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Authors: Wang, Michael Sheng-Hui
Advisors: Hecht, Michael
Contributors: Chemistry Department
Keywords: ATPase
de novo protein
novel enzyme
Subjects: Biochemistry
Issue Date: 2022
Publisher: Princeton, NJ : Princeton University
Abstract: Despite being stunningly diverse, all life on Earth arose from common ancestry. There-fore, although plants and animals (or elephants and amoebae) appear very different, all forms of terrestrial life share a remarkable conservation of genes, proteins, and biochemical reac-tions. The traits we share are similar because in our common ancestor, they were in fact the same. But is it possible for the catalysis that sustains life to be achieved in ways unlike those that came to dominate in life on Earth? A common molecular feature to life on Earth is an interplay between nucleotides, metals, and proteins. This includes nucleotides being used not only to store and repeat information (DNA and RNA), but also as “energy currency” in the form of ATP, and as signaling molecules like cAMP and GTP. Metals are also ubiquitous, with nearly 50% of known enzymes requiring metals, including many that also interact with nucleotides. These interactions are so universal and ancient that they constitute a ‘molecular fossil record’ of the earliest life-essential biochem-istry. In this dissertation, I test the ability of large collections of semi-random proteins to inter-act with metals and nucleotides. Completely designed proteins allow these experiments to probe the potential of proteins in general to perform the functions that sustain life. The results are surprising: sequences unprecedented in nature can nonetheless readily interact with metals and nucleotides. To understand this reactivity, these enzymes underwent detailed biophysical and kinetic characterization. One example is a novel enzyme that depends on Mn2+ to hydrolyze cAMP (unifying pro-tein, metal, and nucleotide). This relationship has been found before in nature, but the novel protein is completely unrelated to any natural enzyme. Unexpectedly, novel proteins were also found that can be active in ways that run counter to biological conventions. For example, a novel enzyme that hydrolyzes ATP only when Mg2+ is absent, whereas natural ATPases act best in the presence of Mg2+. Together, these novel catalysts expand what we know to be possible for life. The implica-tions of these novel proteins are twofold. First, biotechnology applications may be built on these enzymes to make use of their unusual reactivity and stability. Second, understanding this unprecedented biochemistry enriches our understanding of prebiotic evolution and the poten-tial scope of biocatalysis.
Alternate format: The Mudd Manuscript Library retains one bound copy of each dissertation. Search for these copies in the library's main catalog:
Type of Material: Academic dissertations (Ph.D.)
Language: en
Appears in Collections:Chemistry

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