1. Structure Visualization
First & Last Name
June X, 2005
Structure Visualization
Boris Steipe
University of Toronto
3.4
(c) 2005 CGDN

2. Visualizations: abstractions to aid understanding
First & Last Name
June X, 2005
Visualizations: abstractions to aid understanding
Where are we with respect to our objectives ?
CPK
Line
Trace
Cartoon
3.4
(c) 2005 CGDN

3. Visualization of 3D relationships requires stereo vision
First & Last Name
June X, 2005
Visualization of 3D relationships requires 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
3.4
(c) 2005 CGDN

4. Global features of structure
First & Last Name
June X, 2005
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
3.4
(c) 2005 CGDN

5. Distances in protein structure
First & Last Name
June X, 2005
Distances in protein structure
Hydrogen bonds
Size
Bond-lengths
Where are we with respect to our objectives ?
Binding sites
Salt-bridges
Rasmol: set picking distance
3.4
(c) 2005 CGDN

6. Distances from coordinates
First & Last Name
June X, 2005
Distances from coordinates
XYZ coordinates are vectors in an orthogonal coordinate system, in Å.
All the rules of analytical geometry apply.
[...]
ATOM OH TYR
ATOM O ASP
Where are we with respect to our objectives ?
d = [( )2 + ( )2 + ( )2]0.5
= [(2.581)2 + (-0.013)2 + (-0.412)2]0.5
= [ ]0.5
= [ ]0.5
= Å = nm = m
3.4
(c) 2005 CGDN

7. Distances and angles: Ligand binding
First & Last Name
June X, 2005
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)
Where are we with respect to our objectives ? D H A
2.85±0.25 Å
(Hydrogen coordinates are usually inferred !)
3.4
(c) 2005 CGDN

8. Dihedral angles +f i+3 i i+2 i+1 Single bonds:
First & Last Name
June X, 2005
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
Where are we with respect to our objectives ? +f
i+1
Rasmol: set picking torsion
3.4
(c) 2005 CGDN

9. Backbone dihedral angles: Ramachandran plots
First & Last Name
June X, 2005
Backbone dihedral angles: Ramachandran plots   
Where are we with respect to our objectives ?
3.4
(c) 2005 CGDN

10. Sidechain rotamers 3 2 
First & Last Name
June X, 2005
Sidechain rotamers
100 randomly chosen Phe-residues superimposed. 3 2 
Where are we with respect to our objectives ?
Ponder & Richards (1987) J. Mol. Biol. 193,
3.4
(c) 2005 CGDN

11. First & Last Name
June X, 2005
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.
3.4
(c) 2005 CGDN

12. Molecular complementarity
First & Last Name
June X, 2005
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
Where are we with respect to our objectives ?
hydrophobic
positive charge
Phosphorylcholine in antibody binding site
(2MCP.PDB)
3.4
(c) 2005 CGDN

13. Mapping properties on surfaces
First & Last Name
June X, 2005
Mapping properties on surfaces
Properties of atoms (B-factors)
Ensemble properties of residues
(hydrophobicity, conservation)
Geometry (local curvature)
Fields and potentials
(isosurfaces, binding potential)
Where are we with respect to our objectives ?
AChE (1ACL.PDB) color coded by electrostatic potential with GRASP.
edu/grasp/
3.4
(c) 2005 CGDN

14. Visualization tools Rasmol Chime MolMol Cn3D others Molscript ....
First & Last Name
June X, 2005
Visualization tools
Rasmol
Chime
MolMol
Cn3D
others
Molscript
....
ORTEP
POVRay
Where are we with respect to our objectives ?
3.4
(c) 2005 CGDN

15. Tools RasMol Cn3D DeepView VMD First & Last Name June X, 2005 3.4
(c) 2005 CGDN

16. RasMol Work through the Rasmol tutorial !
First & Last Name
June X, 2005
RasMol
Small footprint, easy to install, sufficient functionality for most tasks, widely distributed, powerful commandline interface, scriptable.
Work through the Rasmol tutorial !
Rasmol download
Features
Stereo vision !
Where are we with respect to our objectives ? L R
1DRO.PDB, model 1
3.4
(c) 2005 CGDN

17. Cn3D Work through the Cn3D tutorial !
First & Last Name
June X, 2005
Cn3D
Good integration with NCBI databases, excellent functionality for domain and conservation analysis. Scriptable. No stereo :-(
Work through the Cn3D tutorial !
Where are we with respect to our objectives ?
3.4
(c) 2005 CGDN

18. DeepView (Swiss PDB Viewer)
First & Last Name
June X, 2005
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 !
Where are we with respect to our objectives ?
3.4
(c) 2005 CGDN

19. VMD (http://www.ks.uiuc.edu/Research/vmd/)
First & Last Name
June X, 2005
VMD (
Very powerful, well maintained, good graphics, intuitive use, scriptable and well integrated with NAMD.
Work through the VMD tutorial !
Where are we with respect to our objectives ?
3.4
(c) 2005 CGDN