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Project Progress

We continue to employ both experimental and computational approaches to investigate the evolutionary origins of functional macromolecules. We conducted the first laboratory evolution of a completely new non-biological enzyme that joins two fragments of RNA into a single strand (it acts as an RNA ligase). The enzyme was evolved from a partially randomized non-catalytic scaffold protein. NMR spectroscopy of the purified enzyme shows that most of the protein is well structured. The nature of amino acid substitutions during in vitro evolution indicates that the initial protein structure underwent at least local refolding. The results demonstrate that novel functions (and possibly different structures) can be obtained through a limited number of mutations in sequences of small proteins that might serve as models for ancestral macromolecules. Nature magazine has accepted the manuscript describing this work.

We continued to explore the evolutionary optimization of our previously evolved ATP-binding protein. NMR and X-ray crystallographic studies have revealed an unexpectedly strong role of surface residue interactions in stabilizing this small protein. The results help us to elucidate pathways by which primordial protein sequences attain increased degrees of functionality through the systematic accumulation of point mutations. (2 papers, one in PLoS ONE, and one in press in J. Mol. Biol.)

To explain how primordial proteins could have performed an essential cellular function of transporting ions across cell walls, which is carried out by some of the most complex protein assemblies of modern cells, we studied the antiamoebin channel using molecular dynamics computer simulations. This channel consists simply of 8 identical helices, each 16 amino acids in length. It achieves an efficiency that is comparable to that of a highly evolved voltage-gated potassium channel. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire mechanisms for precise regulation rather than to improve efficiency. Further, the observed dependence of amino acid sequence and function of membrane proteins on the nature of membrane-forming material suggests that channels and membranes might have co-evolved.

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