H. sapiens D. melanogaster C. elegans S. cerevisiae Tamaños milesORFs Mbases Mycoplasma 0.6 Bacterias 3-4 1-4 Levadura 6 16 Humano 70-125 3200 E. coli by D. Devos H. influenzae

6. Sequence, structure and function Function Sequence Structure

7. Why protein structureprediction?

9. Actin DnaK Hsc70 FtsA MreB Hexokinase

10. Structural alignment

11. Protein structure determination USA Northeast Struct. Genomics Research Consor. Rutgers U. NY Struct. Genomics Research Rockefeller U. Southeast Collab. Struct. Genomics U. Georgia Struct. 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. Others CNRS Orsay/Gif-sur-Yvette Protein Structure Factory Berlin NMR facility Oxford Astex Technology Cambridge RIKEN Tokyo Xray crystallography NMR By D. Devos

12. EMBL PDB

13. Physical principles: not in the next few years? Informatics (copying from known cases) - Homology modeling Score = 85.1 bits (208), Expect = 6e-19 Identities = 27/56 (48%), Positives = 42/56 (74%), Gaps = 1/56 (1%) Query: 2 FIAIYDYKAETEEDLTIKKGEKLEIIEKEGD-WWKAKAIGSGEIGYIPANYIAAAE 56 F+A+YDY+A TE+DL+ KGEK +I+ WW+A+++ +GE GYIP+NY+A + Sbjct: 8 FVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD 63 - Threading MAKEFGIPAA VAGTVLNVVE AGGWVTTIV S ILTAVGSGGL SLLAAAGRES IKAYLKKEIK KKGKRAVIAW Fold ranking PDB Pseudo-Energy level? By D. Devos Protein structure prediction MAKEFGIPAA VAGTVLNVVE AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIK KKGKRAVIAW

14. http://folding.stanford.edu/

15. Folding@home: Simulations of the villin headpiece 3 Phe 1 Trp 1 Phe The 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 OFMICROVILLI 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 HIVintegrase 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? Informatics (copying from known cases) - Homology modeling Score = 85.1 bits (208), Expect = 6e-19 Identities = 27/56 (48%), Positives = 42/56 (74%), Gaps = 1/56 (1%) Query: 2 FIAIYDYKAETEEDLTIKKGEKLEIIEKEGD-WWKAKAIGSGEIGYIPANYIAAAE 56 F+A+YDY+A TE+DL+ KGEK +I+ WW+A+++ +GE GYIP+NY+A + Sbjct: 8 FVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD 63 - Threading MAKEFGIPAA VAGTVLNVVE AGGWVTTIV S ILTAVGSGGL SLLAAAGRES IKAYLKKEIK KKGKRAVIAW Fold ranking PDB Pseudo-Energy level? By D. Devos Protein structure prediction MAKEFGIPAA VAGTVLNVVE AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIK KKGKRAVIAW

18. Structure & sequence similarity Lesk & Chothia, 1986 Sander & Schneider, 1991

20. Structure to function (some examples)

21. a1 b1 a2 b2 a4 a3 b3 b4 b5 a5 a6 b6 b7 a7 a8 b8 Hydroxymethylglutaryl-CoA lyase

22. Hydroxymethylglutaryl-CoA lyase R41 D42 a2 a1 S75 D42 L263 S75 L263 a3 E279 a8 C a4 N D204 S201 H233 a7 H233 a5 D204 a6 V70 C S201 S75 E279 H233 R41 D204 D42 L263

23. S201 Y201 H233 D204 R75 S75 D42 Hydroxymethylglutaryl-CoA lyase A B

24. 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. 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 Kinesin is a force-generating enzyme, or motor protein, which convertsthe free energy of the gamma phosphate bond of ATPinto mechanical work. This work is used to power the transport of intracellular organelles along microtubules. http://www.proweb.org/~kinesin/ Liz Greene, Steve Henikoff & Sharyn Endow

27. Kinesin Motility Kinesin itself is an alpha2-beta2 heterotetramer of two heavy and two light chains How does kinesin walk along a MT protofilament? Twisting model Floppy logic model Alternate-sides model Rob Cross & Minia Alonso http://mc11.mcri.ac.uk/wrongtrousers.html

28. Kinesin Motility Neurospora crassa kinesin Song et al. (2001) http://www.mpasmb-hamburg.mpg.de/ktdock/ Mandelkow lab

29. Kinesin Motility Model of kinesin dimer walking along a microtubule protofilament. (Hoenger et al.2000). http://www.mpasmb-hamburg.mpg.de/ktdock/ Mandelkow lab

30. Kinesin Motility Animated Model for Processive Motility by Kinesin Animated Model for Muscle Myosin-Based Motility http://www.scripps.edu/milligan/projects.html Ron Milligan Lab

31. Bioinformatics Lab. Eduardo López Viñas Ugo Bastolla Paulino Gómez-Puertas Centro de Astrobiología (CSIC-INTA)

32. End of slide show