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

by: R. Guigó

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

From DNA sec. to protein

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

Sequence, structure and function

Why protein structure prediction?

Actin DnaK Hsc70 FtsA MreB Hexokinase

Structural alignment

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

EMBL PDB

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

http://folding.stanford.edu/

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.

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.

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

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

Structure to function (some examples)

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

Hydroxymethylglutaryl-CoA lyase N S201 D204 H233 a7 a5 H233 D204 a6 V70 C S201 S75 E279 H233 D42 R41 L263 D204

Hydroxymethylglutaryl-CoA lyase B D42 S75 R75

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.

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.

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. http://www.proweb.org/~kinesin/ Liz Greene, Steve Henikoff & Sharyn Endow

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 http://mc11.mcri.ac.uk/wrongtrousers.html Rob Cross & Minia Alonso

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

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

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

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

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