Protein Architecture

Exercises and Demonstrations

Aidan Budd


Quarternary Protein Structure

Domain-Domain interactions

Demonstration

Human haemoglobin 1DXT - domain-domain interactions between two beta and two alpha chains

Globular Domains and Linear Motifs

Side-chain specificity of a motif-binding groove in a globular domain

Demonstration

The FxDxF motif of Amphiphysin binding to the AP-2 Clathrin Adaptor Alpha-Appendage - the surface of a domain provides a very specific binding groove for the motif, in particular providing a close-fit for one of the phenyalanine side-chains

Different dynamics/flexibility of peptide compared to globular domain

Demonstration

Phosphothreonine peptide binding to the FHA1 domain of Rad53 solved using NMR, 20 different states provided in the PDB record. Quickly displaying the 20 states after one another provides an impression of the much greater mobility/dynamism of the peptide compared to the globular domain.

Conservation of strongly-constrained motif sidechains

Demonstration

MAD1 has been shown to interact with MAD2 via an MAD2-binding motif in MAD1. The 3D structure has been solved for this complex, and the motif shows strong conservation of the regular expression used to describe the binding peptide in the ELM resource, including humans, yeast, and slime mold.


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Copyright Aidan Budd, 2009 (c)