predicción de estructura de proteínas. modelado por...

Paulino Gómez Puertas Bioinformática.

Predicción de estructura de proteínas.Modelado por homología.


Predicción de estructura de proteínas.

¿Por qué predecir la estructura de una proteína?.

¿Cómo predecir la estructura de una proteína?


Kinesin Motility

Model of kinesin dimerwalking along a microtubuleprotofilament.(Hoenger et al.2000).

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


Virtual docking:

carnitine


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 IKAYLKKEIKKKGKRAVIAW

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


“AB INITIO ”


Molecular dynamics simulation.

ab initio methods


Alain Leppinette. CAB.


Epot = Σi Ebonding + Σi Enon-bonding

Σi Ebonding = Σi Ebond + Σi Eangle + Σi Edihedral + Σi Eimproper

Σi Enon-bonding = Σi Eelectrostatic + Σi ELennard-Jones

Molecular Mechanics

Molecular DynamicsF = m · a ; F = m ·v/t ; Epot = F · f(i)

Epot = m · v/t · f(i)

Epot = F · f(i) (Epot grav. = m · g · h)


bonding terms

( )20bbonds

bonds bbk21E −= ∑

( )∑ −=angles

20angle k

21E θθθ

( )[ ]∑ −+=dihedrals

0ddihedral cos1k21E θθ

non-bonding terms

∑=ij ij

ji

0elect r

qq4

1Eεπε

repulsive

atractive

∑ −=−ij

6ij

ij12ij

ijJonesLennard r

BrA

E


PROTEIN UNFOLDING


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.

Thefoldingtime is on the order of 10 micro-seconds.

3 Phe

1 Trp

1 Phe

Folding@home: Simulations of the villin headpiece



Physical principles: not in the next few years?

Informatics (copying from known cases)

- Homology modeling

Score = 85.1 bits (208), Expect = 6e-19Identities = 27/56 (48%), Positives = 42/56 (74%), Gaps = 1/56 (1%)

Query: 2 FIAIYDYKAETEEDLTIK KGEKLEIIEKEGD-WWKAKAIGSGEIGYIPANYIAAAE 56F+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


Protein structure prediction. Flow chart.


Modelado por homología.


protein structure evolution


DnaK

FtsA

Actin

Hexokinase

Hsc70

MreB


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


AlignmentsThe 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)


Rotamers


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 - StructureAlignment

Query-Target Structures

Basic approach in homology modeling

Structuralalignment of target structures

Protein core

Full coordinates 3D Model

�Modeling based onrotamer databases

�Space restriction for the conformational search

Refined 3D Model

Loop search

MD and EM tech.

Rotamer library


Quality check: the Ramachandran plot.


Quality check: Prosa II energy plots


http://modbase.compbio.ucsf.edu


http://swissmodel.expasy.org/repository


Protein structure prediction. Flow chart.


Threading. Reconocimiento de plegamiento. Modelado por homología remota.


Homology Modelling vs Fold Recognition

Fold Recognition Homology Modelling

% seq. ID

0 30 100

Application

Model Quality

Any Sequence >= 30-50% IDwith template

Fold Level Atomic Level

If the sequence is similar to a known structure (>30-50% identity) you can usually move straight onto generating an all atom model by homology modelling.

Target Sequence


Structural space

Sequence space

Homology Modelling Targets

Fold Recognition Targets

Sequence Space vs. Structure Space

The development of fold recognition methods came from the observation that many apparently unrelated sequences had very similar 3-dimensional structures (folds).


Superfolds(Orengo et al.)


Algoritmos de threading. General.

Secuenciaproblema


Count pairs of each residue type at different separations

Algoritmos de threadingPotenciales de contacto

Energy of interaction = -KT ln (frequency of interactions)Boltzmann principle

d

Eco

unts

d

Jones, 1992; Sippl, 1995


Prediction-basedthreading

Algoritmos de threadingCoincidencia de estructura secundaria y accesibilidad

Rost, 1995 http://cubic.bioc.columbia.edu/predictprotein

secondary structure prediction


ALGUNOS SERVIDORES DE THREADING3D-PSSM: http://www.sbg.bio.ic.ac.uk/3dpssm


ALGUNOS SERVIDORES DE THREADINGFUGUE: http://www-cryst.biob.cam.ac.uk/~fugue/


ALGUNOS SERVIDORES DE THREADINGPSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/


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predicción de estructura de proteínas. modelado por...

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