1.3 From 3D Motifs to Multimeric Proteins

It is useful to describe protein structure in a hierarchical fashion. Proteins can be thought of as being built up from:

• Motifs:arrangements of two or three consecutive secondary structure elements

examples:

• alpha-hairpin: 2 antiparallel alpha-helices joined by a 'hairpin' bend changing the chain direction by 180°),
• beta-alpha-beta unit: 2 parallel strands, separated by an alpha-helix antiparallel to them, with 2 hairpins separating the three secondary structures; hydrohpobic residues of the alpha-helix pack against the beta-strands
• Folds: combinations of the supersecondary structural motif

examples:

• four-helix bundle: 2 alpha-hairpin units connected by a loop
• beta-alpha-beta-alpha-beta unit- alias the Rossman fold
• Domains: compact, local semi-independent folding units
• Multiple domains
• Multiple subunits:each subunit is a separate polypeptide chain
• Multi-protein complexes: multi-enzyme complexes, viruses

The bewildering complexity of known protein structures is now also accessible for the non-specialist through organized WWW collections, as will be discussed in section 3.2

2. Experimental 3D Protein Structures