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The complex interplay between sequence, folded structure, and function in a divergently evolving protein family can be reflected in the rate at which individual sites accumulate amino acid replacements. Thus, detecting shifts in the evolutionary rates of individual sites offers a way to identify potential instances of functional divergence among proteins (Benner 1989; Naylor and Gerstein 2000; Gaucher, Miyamoto, and Benner 2001; Marin et al. 2001; Wang and Gu 2001). The covarion model of Fitch and Markowitz (1970) was among the first to consider protein structure and function in this way. The ability to detect rate-shift sites relies on molecular evolutionary approaches (Gu 1999, 2001; Benner and Gaucher 2001; Galtier 2001; Landgraf, Xenarios, and Eisenberg 2001), whereas functional explanations for these changes can be derived from experiments in structural biology (Golding and Dean 1998). This combination defines a powerful approach for studies within the field of functional genomics in general. Gaucher, Miyamoto, and Benner (2001) illustrated how such a combined approach can provide experimentally testable hypotheses that relate individual amino acids to specific functional differences among proteins. They analyzed elongation factor (EF) sequences and identified those sites with shifting rates between the EFTu and eEF1A orthologs from bacteria and eukaryotes, respectively. Their comparisons relied on maximum likelihood (ML) methods to estimate the evolutionary rates of sites in one group, then in the other. Those sites with the greatest rate changes between EF-Tu and eEF1A were identified from a frequency histogram of their individual differences. EF-Tu and eEF1A (formerly known as EF-1a) are essential for translation in bacteria and eukaryotes (Krab and Parmeggiani 1998; Negrutskii and El’skaya 1998). Despite their similar overall roles in translation and very slow rates of evolution, these two orthologous proteins differ in several of their more specific functions. For example, bacterial EF-Tu binds GDP ;100-fold tighter than GTP, in contrast to the near-identical affinities of eEF1A for both. EF-Tu regenerates its active form via the single-subunit nucleotide exchange factor EF-Ts. In contrast, eEF1A is regenerated by the multisubunit nucleotide exchange factor eEF1B (formally known as EF1bgd). eEF1B is composed of the subunits a, b, and g,

The Crystal Structure of eEF1A Refines the Functional Predictions of an Evolutionary Analysis of Rate Changes Among Elongation Factors