URBANA Researchers in the Evolutionary Bioinformatics Laboratory at the University of Illinois in collaboration with German scientists have been using bioinformatics techniques to probe the world of proteins for answers to questions about the origins of life.
Proteins are formed from chains of amino acids and fold into three-dimensional structures that determine their function. According to crop sciences professor Gustavo Caetano-Anolls, very little is known about the evolutionary drivers for this folding.
In collaboration with scientists at the Heidelberg Institute for Theoretical Studies, he has been working at the interface of molecular evolution and molecular dynamics, looking back to when proteins first appeared approximately 3.8 billion years ago to determine changes in folding speed over time.
To do this, they looked at all known protein structures as defined in the Structural Classification of Proteins (SCOP) database and mined their presence in 989 fully sequenced genomes. In a previous study, researchers in Caetano-Anolls's group used SCOP and genomic information to reconstruct phylogenomic trees that describe the history of the protein world. The current research is based on these types of trees.
"They are not the standard trees that people see in phylogenetic analysis," he said. "In phylogenetic analysis, usually the tips of the trees, the leaves, are organisms or microbes. In these, they are entire biological systems."
In contrast, the leaves of these new trees are protein domains, which are compact evolutionary units of structure and function. Proteins are usually complex combinations of several domains.
"We have a world of about 90,000 of these structures, but they seem to be always producing the same designs," he said. Over the last 10 years, he has been part of the effort to map these designs, or folds, because they are determined by the way the protein chains fold on themselves. To date
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University of Illinois College of Agricultural, Consumer and Environmental Sciences