Lecture 09

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Structure Analysis

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Lecture Slides

Slide 001

Lecture 09, Slide 001

Slide 002

Lecture 09, Slide 002

Slide 003

Lecture 09, Slide 003

Slide 004

Lecture 09, Slide 004

Slide 005

Lecture 09, Slide 005
Rotamers are low-energy conformations of side-chain dihedral angles. Only a small number of rotamer states and combinations are significantly populated in natural proteins. This tremendously simplifies protein structure modelling and prediction problems. However it also guides analysis, e.g. in enzyme active sites the rotamers often exist in strained, rare conformations.

Slide 006

Lecture 09, Slide 006
Surfaces represent the parts of a protein that interact with the surroundings. In this example, the electrostatic potential mapping shows how an electrostatic potential gradient attracts the substrate molecule into Acetylcholine-esterase's active site.

Slide 007

Lecture 09, Slide 007
The "Accessible Surface" depends on the probe radius. For solvent accessible surfaces a probe radius of 1.4A is commonly used since this approximates the radius of a water-molecule.

Slide 008

Lecture 09, Slide 008
Motifs represent (presumably) low-energy patterns of conformations. They can be discovered in structure datasets by looking for patterns that recur more frequently than expected by random chance. In almost all cases, they have significant statistical propensities to favour particular amino acids in particular positions.