Postdoctoral Research in Tawfik Lab
Graduate Research in Blaber Lab
Prebiotic Protein Design
In 1953, Stanley Miller and Harold Urey demonstrated that putative early Earth conditions were capable of synthesizing α-carboxy, α-amino acids, critical bio-organic compounds, from inorganic precursors. The Miller-Urey experiment was the first step towards understanding the chemical origin of life, and these results have since been enriched by active research into interstellar chemistry, analysis of carbonaceous chondrites (such as the Murchison meteorite), and deep vent chemistry. In a recent review of the literature, Dr. Michael Blaber and I identify a subset of canonical amino acids that are generated by abiotic physical processes and were likely present at the origin of life: “the prebiotic set.”
The prebiotic set includes only 10 of the 20 canonical amino acids, and does not include either aromatic amino acids or basic amino acids. As such, it is unclear whether the prebiotic set of amino acids comprise a “foldable set.” To address this question, we recently published a paper in which we enriched a de novo designed synthetic β-trefoil protein (“Symfoil”) for the prebiotic amino acid alphabet. This enrichment approached 80% prebiotic composition and the resulting protein (“Primitive Version 2”) was fully foldable, but only within a high-salt (i.e., halophile) environment. Thus, our results suggest that proteogenesis (the origin of proteins) was a potentially early abiogenicevent, and likely occurred within a high-salt environment (e.g., evaporative pond). Both of these conclusions are counter to the existing paradigms of a hydrothermal vent origin of life, and the popular RNA world hypothesis.
Symmetric Protein Folding, Evolution, and Design
Nearly one-third of protein architectures possess significant tertiary structure symmetry (i.e., β-trefoil, β-propeller, TIM barrel), a feature that is presumed to be the result of duplication and fusion events early in the evolution of symmetric protein folds. A principle prediction of the gene duplication and fusion model, however, is that a protein with “pure symmetry” (that is, simultaneous 1° and 3° structure symmetry) is generated immediately after the duplication/fusion/truncation event.
Notably, several workers in the field of protein design have argued that primary sequence symmetry is problematic to foldability and will result in a protein that is prone to aggregation. To resolve this apparent contradiction, we show that purely symmetric 1° structure enables utilization of alternative definitions of the critical folding nucleus in response to gross structural rearrangement. Thus, major replication errors producing 1° structure symmetry can conserve foldability. Our results provide an explanation for the prevalence of symmetric protein folds, and highlight a critical role for 1° structure symmetry in protein evolution.
Foldability Function Trade-off in FGF-1
A “stability/function tradeoff” hypothesis in proteins has been supported by a number of studies over more than a decade; however, a “foldability/function tradeoff” hypothesis is a more recent development with little direct experimental support. To this end, I have performed a Φ-value analysis of fibroblast growth factor-1 (FGF-1) to identify turn regions essential to formation of the critical folding transition state. Although the overall fold of FGF-1 is symmetric (the β-trefoil fold) the distribution of regions forming the folding transition state are highly-asymmetric. Furthermore, regions critical for foldability are segregated from regions known to be responsible for the various functionalities of FGF-1 (e.g., heparin-binding, receptor-binding, and nuclear localization). These results provide unambiguous experimental support for the “foldability/function tradeoff” hypothesis. Importantly, the results identify that only a fraction of the structure is essential for formation of the important folding transition state, and that functional residues are a form of deviation from ideal symmetry within the overall fold.