CAREER: Seeing the invisible: Locating hydrogen atoms in protein crystal structures

University Of Hawaii, Honolulu

Investigators

Abstract

Protein enzymes are the amazing catalysts, essential for the existence of living systems. They are also used extensively in biotechnology industry. They dramatically increase reaction rates, are exquisitely specific and they function in water. The ability to harness enzymes for use in the chemical industry would be a major advance. Unfortunately, one of the most important components of proteins, their hydrogen atoms, are invisible. The long-term goal of the proposed work is to solve this problem and make the location of hydrogen atoms more accessible to researchers. The results will advance efforts to design new catalysts by enzyme engineering. To support the adoption of methods to be developed, a public web server to process user submitted data will be implemented. Additionally, the project strengthens collaborations and training opportunities between the University of Hawaii and world-class facilities at the Department of Energy. The project will also provide new curriculum, outreach and student research opportunities that are integrated in the research plan. Special emphasis is placed on supporting Native Hawaiian and minority STEM students in collaboration with campus student support programs. A new research project-based undergraduate protein biochemistry course will be developed. Student work on expressing, purifying, and crystallizing different ferredoxin mutants add to the research efforts. Ng will serve as a mentor and speaker to minority STEM support programs, conduct outreach activities at local high schools through the Crystal Growing Challenge and train teachers to lead students to explore conditions that maximize the growth of ferredoxin crystals. The research uses novel experimental and computational methods to attain its goal of identify and locating hydrogen atoms in protein structures by applying the proposed computational approach, HyPO (Hydrogen Prediction and Observation) to X-ray and neutron diffraction data. Traditionally, crystallographers determine whether an atom is present in a crystal structure by visual comparison with a contoured electron density map. HyPO takes a fundamentally different, quantitative approach by answering the question: What arrangement of atoms is most probable given a map? The combination of HyPO and powerful new neutron sources at collaborating Oak Ridge National Laboratory will make neutron crystallography more accessible to structural biologists. HyPO will be used to analyze ferredoxin, a key enzyme in photosynthesis whose hydrogen atoms have never been directly observed. HyPO analysis will be applied to the determination of neutron structures of ferredoxin to define how ferredoxin transfers electrons. New insight into the role of hydrogen atoms in ferredoxin will have important applications in other electron transfer proteins and to protein in general.