aim
Structure prediction tries to build models of
3D structures of proteins that could be useful
for understanding structure-function
relationships.
Genbank/EMBL 105.000.000
Uniprot 5.200.000
PDB 47.000
The protein folding problem
The information for 3D structures is coded in
the protein sequence
Proteins fold in their native structure in
seconds
Native structures are both
thermodynamically stables and kinetically
available
ab-initio prediction
Prediction from sequence using first
principles
AVVTW...GTTWVR
Ab-initio prediction
“In theory”, we should be able to build native
structures from first principles using
sequence information and molecular
dynamics simulations: “Ab-initio prediction of
structure”
Simulaciones de 1 s de “folding” de una proteína
modelo (Duan-Kollman: Science, 277, 1793, 1998).
Simulaciones de folding reversible de péptidos (20-200
ns) (Daura et al., Angew. Chem., 38, 236, 1999).
Simulaciones distribuidas de folding de Villin (36-
residues) (Zagrovic et al., JMB, 323, 927, 2002).
... the bad news ...
It is not possible to span simulations to the
“seconds” range
Simulations are limited to small systems and
fast folding/unfolding events in known
structures
steered dynamics
biased molecular dynamics
Simplified systems
typical shortcuts
Reduce conformational space
1,2 atoms per residue
fixed lattices
Statistic force-fields obtained from known
structures
Average distances between residues
Interactions
Use building blocks: 3-9 residues from PDB
structures
Results
from ab-initio
Average error 5 Å -
10 Å
Function cannot be
predicted
Long simulations
Some protein from [Link]
predicted at 7.6 Å
(CASP3, [Link])
comparative modelling
The most efficient way to predict protein
structure is to compare with known 3D
structures
Protein folds
Basic concept
In a given protein 3D structure is a more
conserved characteristic than sequence
Some aminoacids are “equivalent” to each
other
Evolutionary pressure allows only aminoacids
substitutions that keep 3D structure largely
unaltered
Two proteins of “similar” sequences must
have the “same” 3D structure
Possible scenarios
1. Homology can be recognized using sequence comparison
tools or protein family databases (blast, clustal, pfam,...).
Structural and functional predictions are feasible
2. Homology exist but cannot be recognized easily (psi-blast,
threading)
Low resolution fold predictions are possible. No functional
information.
3. No homology
1D predictions. Sequence motifs. Limited functional
prediction. Ab-initio prediction
fold prediction
3D struc. prediction
1D prediction
Prediction is based on averaging aminoacid
properties
AGGCFHIKLAAGIHLLVILVVKLGFSTRDEEASS
Average over a
window
1D prediction. Properties
Secondary structure propensitites
Hydrophobicity (transmembrane)
Accesibility
...
Propensities Chou-Fasman
Biochemistry 17, 4277 1978
Aminoacido P() P() P(turn)
Ala 1.29 0.9 0.78
Cys 1.11 0.74 0.8
Leu 1.3 1.02 0.59
Met 1.47 0.97 0.39
Glu 1.44 0.75 1
Gln 1.27 0.8 0.97
His 1.22 1.08 0.69
Lys 1.23 0.77 0.96
Val 0.91 1.49 0.47
Ile 0.97 1.45 0.51
Phe 1.07 1.32 0.58
Tyr 0.72 1.25 1.05
Trp 0.99 1.14 0.75
Thr 0.82 1.21 1.03
Gly 0.56 0.92 1.64
Ser 0.82 0.95 1.33
Asp
Asn
1.04
0.9
0.72
0.76
1.41
1.23 turn
Pro 0.52 0.64 1.91
Arg 0.96 0.99 0.88
Some programs ([Link])
BCM PSSP - Baylor College of Medicine
Prof - Cascaded Multiple Classifiers for Secondary Structure
Prediction
GOR I (Garnier et al, 1978) [At PBIL or at SBDS]
GOR II (Gibrat et al, 1987)
GOR IV (Garnier et al, 1996)
HNN - Hierarchical Neural Network method (Guermeur, 1997)
Jpred - A consensus method for protein secondary structure
prediction at University of Dundee
nnPredict - University of California at San Francisco (UCSF)
PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology,
PHDthreader, MaxHom, EvalSec from Columbia University
PSA - BioMolecular Engineering Research Center (BMERC) / Boston
PSIpred - Various protein structure prediction methods at Brunel
University
SOPM (Geourjon and Deléage, 1994)
SOPMA (Geourjon and Deléage, 1995)
AGADIR - An algorithm to predict the helical content of peptides
1D
Prediction
Original methods: 1 sequence and uniform
parameters (25-30%)
Original improvements: Parameters specific
from protein classes
Present methods use sequence profiles
obtained from multiple alignments and neural
networks to extract parameters (70-75%, 98%
for transmembrane helix)
Methods for remote homology
Homology can be recognized using PSI-Blast
Fold prediction is possible using threading
methods
Acurate 3D prediction is not possible: No
structure-function relationship can be
inferred from models
Threading
Unknown sequence is “folded” in a number of
known structures
Scoring functions evaluate the fitting
between sequence and structure according to
statistical functions and sequence comparison
..........
10.5 > .......... 5.2
SELECTED HIT
ATTWV....PRKSCT Sequence
HHHHH....CCBBBB Pred. Sec. Struc.
eeebb....eeebeb Pred. accesibility
..........
Sequence GGTV....ATTW ........... ATTVL....FFRK
Obs SS BBBB....CCHH ........... HHHB.....CBCB
Obs Acc. EEBE.....BBEB ........... BBEBB....EBBE
Threading accurancy
0.35
% 0.3
A 0.25
C
0.2
I
E 0.15
R
T 0.1
O
S 0.05
0
5 10 15 20 25
% IDENTIDAD SECUENCIAS
Comparative modelling
Good for homology >30%
Accurancy is very high for homology > 60%
Reminder
The model must be USEFUL
Only the “interesting” regions of the protein
need to be modelled
Expected accurancy
Strongly dependent on the quality of the sequence
alignment
Strongly dependent on the identity with
“template” structures. Very good structures if
identity > 60-70%.
Quality of the model is better in the backbone than
side chains
Quality of the model is better in conserved regions
Quality test
No energy differences between a correct or
wrong model
The structure must by “chemically correct” to
use it in quantitative predictions
Analysis software
PROCHECK
WHATCHECK
Suite Biotech
PROSA
Prediction software
SwissModel (automatic)
[Link]
SwissModel Repository
[Link]
3D-JIGSAW ([Link])
[Link]
Modeller ([Link])
[Link]
MODBASE (A. Sali)
[Link]
Final test
The model must justify experimental data (i.e.
differences between unknown sequence and
templates) and be useful to understand
function.