Modelado 3D. “Introducción”bioweb.cbm.uam.es/courses/MasterVirol2013/intro... · Modelado 3D....

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.


Predicción de estructura de proteínas.

¿Por qué predecir la estructura de una proteína?.

¿Cómo predecir la estructura de una proteína?


Molecular chaperonin

GroEL

subunit

heptamer

(Dr Jianpeng Ma, Harvard Univ.)

ATP


Protein structure determination

Xray crystallography NMR

By D. Devos


EMBL

PDB


Predicción de estructura de proteínas.

¿Por qué predecir la estructura de una proteína?.

¿Cómo predecir la estructura de una proteína?


MAKEFGIPAA

VAGTVLNVVE

AGGWVTTIVS

ILTAVGSGGL

SLLAAAGRES

IKAYLKKEIK

KKGKRAVIAW

Physical principles: not in the next few years? Protein structure prediction


PLEGAMIENTO DE PROTEÍNAS

“AB INITIO ”


Molecular dynamics simulation.

ab initio methods


Alain Leppinette. CAB.


bonding terms

20b

bonds

bonds bbk2

1E

angles

20angle k

2

1E

dihedrals

0ddihedral cos1k2

1E

ij ij

ji

0elect

r

qq

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.

../../../../2005/BioInfo2005/Curso_UAM_2002/Mol_dyn/EmbNet/abt.gif


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


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


Protein structure prediction. Flow chart.


Predicción de estructura de proteínas. Modelado por homología.


protein structure evolution


Structural alignment


Lesk & Chothia, 1986

Structure & sequence similarity


Sander & Schneider, 1991


alignment

AHPLTSDFGGHTERDLHA

AHTLTSEGGGHTEADVHA || |||: ||||| |:||

template (1ndb)

model (hCPTI)


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


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)


Alignments and introduced errors


Modeling

protein cores


Modeling loops (deletions &

insertions)

by Luis Sanchez-Pulido, 2000


Modeling side chains (rotamer libraries)


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


Quality check: the Ramachandran plot.


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


http://modbase.compbio.ucsf.edu


http://swissmodel.expasy.org/repository


Protein structure prediction. Flow chart.


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