Quantitative Molecular Dynamics of Extremophile Metalloproteins -- Combining Experiment and Computation

Seti Institute, Mountain View CA

Investigators

Abstract

This is a collaborative research project between the SETI Institute, San Jose State University, PCOM Georgia, and Georgetown University to study proteins from ‘extremophiles’. These are organisms that can thrive in extreme environments, such as low temperature (<0°C, ‘psychrophiles’), high temperature (>100°C, ‘hyperthermophiles’), or high pressure (>1100 atm, ‘piezophiles’), as well as other extremes of pH, salt concentration, and radiation. Understanding how living things can flourish under extreme conditions is important for guiding the search for life elsewhere in the universe. It also has many practical applications, since the enzymes from these microorganisms, ‘extremozymes’, are extraordinarily useful. Their stability under extreme conditions has enabled numerous applications, such as enzymes included in cold-water ‘biodetergents’, high temperature ‘bio-pulping’ enzymes for more eco-friendly paper-processing, and high-pressure enzymes for food processing. Despite their numerous applications, the factors that lead to extremozyme stability are still not completely understood. Some theories propose that the molecular motion within these proteins determines the ranges of stability and activity. However, there is not enough good quantitative information about extremozyme motion under different conditions. For this project, proteins from various extremophiles will be produced by undergraduates at San Jose State and PCOM Georgia. The motion in these proteins will be measured by SETI scientists using novel x-ray techniques. The results will be tested against theoretical calculations by graduate students at Georgetown University. Underrepresented high school and undergraduate students from local schools will be involved in field trips and summer research projects. This project is undertaken to gain experimental data on atomic motion in proteins from psychrophiles to hyperthermophiles and from mesophiles to obligate piezophiles, under a range of temperatures and pressures. Experiments performed by using nuclear resonance vibrational spectroscopy (NRVS) will provide information on motion of Fe atoms at the active sites of rubredoxin and cytochrome P450 and Te atoms in the middle or on the periphery of the target proteins. X-ray diffraction and nuclear resonant time domain interferometry (NR-TDI) will quantify motion in polypeptide helices and loops of these proteins. The data will test two hypotheses concerning protein dynamics. The project will specifically look for ‘protein glass transitions’, which are proposed Temperature-dependent changes in protein flexibility over the range of 180-220 K. The project will also test the ‘corresponding states’ paradigm, which says that proteins in an extremophile have been adapted to maintain equivalent flexibility under the different environmental conditions favored for each organism. Finally, the project is aimed to determine the best combination of force fields and water models for molecular dynamics (MD) simulations to reproduce and interpret the experimental data collected for a set of proteins. This research is expected to expand the knowledge of molecular motion in extremophile proteins and the fundamental factors that contribute to life under extreme conditions. This project was funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.