@article{buck_atchley_2005, title={Networks of coevolving sites in structural and functional domains of serpin proteins}, volume={22}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msi157}, abstractNote={Amino acids do not occur randomly in proteins; rather, their occurrence at any given site is strongly influenced by the amino acid composition at other sites, the structural and functional aspects of the region of the protein in which they occur, and the evolutionary history of the protein. The goal of our research study is to identify networks of coevolving sites within the serpin proteins (serine protease inhibitors) and classify them as being caused by structural-functional constraints or by evolutionary history. To address this, a matrix of pairwise normalized mutual information (NMI) values was computed among amino acid sites for the serpin proteins. The NMI matrix was partitioned into orthogonal patterns of amino acid variability by factor analysis. Each common factor pattern was interpreted as having phylogenetic and/or structural-functional explanations. In addition, we used a bootstrap factor analysis technique to limit the effects of phylogenetic history on our factor patterns. Our results show an extensive network of correlations among amino acid sites in key functional regions (reactive center loop, shutter, and breach). Additionally, we have discovered long-range coevolution for packed amino acids within the serpin protein core. Lastly, we have discovered a group of serpin sites which coevolve in the hydrophobic core region (s5B and s4B) and appear to represent sites important for formation of the "native" instead of the "latent" serpin structure. This research provides a better understanding on how protein structure evolves; in particular, it elucidates the selective forces creating coevolution among protein sites.}, number={7}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Buck, MJ and Atchley, WR}, year={2005}, month={Jul}, pages={1627–1634} }
 @article{buck_atchley_2003, title={Phylogenetic analysis of plant basic helix-loop-helix proteins}, volume={56}, DOI={10.1007/s00239-002-2449-3}, abstractNote={The basic helix-loop-helix (bHLH) family of proteins is a group of functionally diverse transcription factors found in both plants and animals. These proteins evolved early in eukaryotic cells before the split of animals and plants, but appear to function in 'plant-specific' or 'animal-specific' processes. In animals bHLH proteins are involved in regulation of a wide variety of essential developmental processes. On the contrary, bHLH proteins have not been extensively studied in plants. Those that have been characterized function in anthocyanin biosynthesis, phytochrome signaling, globulin expression, fruit dehiscence, carpel and epidermal development. We have identified 118 different bHLH genes in the completely sequenced Arabidopsis thaliana genome and 131 bHLH genes in the rice genome. Here we report a phylogenetic analysis of these genes, including 46 genes from other plant species and a classification of these proteins into 15 distinct plant clades. Results imply a polyphyletic origin for the plant bHLH proteins related only by their bHLH DNA binding motif. We suggest that plant bHLH proteins are under weaker selective constraints than their animal counterparts and that lineage specific expansions and subfunctionalization have fashioned regulatory proteins for plant specific functions.}, number={6}, journal={Journal of Molecular Evolution}, author={Buck, M. J. and Atchley, W. R.}, year={2003}, pages={742–750} }
 @article{buck_squire_andrews_2002, title={Coordinate expression of the PDK4 gene: a means of regulating fuel selection in a hibernating mammal}, volume={8}, ISSN={["1094-8341"]}, DOI={10.1152/physiolgenomics.00076.2001}, abstractNote={Hibernation in mammals requires a metabolic shift away from the oxidation of carbohydrates and toward the combustion of stored fatty acids as the primary source of energy during torpor. A key element involved in this fuel selection is pyruvate dehydrogenase kinase isoenzyme 4 (PDK4). PDK4 inhibits pyruvate dehydrogenase and thus minimizes carbohydrate oxidation by preventing the flow of glycolytic products into the tricarboxylic acid cycle. This paper examines expression of the PDK4 gene during hibernation in heart, skeletal muscle, and white adipose tissue (WAT) of the 13-lined ground squirrel, Spermophilus tridecemlineatus. During hibernation PDK4 mRNA levels increase 5-fold in skeletal muscle and 15-fold in WAT compared with summer-active levels. Similarly, PDK4 protein is increased threefold in heart, fivefold in skeletal muscle, and eightfold in WAT. High levels of serum insulin, likely to have an inhibitory effect on PDK4 gene expression, are seen during fall when PDK4 mRNA levels are low. Coordinate upregulation of PDK4 in three distinct tissues suggests a common signal that regulates PDK4 expression and fuel selection during hibernation.}, number={1}, journal={PHYSIOLOGICAL GENOMICS}, author={Buck, MJ and Squire, TL and Andrews, MT}, year={2002}, month={Feb}, pages={5–13} }