Limits...
3D complex: a structural classification of protein complexes.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA - PLoS Comput. Biol. (2006)

Bottom Line: We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones.This is because most complexes contain four subunits or less, and the large majority are homomeric.In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. elevy@mrc-lmb.cam.ac.uk

ABSTRACT
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Show MeSH
Distribution of Protein Complex Size in the HierarchyHistogram of the number of subunits per protein complex. Smaller complexes are more abundant than larger complexes, and complexes with even numbers of subunits tend to be more abundant than complexes with odd numbers of subunits, at both levels of the hierarchy.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1636673&req=5

pcbi-0020155-g004: Distribution of Protein Complex Size in the HierarchyHistogram of the number of subunits per protein complex. Smaller complexes are more abundant than larger complexes, and complexes with even numbers of subunits tend to be more abundant than complexes with odd numbers of subunits, at both levels of the hierarchy.

Mentions: The first, as shown in Figure 4, is that most complexes contain a small number of chains and can therefore adopt a very restricted number of topologies. In the PDB set, we observe a sharp decrease in the proportion of complexes as the number of their chains increases, so that 94% of the structures contain four chains or less and are found in ten QSTs only.


3D complex: a structural classification of protein complexes.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA - PLoS Comput. Biol. (2006)

Distribution of Protein Complex Size in the HierarchyHistogram of the number of subunits per protein complex. Smaller complexes are more abundant than larger complexes, and complexes with even numbers of subunits tend to be more abundant than complexes with odd numbers of subunits, at both levels of the hierarchy.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636673&req=5

pcbi-0020155-g004: Distribution of Protein Complex Size in the HierarchyHistogram of the number of subunits per protein complex. Smaller complexes are more abundant than larger complexes, and complexes with even numbers of subunits tend to be more abundant than complexes with odd numbers of subunits, at both levels of the hierarchy.
Mentions: The first, as shown in Figure 4, is that most complexes contain a small number of chains and can therefore adopt a very restricted number of topologies. In the PDB set, we observe a sharp decrease in the proportion of complexes as the number of their chains increases, so that 94% of the structures contain four chains or less and are found in ten QSTs only.

Bottom Line: We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones.This is because most complexes contain four subunits or less, and the large majority are homomeric.In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. elevy@mrc-lmb.cam.ac.uk

ABSTRACT
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Show MeSH