title: Predicting functional divergence in protein evolution by site-specific rate shifts.
abstract: Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.
authors.affiliation: NASA Astrobiology Institute, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Gaucher
authors.forename: Xun
authors.initials: X
authors.lastname: Gu
authors.forename: Michael M
authors.initials: MM
authors.lastname: Miyamoto
authors.forename: Steven A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed / Q000235:genetics*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins