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Paulino Gomez-Puertas Bioinformática. 2012
Modelado 3D.
“Introducción”
http://www.cbm.uam.es/bioweb
Paulino Gómez Puertas.
Centro de Biología Molecular "Severo Ochoa"
CSIC-UAM, Madrid
Centro de Investigacion y Tecnologia
Agroalimentaria. CITA - DGA.
Paulino Gomez-Puertas Bioinformática. 2012
Predicción de estructura de proteínas.
¿Por qué predecir la estructura de una proteína?.
¿Cómo predecir la estructura de una proteína?
Paulino Gomez-Puertas Bioinformática. 2012
Molecular chaperonin
GroEL
subunit
heptamer
(Dr Jianpeng Ma, Harvard Univ.)
ATP
Paulino Gomez-Puertas Bioinformática. 2012
Protein structure determination
Xray crystallography NMR
By D. Devos
Paulino Gomez-Puertas Bioinformática. 2012
EMBL
PDB
Paulino Gomez-Puertas Bioinformática. 2012
Predicción de estructura de proteínas.
¿Por qué predecir la estructura de una proteína?.
¿Cómo predecir la estructura de una proteína?
Paulino Gomez-Puertas Bioinformática. 2012
MAKEFGIPAA
VAGTVLNVVE
AGGWVTTIVS
ILTAVGSGGL
SLLAAAGRES
IKAYLKKEIK
KKGKRAVIAW
Physical principles: not in the next few years? Protein structure prediction
Paulino Gomez-Puertas Bioinformática. 2012
PLEGAMIENTO DE PROTEÍNAS
“AB INITIO ”
Paulino Gomez-Puertas Bioinformática. 2012
Molecular dynamics simulation.
ab initio methods
Paulino Gomez-Puertas Bioinformática. 2012
Alain Leppinette. CAB.
Paulino Gomez-Puertas Bioinformática. 2012
Alain Leppinette. CAB.
Paulino Gomez-Puertas Bioinformática. 2012
bonding terms
20b
bonds
bonds bbk2
1E
angles
20angle k
2
1E
dihedrals
0ddihedral cos1k2
1E
ij ij
ji
0elect
r
4
1E
repulsive
atractive
ij6ij
ij
12ij
ijJonesLennard
r
B
r
AE
non-bonding terms
Molecular Mechanics and Dynamics as tools for research in Biomedicine.
Paulino Gomez-Puertas Bioinformática. 2012
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
Paulino Gomez-Puertas Bioinformática. 2012
MAKEFGIPAA
VAGTVLNVVE
AGGWVTTIVS
ILTAVGSGGL
SLLAAAGRES
IKAYLKKEIK
KKGKRAVIAW
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
MAKEFGIPAA
VAGTVLNVVE
AGGWVTTIV
S ILTAVGSGGL
SLLAAAGRES
IKAYLKKEIK
KKGKRAVIAW
Pseudo-Energy level?
PDB
Fold
ranking
By D. Devos
Protein structure prediction
Paulino Gomez-Puertas Bioinformática. 2012
Protein structure prediction. Flow chart.
Paulino Gomez-Puertas Bioinformática. 2012
Predicción de estructura de proteínas. Modelado por homología.
Paulino Gomez-Puertas Bioinformática. 2012
protein structure evolution
Paulino Gomez-Puertas Bioinformática. 2012
Structural alignment
Paulino Gomez-Puertas Bioinformática. 2012
Structural alignment
Paulino Gomez-Puertas Bioinformática. 2012
Lesk & Chothia, 1986
Structure & sequence similarity
Paulino Gomez-Puertas Bioinformática. 2012
Sander & Schneider, 1991
Paulino Gomez-Puertas Bioinformática. 2012
Paulino Gomez-Puertas Bioinformática. 2012
alignment
AHPLTSDFGGHTERDLHA
AHTLTSEGGGHTEADVHA || |||: ||||| |:||
template (1ndb)
model (hCPTI)
Paulino Gomez-Puertas Bioinformática. 2012
Classical homology modeling algorithm
Generate alignment query - target
Replace conserved amino acid side-chains
Replace other amino acids
- use most common rotamers
- keep as many atoms in positions as possible
Model loops regions (insertions and deletions)
Optimize packing
Quality check
Paulino Gomez-Puertas Bioinformática. 2012
Alignments
The quality of the alignment is the key step in homology modeling
pairwise alignments
multiple sequence alignments
profile based alignments
Match of secondary structure elements *observed/predicted
Match structural environments and residue properties
Optimal structural position of gaps in the alignments
minimal number of gaps
better place them in loops / exposed regions
and close in structure (possible to model)
Paulino Gomez-Puertas Bioinformática. 2012
Alignments and introduced errors
Paulino Gomez-Puertas Bioinformática. 2012
Modeling
protein cores
Paulino Gomez-Puertas Bioinformática. 2012
Modeling loops (deletions &
insertions)
by Luis Sanchez-Pulido, 2000
Paulino Gomez-Puertas Bioinformática. 2012
Modeling side chains (rotamer libraries)
Paulino Gomez-Puertas Bioinformática. 2012
Similarity
Search
Database of 3D
structures
•Substitution of side-chains of internal residues
•Substitution of other
side-chains
3D Model
of the
protein core
Protein query
Sequence - Structure
Alignment
Query-
Target Structures
Basic approach in homology
modeling
Structural
alignment
of target
structures
Protein
core
Full
coordinates
3D Model
•Modeling based on rotamer databases
•Space restriction for
the conformational
search
Refined 3D
Model
Loop
search
MD and
EM tech.
Rotamer library
Paulino Gomez-Puertas Bioinformática. 2012
Quality check: the Ramachandran plot.
Paulino Gomez-Puertas Bioinformática. 2012
0 -20
-15
-10
-5
0
5
10
200 400 600 800 1000
X-ray
NMR
Z-S
co
re
Number of residues
Z-Score: -11.17
1000 0 -20
-15
-10
-5
0
5
10
200 400 600 800
Z-S
co
re
Number of residues
Z-Score: -11.88
X-ray
NMR
PROSA: Wiederstein & Sippl, NAR, 2007 ; Sippl, Proteins,1993
1NDB:A 1XL8:B
Kn
ow
led
ge
-based
en
erg
y
Sequence position
-3
-2
-1
0
1
2
3
Window size 10
Window size 40
625 30
Kn
ow
led
ge
-based
en
erg
y
Sequence position -3
-2
-1
0
1
2
3
612 11
Window size 10
Window size 40
Z-Score: -9.65
0 -20
-15
-10
-5
0
5
10
200 400 600 800 1000
Z-S
co
re
Number of residues
X-ray
NMR
Kn
ow
led
ge
-based
en
erg
y
Sequence position
-3
-2
-1
0
1
2
3
772 166
Window size 10
Window size 40
CPT1A_HUMAN model
[dominio CCAT] [ sw|P50416 ]
Calidad estructural: ProSA-web
Paulino Gomez-Puertas Bioinformática. 2012
http://modbase.compbio.ucsf.edu
Paulino Gomez-Puertas Bioinformática. 2012
http://swissmodel.expasy.org/repository
Paulino Gomez-Puertas Bioinformática. 2012
Protein structure prediction. Flow chart.
Paulino Gomez-Puertas Bioinformática. 2012
Cuestiones…
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