Structure Visualization

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Structure Visualization

• Boris Steipe
• University of Toronto
• boris.steipe_at_utoronto.ca

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Visualizations abstractions to aid understanding

• Line

CPK
Trace
Cartoon
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Visualization of 3D relationshipsrequires stereo
vision
1CDL.PDB

• Practice regularily
• Increase image size
• Increase viewing distance
• Increase complexity

set stereo -5 select protein color chain select
.ca and hetero color 0,180,255 select within
(3.0, (.ca and hetero)) and .O color red
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Global features of structure
quarternary structure
global fold ? machine metaphore, mimicry
residues that participate in ligand binding
interfaces
surprising structural similarity ? homology
unusual surface and core residues
location of SNPs or sites and context of
mutations, PTM sites
shape ? clefts, pockets, protrusions
conformational changes ? molecular mechanisms
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Distances in protein structure
Hydrogen bonds
Size
Bond-lengths
Binding sites
Salt-bridges
Rasmol set picking distance
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Distances from coordinates
XYZ coordinates are vectors in an orthogonal
coordinate system, in Å.
All the rules of analytical geometry apply.
... ATOM 687 OH TYR 86 7.415
62.584 32.900 1.00 3.37 ... ATOM 651 O
ASP 82 9.996 62.571 32.488 1.00
5.18 ...
d (9.996-7.415)2 (62.571-62.584)2
(32.488-32.900)20.5 (2.581)2 (-0.013)2
(-0.412)20.5 6.661561 0.0000169
0.1697440.5 6.8314740.5 2.614 Å
0.2614 nm 2.614 . 10-10 m
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Distances and angles Ligand binding
H-bonds have specific geometric requirements with
respect to distance and angles. They confer
conformational specificity to proteins. More than
90 of H-bond "valences" are usually satisfied
and geometries cluster closely around consensus
distances and angles.
30
70
Chelation Calcium bound in Calmodulin (1CLL.PDB)
A
H
D
2.850.25 Å
(Hydrogen coordinates are usually inferred !)
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Dihedral angles
i3
Single bonds Freely rotable, but constrained
by steric overlap.
i
Double bonds Constrained to planar geometry.
Large energetic barrier to isomerization.
i2
f
i1
Rasmol set picking torsion
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Backbone dihedral angles Ramachandran plots
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Sidechain rotamers
100 randomly chosen Phe-residues superimposed.
?3
?2
??
Ponder Richards (1987) J. Mol. Biol. 193,
775-791
http//www.fccc.edu/research/labs/dunbrack/sidecha
in.html
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B-factors
B-factors are isotropic temperature factors, i.e.
they model the relation-ship between observed and
theoreti-cal electron density of an atom at rest
by applying a spherically symmetrical thermal
distribution to the density until it best matches
the experiment. "Real" devitions from ideality
are neither isotropic nor ther-mally distributed,
they can corres-pond to discrete disorder,
dynamic mobility and will be influenced by
experimental error of measurement and refinement
problems.
2IMM.PDB Rasmol, CPK, color by temperature, slab
mode.
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Molecular complementarity
Tight and specific binding implies that all
features of the ligand will be recognized by the
protein.
Arg H52
Tyr L100
Tyr H33
Trp H107
negative charge
distance
hydrophilic
Asp L97
hydrophobic
positive charge
Phosphorylcholine in antibody binding
site (2MCP.PDB)
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Mapping properties on surfaces

• Properties of atoms (B-factors)
• Ensemble properties of residues
• (hydrophobicity, conservation)
• Geometry (local curvature)
• Fields and potentials
• (isosurfaces, binding potential)

AChE (1ACL.PDB) color coded by electrostatic
potential with GRASP. http//trantor.bioc.columbi
a. edu/grasp/
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Visualization tools
Rasmol Chime MolMol Cn3D others
Molscript ....
ORTEP
POVRay
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Tools

• RasMol
• Cn3D
• DeepView
• VMD

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RasMol
Small footprint, easy to install, sufficient
functionality for most tasks, widely distributed,
powerful commandline interface, scriptable.
Work through the Rasmol tutorial !
http//biochemistry.utoronto.ca/steipe/bioinformat
ics

• Rasmol download
• Features
• Stereo vision !

L
R
1DRO.PDB, model 1
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Cn3D
Good integration with NCBI databases, excellent
functionality for domain and conservation
analysis. Scriptable. No stereo -(
Work through the Cn3D tutorial !
http//ncbi.nih.gov/Structure/CN3D/cn3dtut.shtml
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DeepView (Swiss PDB Viewer)
Excellent tool for homology modeling, structure
manipulation, structure alignment and analysis of
sequence alignments. Calculates surfaces and
electrostatics. Creates PovRay scenes. Good
integration with SwissModel.
Work through either DeepView tutorial !
http//ca.expasy.org/spdbv/text/tutorial.htm http
//www.usm.maine.edu/rhodes/SPVTut/
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VMD (http//www.ks.uiuc.edu/Researc
h/vmd/)
Very powerful, well maintained, good graphics,
intuitive use, scriptable and well integrated
with NAMD.
Work through the VMD tutorial !
http//www.ks.uiuc.edu/Research/vmd/vmd-1.8.2/tuto
rial/html/vmd-tutorial.html