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

2. by: R. Guigó

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

4. From DNA sec. to protein

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

6. Sequence, structure and function

7. Why protein structure prediction?

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?
Protein structure prediction
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 FIAIYDYKAETEEDLTIK KGEKLEIIEKEGD-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
Pseudo-Energy level?
PDB
Fold
ranking
By D. Devos
MAKEFGIPAA VAGTVLNVVE
AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIK
KKGKRAVIAW

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 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 prediction
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 FIAIYDYKAETEEDLTIK KGEKLEIIEKEGD-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
Pseudo-Energy level?
PDB
Fold
ranking
By D. Devos
MAKEFGIPAA VAGTVLNVVE
AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIK
KKGKRAVIAW

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

20. Structure to function
(some examples)

21. Hydroxymethylglutaryl-CoA lyaseb1 b2 a2 a4 b5 a3 b4 b3 a6 b7 b6 a5 a8 b8 a7

22. Hydroxymethylglutaryl-CoA lyaseN
S201
D204
H233 a7 a5
H233
D204 a6
V70 C
S201
S75
E279
H233
D42
R41
L263
D204

23. Hydroxymethylglutaryl-CoA lyaseB
D42
S75
R75

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 chains
How does kinesin walk along a MT protofilament?
Twisting
model
Floppy logic model
Alternate-sides model
Rob Cross & Minia Alonso

28. Kinesin Motility Song et al. (2001) Neurospora crassa kinesin
Mandelkow lab

29. Kinesin Motility
Model 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 Kinesin
Animated Model for Muscle Myosin-Based Motility
Ron Milligan Lab

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

32. End of slide show