Evolution of protein structures

When protein sequences mutate, they may change structure and function, and natural selection acts on these changes.
We found that conservation of protein function implies very strong conservation of protein function, whereas changes of protein function are related with changes of the rate of evolution of protein structures, possibly due to the action of positive selection.
When the evolution of protein structures proceeds through gene duplication events followed by diversification according to a molecular clock, protein structures can be classified into a phylogenetic tree, protein folds can be objectively defined as equivalence classes of protein structures, and protein structural space is discrete. However, if recombination processes occur, protein structure space is continuous and protein structures cannot be objectively classified.

Publications on the evolution of protein structures:

Selected:

1. Pascual-García A, Arenas M, Bastolla U. The molecular clock in the evolution of protein structures. Mol Biol Evol, submitted (2017). [PDF]

2. A. Pascual-Garcia; D. Abia; R. Méndez; G.S. Nido and U. Bastolla Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation. Proteins. 2010 78:181-96 . [Pubmed]

3. Pascual-Garcia, A.; Abia, D.; Ortiz, A.R. and Bastolla, U. Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.
   PLoS Comput Biol, 5, e1000331. [Pubmed] [PDF]

4. Leo-Macias, A.; Lopez-Romero, P.; Lupyan, D.; Zerbino, D. ; Ortiz, A.R. An analysis of core deformations in protein superfamilies. Biophys J (2005) 88, 1291-9. [Pubmed] [PDF]