Predicting Protein Structure:

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Predicting Protein Structure Comparative
Modeling (homology modeling)
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Predicting Protein Structure Comparative
Modeling (formerly, homology modeling)
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Structure prediction

• In an ideal world, we would be able to accurately
  predict protein structure from the sequence only!
• Because of the myriad possible configurations of
  a protein chain This goal cant reliably be
  achieved, yet.
• Knowledge based prediction vs. Simulation based
  on physical forces.
• Here we will only concern ourselves with
  knowledge-based methods, although we might use
  simulation in order to optimize our models.

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Can we predict protein structures ?

• ab initio folding simulation not yet ...
• Rosetta approach neither ...
• Fold recognition (threading)
• Often works, but ...
• ???

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Approaches to predicting protein structures
obtain sequence (target)
fold assignment
comparative modeling
ab initio modeling
build, assess model
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Homology Modelling of Proteins

• Definition
• Prediction of three dimensional structure of a
  target protein from the amino acid sequence
  (primary structure) of a homologous (template)
  protein for which an X-ray or NMR structure is
  available.
• Why a Model
• A Model is desirable when either X-ray
  crystallography or NMR spectroscopy cannot
  determine the structure of a protein in time or
  at all. The built model provides a wealth of
  information of how the protein functions with
  information at residue property level. This
  information can than be used for mutational
  studies or for drug design.

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Homology modeling
Comparative protein modeling Knowledge-based
modeling
Idea Extrapolation of the structure for a new
(target) sequence from the known 3D-structures of
related family members (templates).
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Homology models can be very smart!
Homology models have RMSDs less than 2Å more than
70 of the time.
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Sequence similarity implies structural similarity?
.
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Step 1 in Homology Modeling - Fold Identification
Aim To find a template or templates structures
from protein data base
pairwise sequence alignment - finds high homology
sequences BLAST http//www.ncbi.nlm.nih.gov/BLAST/
Improved Multiple sequence alignment methods
improves sensitivity - remote homologs PSIBLAST,
CLUSTAL
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Comparative Modeling

• Protein Data Bank PDB http//www.pdb.org
• Database of templates
• Separate into single chains
• Remove bad structures (models)
• Create BLAST database

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Model Building from template
Core conserved regions
Protein Fold
Variable Loop regions
Side chains
Calculate the framework from average of all
template structures
Multiple templates
Generate one model for each template and evaluate
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I. Manual Modeling
http//www.expasy.org/spdbv/
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II. Template based fragment assembly
a) Build conserved core framework

• averaging core template backbone atoms
  (weighted by local sequence similarity with the
  target sequence)
• Leave non-conserved regions (loops) for later .

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Dressing up the Core Model
Core Model-Rigid Body Assembly
Add loops
Add Side chains
End Game in protein folding - Molecular dynamics
of all atoms in explicit solvent
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II. Template based fragment assembly
b) Loop modeling

• use the spare part algorithm to find
  compatible fragments in a Loop-Database
• ab-initio rebuilding of loops (Monte Carlo,
  molecular dynamics, genetic algorithms, etc.)

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Loop Builders
Loops result from substitutions, insertions and
deletions in the same family
Mini protein folding problem- 3 to 10 residues
longer in membrane proteins
Some Homology modeling methods have less number
of loops to be added because of extensive
multiple sequence alignment of profiles
Ab Initio methods - generates various random
conformations of loops and score
Compare the loop sequence string to DB and get
hits and evaluate.
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Construction of loops might be done by
Using database of loops which appear in known
structures. The loops could be catagorised by
their length or sequence
Ab initio methods - without any prior knowledge.
This is done by empirical scoring functions that
check large number of conformations and evaluates
each of them.
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II. Template based fragment assembly
c) Side Chain placement

• Find the most probable side chain
  conformation, using
• homologues structures
• back-bone dependent rotamer libraries
• energetic and packing criteria

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II. Template based fragment assembly
d) Energy minimization

• modeling will produce unfavorable contacts and
  bonds
• ? idealization of local bond and angle geometry
• extensive energy minimization will move
  coordinates away
• ? keep it to a minimum
• SwissModel is using GROMOS 96 force field for a
  steepest descent

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II. Template based fragment assembly
d) Energy minimization
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Homology Modeling Programs

• Modeller (http//guitar.rockefeller.edu/modeller)
  
• Swiss-Model (http//www.expasy.ch/swissmod)
• Whatif (http//www.cmbi.kun.nl/whatif)

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Swiss-Model

• Method Knowledge-based approach.
• RequirementsAt least one known 3D-structure of
  a related protein. Good quality sequence
  alignements.
• ProceduresSuperposition of related
  3D-structures. Generation of a multiple a
  alignement.Generation of a framework for the new
  sequence. Rebuild lacking loops. Complete and
  correct backbone. Correct and rebuild side
  chains. Verify model structure quality and check
  packing. Refine structure by energy minimisation
  and molecular dynamics.

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Model Confidence Factors

• The Model B-factors are determined as follows
• The number of template structures used for model
  building.
• The deviation of the model from the template
  structures.
• The Distance trap value used for framework
  building.
• The Model B-factor is computed as
• 85.0 (1/ selected template str.)
  (Distance trap / 2.5)
• and
• 99.9 for all atoms added during loop and
  side-chain building

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Verifying the Model

• PROCHECK

• WHAT IF

• PROSA II

• VERIFY 3D, Profile3D

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Errors in Models !!!

• Incorrect template selection

• Incorrect alignments

• Errors in positioning of sidechains and loops

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General Structure Prediction Scheme
Any given protein sequence
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Baker and Sali (2000)
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Model Accuracy Evaluation
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Several web pages for homology modeling
COMPOSER felix.bioccam.ac.uksoft-base.html
MODELLER guitar.rockefeller.edu/modeller/modelle
r.html
WHAT IF www.sander.embl-heidelberg.de/whatif/
SWISS-MODEL www.expasy.ch/SWISS-MODEL.html