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Project Progress

As previously reported, we have used messenger ribonucleic acid (mRNA)-display to select four new adenosine triphosphate (ATP)-binding proteins from a population of >10¹² random polypeptides. Proteins from one family have been characterized – they are highly selective, and do not bind either guanosine triphosphate (GTP) or deoxyadenosine triphosphate (dATP). They do not contain any known ATP-binding motifs, but require zinc ions and contain conserved cysteine residues, suggesting a possible structural similarity to zinc finger proteins. In order to test this possibility, and more generally to determine if these de novo evolved proteins resemble biological protein, we have evolved mutants that are suitable for biophysical studies by continued selection for ATP binding in the presence of guanidine. Guanidine is a denaturant of protein structure and its presence in solution favors selection of proteins with stable folded states. As expected, more of the newly selected proteins stay soluble in the presence of ATP, presumably because ATP binding stabilizes the folded state of the protein. We have established that some proteins remain stable as monomers. We have optimized a rapid, efficient purification scheme that allows for generating a sufficient amount of proteins for biophysical characterization.

We also initiated efforts to use in vitro selection to evolve novel enzymes. Our initial efforts have concentrated on enzymes that catalyze Diels-Alder reactions. The initial library of random-sequence proteins has been created and selection is in progress.

To simulate self-organization of protobiological proteins into metabolic networks capable of evolution towards increasing complexity, we develop a computational approach for describing systems with many species and reaction channels. This approach is based on Next Reaction Method, an exact and efficient approach to simulating coupled chemical reactions. The method is not limited to chemical reactions and allows for incorporation of other cellular processes such as channel-mediated transport and cell growth and division.