This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). Support from the MRI-R2 program has been awarded to SUNY at Buffalo to develop two complimentary instruments: Spectral Terahertz Imaging Microscopy (STIM) and Dynamic Alignment Terahertz Spectroscopy (DATS). This pair of instruments is essential to address a fundamental question: what is the role of collective motions in protein function? Answering this question has an immediate impact on biological physics, and bioengineering. STIM enables terahertz imaging of protein crystals and solid state samples with < 1 micron resolution, 0.2-7.0 THz bandwidth, 4.2 K - 300 K and in fields up to 10 T. DATS enables terahertz spectroscopy of electrostatically aligned molecular systems and structural measurements of non-crystallizing molecular systems. Proteins and RNA-systems lay at the intersection between highly structured and amorphous systems. Traditional approaches to studying these systems are limited by background from the relaxational contribution of surface side chains and solvent, and by the broad spectrum of overlapping modes. STIM and DATS address these limitations through molecular alignment and polarization modulation and thereby establish the functional importance of structural vibrational motion. This instrumentation significantly improves our understanding of protein dynamics. Also, magnetic excitations, phonon frequencies and carrier transport times for technologically emerging materials lie in the terahertz frequency range. As device size shrinks, one cannot assume bulk material properties and local characterization is essential. Further, emerging materials often do not have sufficient sample size or uniformity for bulk characterization. To probe nonuniformity, localized states and phase transitions require terahertz microscopy. STIM is a high resolution, high quality spectroscopy system for measurement of nanosystems. The development of STIM and DATS enables critical measurements in fields as diverse as structural biology and condensed matter research. The instrumentation directly addresses needs that other current terahertz instrumentation does not: 1) need to discriminate structural motion from diffusive surface motion in proteins; 2) need for spatially resolved conductivity tensor and spin spectroscopy of electronic materials 3) need for structural determination for non-crystallizing molecules. This MRI-R2 project fosters interdisciplinary work among multiple departments, schools and agencies. The system development offers unique training opportunities for graduate and undergraduate researchers. This MRI-R2 activity also includes a new microscopy exhibit for our GGEMS on the GO program for 7-12 graders and an undergraduate Discovery Seminar Series: Bringing Science and Engineering to Life. Results of the development effort, and of the research enabled by the new instruments, will be published in peer-reviewed journals and disseminated through student and faculty presentations at regional and national meetings.
This funding enabled the development of new instruments that for the first time allow us to measure the internal vibrations of proteins. Proteins are very large molecules that participate in all cellular processes. For example the protein lysozyme can be visualized like a pacman from the video game. Lysozyme destroys bacteria by chomping down on carbohydrates in the bacterial cell walls. The question is how does lysozyme clamp down on the carbohydrates? It is a molecule. It doesn’t have eyes to see the bacteria. One suggestion is that the lysozyme is constantly bouncing between open and closed, and when it happens to encounter the right carbohydrate it locks down on the carbohydrate until it falls apart and then the lysozyme goes back to bouncing again. This bouncing is a vibration of the molecule. However before this work there was no simple method to measure if this vibration is present. Vibrations in molecules are often measured with light. Many people are familiar with this from television shows on forensics, where investigators identify chemicals from the crime scene using lab measurements with mid infrared light. This light has lower energy than infrared light (infrared vision goggles) and cannot be detected by human eyes. The molecules identified using mid infrared light are very small in comparison to proteins. The light that is expected to detect protein vibrations is far infrared light, which is even lower energy than mid infrared light. Only recently have instruments in the far infrared been developed similar to those in the mid infrared. Unfortunately these instruments don’t just measure the protein vibrations, they also measure water rotations, which are always present for proteins in their native environment. In fact the existing far infrared light instruments are much more sensitive to water rotations, so trying to see the protein vibrations using these instruments is like trying to find white toothpicks in a snow bank. We addressed this problem by using polarized light and special protein samples, protein crystals. Many people use crystals every day, in the form of sugar crystals. What is special about crystals is that the molecules in a crystal are arranged in a regular way, like a marching band. Going back to our snow bank analogy, using a protein crystal would be like having all our toothpicks pointing in the same direction. This wouldn’t seem to help, since the white toothpicks would still blend in with the snow. However, if we use light that is polarized, the snow will look the same no matter what polarization of the light, but the toothpicks will only show up when the polarization direction is along the same direction as the toothpick. Thus by looking at the snow with different polarizations we can easily see our toothpicks. Our instrument has worked very well, making it very easy to see the lysozyme vibrations! We now are working at determining what part of the protein is vibrating and apply the new instrument to a wide variety of interesting questions. By being able to measure these motions we can understand how proteins interact and how we might control how they interact. In particular we can use our instrument to study regulation in cells. That is we will now use our instrument to see if the cell’s machinery uses control of these protein vibrations to turn on and off DNA transcription, cell division and immune response. During the development of our instrument we have been able to train many undergraduate and graduate students. In addition children from kindergarten to 8th grade have participated in our workshops and demonstrations to see how exciting and fun physical science can be.
