Intellectual Merit. How the first protein enzymes evolved from a primordial pool of random sequences remains a fundamental unanswered question in biology. One possibility is that enzymes, by chance, had some intrinsic catalytic function that was optimized by natural selection. An alternative scenario is that enzymes evolved from proteins that initially only bound their substrates and later adapted to catalyze reactions with those substrates. To address this question, this project combines the principles of Darwinian evolution with X-ray crystallography to study the mechanism by which proteins evolve function. Through this process, a protein from random sequence origin was discovered that catalyzes a reaction with the substrate for which it was selected. Based on this observation, it was speculated that many enzymes may have originated from proteins that initially only bound their substrates and later acquired the ability to catalyze reactions with those substrates. This may be the first example of a functional enzyme from random sequence origin. The practical value of studying how proteins evolve function is that this knowledge could one day be used to create tailor-made enzymes in the laboratory. In this regard, the approach of this research project is ideal for evaluating the amount of information that is needed to specify a polypeptide with a desired functional property and the requirements needed to change or improve an existing function. The focus of this research is to investigate the evolutionary path by which a synthetic, non-biological protein evolved catalytic function. Broader Impact. This research has the potential to provide broad scientific impact by developing new insight into the diversity of structures and functions distributed across the protein universe. By removing many of the intrinsic biases associated with biology, the PI was able to search sparse regions of protein sequence space for unique independent solutions to a given functional problem. This approach led to the discovery that synthetic proteins obtained from non-biological origins have the ability to adopt novel folds possessing discrete chemical functions, which includes enzyme catalysis. Continued research in this area is expected to improve the fundamental understanding of the chemical basis of biological evolution by developing new constraints on models that describe the evolution of biological proteins. This area of research is also expected to reveal new strategies for evolving tailor-made enzymes in the laboratory, which remains a major problem in chemical and synthetic biology. In addition, this project also contains a significant educational component designed to implement a proactive university effort to attract and maintain student interest in the physical sciences, and improve the participation of underrepresented minorities in math and science. As part of this project, the PI plans to continue synergistic activities that involve training high school and undergraduate students in laboratory techniques that allow them to tackle significant problems in health and science. Through this work, the PI has developed a relationship with Dr. Sandra Simpkins in the Center for Social and Family Dynamics at ASU to help understand the values that children place on science.
The goal of our study was to examine possible mechanisms that nature may have used to evolve protein catalysts. One possibility is that primordial enzymes, by chance, had some intrinsic catalytic function that was optimized by natural selection. An alternative scenario is that modern enzymes evolved from proteins that initially only bound their substrates and later adapted to catalyze reactions with those substrates. To address this question, we combined the principles of Darwinian evolution with X-ray crystallography to study the mechanism by which proteins evolve function. Through this process, we discovered a protein from random sequence origin that catalyzes a reaction with the substrate for which it was selected. Based on this observation, we postulate that many early enzymes may have originated from proteins with simple ligand binding activity. To our knowledge, this is the first example where a functional enzyme was produced from random sequence origin. The practical value of studying how proteins evolve function is that this knowledge could one day be used to create tailor-made enzymes in the laboratory. In this regard, our approach is ideal for evaluating the amount of information that is needed to specify a polypeptide with a desired functional property and the requirements needed to change or improve an existing function.
