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Structure Visualization
Boris Steipe
University of Toronto
[email protected]
3.4
1
Visualizations: abstractions to aid understanding
CPK
3.4
Line
Trace
Cartoon
2
Visualization of 3D relationships
requires stereo vision
1CDL.PDB
• Practice regularily
• Increase image size
• Increase viewing distance
• Increase complexity
3.4
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
3
Global features of structure
quarternary
structure
global fold 
machine metaphore,
mimicry
interfaces
surprising
structural similarity 
homology
unusual surface and
core residues
location of SNPs or
sites and context of
mutations, PTM sites
3.4
residues
that
participate
in ligand
binding
conformational changes 
molecular mechanisms
shape 
clefts, pockets,
protrusions
4
Distances in protein structure
Size
Hydrogen bonds
Bond-lengths
Binding sites
Rasmol: set
3.4
picking distance
Salt-bridges
5
Distances from coordinates
XYZ coordinates are vectors in an orthogonal coordinate system, in Å.
All the rules of analytical geometry apply.
[...]
ATOM
[...]
ATOM
[...]
d =
=
=
=
=
3.4
687
OH
TYR
86
7.415
62.584
32.900
1.00
3.37
651
O
ASP
82
9.996
62.571
32.488
1.00
5.18
[(9.996-7.415)2 + (62.571-62.584)2 + (32.488-32.900)2]0.5
[(2.581)2 + (-0.013)2 + (-0.412)2]0.5
[6.661561 + 0.0000169 + 0.169744]0.5
[6.831474]0.5
2.614 Å = 0.2614 nm = 2.614 . 10-10 m
6
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 Hbond "valences" are usually satisfied and geometries
cluster closely around consensus distances and angles.
±30°
Chelation: Calcium bound
in Calmodulin
(1CLL.PDB)
D
±70°
H
A
2.85±0.25 Å
(Hydrogen coordinates are usually inferred !)
3.4
7
Dihedral angles
i+3
Single bonds:
Freely rotable, but constrained by
steric overlap.
i
Double bonds:
Constrained to planar geometry.
Large energetic barrier to
isomerization.
i+2
i+1
+f
Rasmol: set
3.4
picking torsion
8
Backbone dihedral angles:
Ramachandran plots

f

3.4
9
Sidechain rotamers
3
2

100 randomly chosen
Phe-residues
superimposed.
Ponder & Richards (1987) J. Mol. Biol. 193, 775-791
http://www.fccc.edu/research/labs/dunbrack/sidechain.html
3.4
10
B-factors
B-factors are isotropic temperature
factors, i.e. they model the relationship between observed and theoretical 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 thermally distributed, they can correspond to discrete disorder, dynamic
mobility and will be influenced by
experimental error of measurement
and refinement problems.
3.4
2IMM.PDB: Rasmol, CPK, color by
temperature, slab mode.
11
Molecular complementarity
Tyr H33
Arg H52
Tyr L100
Tight and specific binding implies
that all features of the ligand will be
recognized by the protein.
Trp H107
negative
charge
hydrophilic
Asp L97
hydrophobic
Phosphorylcholine in
antibody binding site
(2MCP.PDB)
3.4
positive
charge
12
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.columbia. edu/grasp/
3.4
13
Visualization tools
ORTEP
3.4
Rasmol
Chime
MolMol
Cn3D
others
Molscript
....
POVRay
14
Tools
•
•
•
•
3.4
RasMol
Cn3D
DeepView
VMD
15
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/bioinformatics
• Rasmol download
• Features
• Stereo vision !
L
R
1DRO.PDB, model 1
3.4
16
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
3.4
17
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/
3.4
18
VMD
(http://www.ks.uiuc.edu/Research/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/tutorial/html/vmd-tutorial.html
3.4
19