Download Lecture 10 Protein Tertiary (3D) Structure

Introduction to Bioinformatics
for Medical Research
Gideon Greenspan
[email protected]
Lecture 10
Protein Tertiary (3D) Structure
Protein Tertiary Structure
• Defining Structure
• Determining experimentally
– PDB
• Predicting Structure
– TOPITS
– GenTHREADER
• Structural classification
– SCOP
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Defining Structure
Atomic symbol
1 N
2 CA
3 C
4 O
5 CB
6 CG
7 SD
8 CE
9 1H
10 2H
MET
MET
MET
MET
MET
MET
MET
MET
MET
MET
A
A
A
A
A
A
A
A
A
A
Hydrogen number
Remoteness
1
1
1
1
1
1
1
1
1
1
Residue number
-14.830
-14.608
-15.821
-15.713
-13.372
-13.531
-12.739
-13.839
-15.554
-13.942
Residue
-2.121
-1.535
-1.799
-2.464
-2.254
-3.764
-4.636
-6.072
-2.865
-2.531
Chain
10.034
8.679
7.781
6.770
8.135
8.330
6.956
6.937
9.976
10.386
3D co-ords
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X-ray Crystallography
• Create repetitive crystal of molecule
– Often difficult, especially hydrophobic portions
• X-rays generate diffraction pattern
– Pattern represents electron density
• Generate comparison patterns
– Add ions or change wavelength
• Obtain electron density map
– Fit protein sequence to map
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Nuclear Magnetic Resonance
• Dissolve molecules in water
– Allows free tumbling and vibration
• Detect activity of atoms with quantum spin
– 1Hydrogen (natural), 13Carbon, 15Nitrogen
• Defines set of atomic
distance constraints
– Ensemble of models
• Can detect motion
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PDB
• Database of molecular structures
– Obtained by crystallography or NMR
– Carefully curated and validated
• Founded in 1971
– 19375 proteins, 2117 other structures
• Additional protein information
– Secondary structure
– References, external links
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PDB: Summary Information
Molecule in PDB entry
Chains in molecule
Experimental
method
Link to SCOP
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PDB: 3D Structure
• Still images at fixed orientation
– Generate at any size
• Interactive molecule explorer
– Requires Java or Chime plug-in
• Download structure file
– Display in RasMol,
Swiss-PDBViewer, etc…
• Demonstration
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Predicting 3D Structure
• Outstanding difficult problem
• Based only on protein sequence
– Comparative modeling (homology)
– Ab-initio modeling
• Based on secondary structure
– Fold recognition
– Protein threading
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Comparative Modeling
• Similar sequence suggests similar structure
– Amino acid characteristics determine folding
• Similarity particularly high in core
– Alpha helices and beta sheets preserved
– But even near-identical sequences vary in loops
• Effectiveness depends on protein length
– Longer fi less sequence similarity required
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Ab Initio Modeling
• Compute molecular structure from laws of
physics and chemistry alone
– Ideal solution (theoretically)
• Simulate process of protein folding
– Apply minimum energy considerations
• Practically nearly impossible
– Exceptionally complex calculations
– Biophysics understanding incomplete
11
Protein Folds
• A combination of secondary structural units
– Forms basic level of classification
• Each protein family belongs to a fold
– Estimated 700–1500 different folds
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Fold Recognition / Threading
• Compare sequence against known structures
– Try to ‘thread’ sequence along chain
• Score suitability of the threading
– Can adjacent amino acids bond?
– Are amino acids close to or far from water?
– Are secondary structures similar?
• Examine list of most threadable structures
– Correct answer is often in top 10 or so
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Threading Example
Query
sequence
Gaps in
threading
Known
structure
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TOPITS Output (1)
Alignment
score
Length
of indels
Alignment
length
Number
of indels
% sequence
identity
Alignment
significance
Matched
sequence
Length of
sequence
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TOPITS Output (2)
Predicted
structure
Amino acid
matches
Query
sequence
Database
sequence
Buried /
Outside
Database known
secondary structure
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GenTHREADER Output
Prediction
confidence
Score from
neural network
Energy
measurements
Expected
errors
Sequence alignment
score and length
Length of
sequence
Structure
from PDB
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Prediction Flowchart
PSIBLAST
TOPITS,
GenTHREADER
PHDsec,
PSIpred
Ab initio
methods
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Structure Classification
• Class
– All alpha, all beta, alpha/beta, alpha+beta
• Fold
– Strong structural similarity
• Superfamily
– Probably common evolutionary origin
• Family
– Evolutionary relationship, sequence similarity
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SCOP
• Structural Classification of Proteins
– Based on known protein structures
– Manually created by visual inspection
• Hierarchical database structure
– Class, fold, superfamily, family
– Proteins/domains, species instances
• Founded in 1995
– 765 folds, 1232 superfamilies, 2164 families
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SCOP: Navigation
Node
name
Node
description
Path from
root to node
Children
of node
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Other Resources
• CATH (classification of protein domains)
– http://www.biochem.ucl.ac.uk/bsm/cath/
• SWISS-MODEL (comparative modeling)
– http://www.expasy.ch/swissmod/
• CASP (structure prediction competition)
– http://predictioncenter.llnl.gov/
• GTSP (guide to structure prediction)
– http://speedy.embl-heidelberg.de/gtsp/
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