Paulino Gómez Puertas Centro de Astrobiología Master Bioinformática. Abril 2003. Predicción de...

Paulino Gómez PuertasCentro de Astrobiología

Master Bioinformática.Abril 2003.

Predicción de estructura de proteínas.

Centro de Astrobiología. CSIC-INTA

Abril 2003

Paulino Gómez-Puertas.

MASTER BIOINFORMÁTICA 2003.



by: R. Guigó



Molecular chaperonin GroEL

subunit

heptamer

(Dr Jianpeng Ma, Harvard Univ.)

ATP



From DNA sec. to protein



by D. Devos

Genome sequencing.

Tamaños milesORFs MbasesMycoplasma 0.6 Bacterias 3-4 1-4Levadura 6 16Humano 70-125 3200

Growth of EMBL

1994 1995 1996 1997 1998 1999 2000 20011,00E+02

1,00E+03

1,00E+04

1,00E+05

1,00E+06

1,00E+07

H. sapiens

E. coli

S. cerevisiae

C. elegans

D. melanogaster

H. influenzae



Function

Sequence

Structure

Sequence, structure and function



Why protein structure prediction?



DnaK

FtsA

Actin

Hexokinase

Hsc70

MreB



Structural alignment



Protein structure determination

Xray crystallography NMR

By D. Devos

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 Tokyo



EMBL

PDB



MAKEFGIPAA VAGTVLNVVE AGGWVTTIVS ILTAVGSGGL SLLAAAGRES IKAYLKKEIKKKGKRAVIAW

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 FIAIYDYKAETEEDLTIK KGEKLEIIEKEGD-WWKAKAIGSGEIGYIPANYIAAAE 56 F+A+YDY+A TE+DL+ KGEK +I+ WW+A+++ +GE GYIP+NY+A +Sbjct: 8 FVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVD 63

- Threading


Pseudo-Energy level?

PDB

Fold ranking

By D. Devos

Protein structure prediction



http://folding.stanford.edu/



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.

The folding time is on the order of 10 micro-seconds.

3 Phe

1 Trp

1 Phe

Folding@home: Simulations of the villin headpiece



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?

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


Pseudo-Energy level?

PDB

Fold ranking

By D. Devos

Protein structure prediction



Lesk & Chothia, 1986

Structure & sequence similarity

Sander & Schneider, 1991



Structure to function

(some examples)



Hydroxymethylglutaryl-CoA lyase




S75

D42R41

L263

E279

H233

D204

S201

E279S75

V70

S201

L263D42 R41H233

D204

H233

D204

S75D42

L263

NC

C




R75

D42

S75

S201

H233D204

Y201

B

A



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. 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 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.

Kinesin Motility

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



Kinesin itself is an alpha2-beta2 heterotetramer of two heavy and two light chains

How does kinesin walk along a MT protofilament?

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

Floppy logic model

Twisting

model

Alternate-sides model

Kinesin Motility



Neurospora crassa kinesin

Mandelkow lab

Song et al. (2001)

http://www.mpasmb-hamburg.mpg.de/ktdock/

Kinesin Motility



Kinesin Motility

Model of kinesin dimer walking along a microtubule protofilament. (Hoenger et al.2000).

Mandelkow lab http://www.mpasmb-hamburg.mpg.de/ktdock/



Kinesin Motility

Ron Milligan Labhttp://www.scripps.edu/milligan/projects.html

Animated Model for Muscle Myosin-Based Motility

Animated Model for Processive Motility by Kinesin



Centro de Astrobiología (CSIC-INTA)

Bioinformatics Lab.

Eduardo López ViñasUgo BastollaPaulino Gómez-Puertas



End of slide show

Paulino Gómez Puertas Centro de Astrobiología Master Bioinformática. Abril 2003. Predicción de...

Documents

Transcript of Paulino Gómez Puertas Centro de Astrobiología Master Bioinformática. Abril 2003. Predicción de...