title: Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins.
abstract: Recreating ancestral proteins in the laboratory increasingly is being used to study the evolutionary history of protein function. More efficient gene synthesis techniques and the decreasing costs of commercial oligosynthesis are making this approach both simpler and less expensive to perform. Developments in ancestral reconstruction methods, particularly more realistic likelihood models of molecular evolution, allow for the accurate reconstruction of more ancient proteins than previously possible. This chapter reviews phylogenetic methods of ancestral inference, strategies for investigating alternative reconstructions, gene synthesis, and design, and an application of these methods to the reconstruction of an ancestor in the green fluorescent protein family.
authors.affiliation: Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.
authors.forename: Belinda S W
authors.initials: BS
authors.lastname: Chang
authors.forename: Juan A
authors.initials: JA
authors.lastname: Ugalde
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Matz
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D037421:Anthozoa / Q000235:genetics; D003116:Color; D019143:Evolution, Molecular; D049452:Green Fluorescent Proteins / Q000138:chemical synthesis / Q000235:genetics* / Q000502:physiology; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid
chemical_list: D049452:Green Fluorescent Proteins