ENIGMA: Evolution of Nanomachines In Geospheres and Microbial Ancestors. This NAI team will explore catalysis of electron transfer reactions by prebiotic peptides to microbial ancestral enzymes to modern nanomachines, integrated over four and a half billion years of Earth’s changing geosphere. Theme 1 focuses on the synthesis and function of the earliest peptides capable of moving electrons on Earth and other planetary bodies. Theme 2 focuses on the evolutionary history of “motifs” in extant protein structures. Theme 3 focuses on how proteins and the geosphere co-evolved through geologic time.
Life on Earth is electric. The electronic circuitry is catalyzed by a small subset of proteins that function as sophisticated nanomachines. Currently, very little is known about the origin of these proteins on Earth or their evolution in early microbial life. To fill this knowledge gap, the ENIGMA research team proposes to conduct integrated and coordinated experimental, bioinformatic, and data-driven studies to explore the origin of catalysis, the evolution of protein structures in microbial ancestors, and the co-evolution of proteins and the geosphere. ENIGMA has three integrated research themes focused on understanding the evolution of proteins involved in electron transfer and energy generation:
Synthesis of Nanomachines in the Origin of Life
Theme 1 seeks to understand how complex extant nanomachines that catalyze electron transfer emerged from simple prebiotic chemical processes. Two possible biochemical origins scenarios will be explored: on the early Earth at the beginning of the Archean eon, and on other planets where different amino acid alphabets and chemical constraints might likely be present. Central to both scenarios is the hypothesis that the first functional molecules were small low-complexity metal-binding peptides that were capable of primitive electron transfer and catalysis, and that these functional peptides subsequently evolved into larger proteins. Since no direct physical fossils of these earliest peptides exist, we will instead turn to databases containing thousands of high resolution extant protein structures and powerful computer simulation tools for engineering small peptides from basic physical principles. This will essentially re-invent plausible candidates for early-life peptides.
In Theme 1, terrestrial peptides will be constructed from the twenty natural amino acids, whereas extraterrestrial peptides will incorporate a much broader alphabet, informed by amino acid distributions found in meteorites and prebiotic chemical simulations such as the classic Urey-Miller experiments. Early peptides are proposed to have assembled into circuits capable of conducting electricity where electron transfer occurred primarily through the metals coordinated by peptides. Thus, it would be critical for peptides to preserve structure and metal binding as these sites assume transient oxidized or reduced excited states. In order to assess their functional potential, candidate molecules will be synthesized and tested for metal binding using a number of spectroscopic, scattering and microscopy methods. High resolution structures will be determined by X-ray diffraction and solution NMR methods to ascertain how similar early peptides are to subsets of extant oxidreductases. A series of functional assays that range from electron transfer and catalysis to the ability to act as metabolic surrogates will be used to evaluate the functional capacity of these small peptides. The resulting peptide designs will be used to root protein evolutionary trees and to inform powerful machine learning tools that will link information gathered on early peptides, extant proteins and Earth’s geochemical cycles across all three Themes.
The proposed team is dedicated to understanding how nature formed catalysts that serve as the pervasive nanomachines of life on Earth, and how analogous processes may have evolved on other planetary bodies within or beyond our solar system. The results of our research will advance our knowledge of how biochemistry emerged from geochemistry—specifically, the enzymatic functions of metal-bearing proteins emerged approximately 4 billion years ago from a geochemical and mineralogical milieu that in some respects mimicked the emergent biochemistry. This concept is of significance to the astrobiology context of all NASA missions, as we attempt to characterize critical features of near-surface environments in which life might emerge. Ultimately, our goal is for the proposed effort to inform future NASA missions about detection of life on planetary bodies in habitable zones. Our effort provides a unique window to potential planetary-scale chemical characteristics that might arise from abiotic chemistry, which must be understood if we are to recognize unique biosignatures on other worlds.