Transcript General recombination (i.e. homologous recombination)

Folding@home and
SWISS-MODEL
Two Different Approaches to
Protein Structure Modeling
Taru Tukiainen ja Sini Sipponen
S-114.2500
13.12.2006
Outline
Introduction to protein modelling
 Modelling the folding process with
Folding@home
 Comparative modelling with SWISSMODEL

Introduction
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Proteins are formed from a
sequence of amino acids
Primary structure = polypeptide
chain
Secondary structure
 alpha helix
 beta sheet
Tertiary structure is 3D
Quaternary structure is comprised
of several tertiary structures
Native state is the functional form
Hydrophobic effect on Folding
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Important force affecting the
forming of the tertiary structure
Many residues of amino acids are
hydrophobic
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leads to the formation of a
hydrophobic core
After folding, entropy of protein
decreases, but the entropy of
system decreases
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Entropy promotes the folding
process
Misfolding
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Prions are result of
faulty folding
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Little known about
how they form
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Can convert normal
protein molecules
to prions
The Problems
1.
2.
3.
Impossible to predict 3D
structures from
polypeptide chains
Folding processes and
mechanisms are mostly
unknown
the 3D, native state is
very expensive and time
consuming to solve
Modeling the Folding Process

Proteins fold in about 10 µs
 Simulation would take dozens of years

Proteins are formed of thousands of atoms
 Presented often as force fields
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E.g. temperature, pH, covalent bonds between
residues and hydrophobic effect must be taken in
consideration
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Proposed that the native state = minimum of
potential energy curve
Folding@home
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Objective to study the
dynamics of protein
folding and misfolding
and the ensuing diseases
Uses distributed
computing, volunteers
let their PC to be utilized
when they aren’t needed
Program is a screen
saver
Uses packages

AMBER, TINKER and
GROMAS
Ensemble Dynamics Method
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Polypeptide chain is considered as a system waiting for
enough free energy to overcome the free energy barrier
(= the folding)
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Group of several molecules M is simulated at the same
time
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simulation rate is then M times faster than a single
simulation
 The simulations are completed in hours not in years
Wait until the first one of the simulations overcomes the
energy barrier
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All the simulations are restarted from the new energy level
Comparative modelling
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aims at building a 3D model for a protein with
unknown structure
relies on detectable similarities between the
protein sequence being modelled (the target)
and at least one empirically determined
protein structure (the template)
a small change in the protein sequence usually
results only in a small change in its 3D
structure
SWISS-MODEL
fully automated web-server for protein
structure modelling
 developed in 1993
 nowadays the most widely-used free webbased automated facility

Using SWISS-MODEL
User-friendly
 User only submits the amino acid sequnce
on a web form
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optionally templates can be submitted as well
Results in 15-60 min by e-mail
How SWISS-MODEL works?
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Five steps that can be repated iteratively
1
2
3
4
5
Search for suitable
templates
Check sequence identity with
target
Create ProModII
jobs
Generate models with
ProModII
Energy
minimisatio
n with
Gromos96
First Approach Mode (regular)
First Approach Mode (with user-defined templates)
Optimise Mode
How SWISS-MODEL works?
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Step 1
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search for suitable templates from ExNRL3D
program used: BLASTP2
Step 2
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find sequences with good degree of similarity
(>25%)
aling target and template sequences
program used: SIM
How SWISS-MODEL works?
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Step 3
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Step 4
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create ProModII input files
generate models
program used: ProModII
Step 5
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minimize energy
program used: Gromos96
Are there problems with SWISSMODEL?
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Results must be concidered with care
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procedure is non-experimental
no human intervention during model building
Chosen template affects the results
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the more the template and the target
sequence share identity the more accurate the
results will be
Accuracy of SWISS-MODEL