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| Title: | Midnight zone of protein structure evolution OR: Protein structures evolve at random - almost |
| Author: | Burkhard Rost, Sean I. O'Donoghue , and Chris Sander |
| Quote: | Preprint |
Today, we have a detailed and ever-widening knowledge of the evolution of DNA sequences, but what do we really know about the evolution of protein structure? Until recently, the answer was: not much. The first detailed structures were determined 26 years ago; 13 years ago, the database of atomic-resolution protein structures contained just 312 structures (PDB). Since then, due to advances in determination methods, the PDB has grown exponentially; presently it holds over 4000 entries. With this size, we can just begin to analyse the evolution of protein structure. Here, we report an analysis of all pairs of proteins in the PDB which have similar three-dimensional (3D) structures. For each pair, we aligned the 3D structures, and measured the sequence identity (pairwise identical residues) in the aligned regions. The resulting distribution of pair identity scores shows one prominent and unexpected feature: most pairs cluster in an approximately Gaussian peak centred at 8-9% sequence identity. The distribution is surprisingly similar to that expected for `random' pairs of completely unrelated sequences. This result has implications for our understanding of protein folding, and of the effect of convergent (different ancestor) and divergent (same ancestor) evolution on protein structure.
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