In protein structures, helices and strands
may be connected and combined in many ways to form a domain. However, from known protein three-dimensional structures, we have learned that there is only a limited number of ways by which secondary structure elements are combined in proteins. These different ways are called folds (or Topology according to CATH database classification). Therefore, we will examine typical examples of connectivity and packing secondary structure elements within 3D structures. This type of analysis simplifies the comparison of protein structures and reveals similarities and differences, opening the way for structure classification.
Defining a domain
A domain may be characterized by the following:
1- Spatially separated unit of the protein structure
2- Often has sequence and/or structural resemblance to other protein structures or domains.
3- Often has a specific function associated with it.
Some proteins (examples include triose phosphate isomerase
, and hemoglobin
) contain one single domain. However, a large number of proteins are multidomain proteins that may contain two or more domains. Here, we start by analyzing single domains, normally found within multidomain proteins. The helix bundle domain
One of the common domains is the helix bundle domain
(the images below show two different bundles). Helix bundles are often found as separate domains within larger, multidomain proteins. On the left image is the crystal structure of a De Novo
designed protein (PDB 1MFT). In this case, the helices within the bundle are connected by short loops and packed to form a hydrophobic core in the middle of the bundle. On the right is a solution structure of the headpiece domain of chicken villin
(PDB 1QQV). Here the arrangement of the helices is very different, and the loops are much longer. Clicking the images will take you to the RCSB PDB 3D-viewer, where you can rotate the structures to get a better impression of how they are built: