The discovery of anammox bacteria in the 1990's has dramatically changed our understanding of the global nitrogen cycle. These bacteria perform ANaerobic AMMonium Oxidation (ANAMMOX), combining ammonium with nitrite into molecular dinitrogen (N2) and water, yielding energy for the cell. This process relies on highly unusual intermediates such as hydrazine. We are studying the molecular mechanism of the ANAMMOX process using structural biology.[mehr]
ACTIVITIES. Bruce Doak and his group invent and develop novel methods of sample delivery for use at advanced X-ray sources, including X-ray Free-Electron Lasers (XFEL) and fourth generation synchrotrons. Based on their research and development, they design and fabricate well-engineered sample injectors for X-ray scattering facilities worldwide.
Viruses are the most abundant biological entities on the planet and have actively influenced the evolution of life since its very beginnings. Whereas viruses as pathogens of humans and livestock have been intensely studied for a century, much less is known about the majority of viruses – especially those that infect microbes. Protists are unicellular eukaryotes and harbor a wide spectrum of viruses, from small RNA viruses to giant DNA viruses.[mehr]
Attaining a well defined three dimensional structure and thus functionality can be a serious challenge in the early life of many proteins. Although the final structure is energetically favored, many side reactions can occur mostly leading to aggregation that prevent the formation of the native protein structure. Molecular chaperones are ubiquitous in prokarytic/eukaryotic organisms and form cellular networks which assist protein folding in the cell.[mehr]
Since light is an important environmental variable, many organisms have evolved signaling pathways that not only sense, but also transmit and thereby translate this stimulus into various biochemical activities. We study a variety of photoreceptor proteins that use different chromophors for light absorption. A major focus is on blue-light absorbing flavin-based photosensors that are coupled to an array of other domains such as kinases and transcription factors. To characterize the light-induced structural changes in the sensor domain and to understand how they activate the regulated output domain, we use biochemical and biophysical approaches including various structural methods, such as hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS), static and time-resolved X-ray diffraction and solution scattering. This is supported by computational studies performed in Tatiana Domratcheva’s group. Together with spectroscopic data, this allows us to understand on a molecular level how absorption of a photon results in a specific structural change of the protein that triggers a secondary signal resulting in a biological event.
Structural biology, and in particular scattering-based techniques making use of X-rays and electrons, have provided high-resolution insight in the structure and function of molecules, molecular assemblies, and cells. Despite a lot of advances in instrumentation, radiation damage limits high resolution imaging of biological material using conventional X-ray or electron based approaches and can change in particular redox sensitive cofactors, compromising chemical insight in reaction mechanisms. X-ray free-electron lasers (XFELs) exceed the peak brilliance of conventional synchrotrons by almost 10 billion times. They promise to break the nexus between radiation damage, sample size, and resolution by providing extremely intense femtosecond X-ray pulses that pass the sample before the onset of significant radiation damage.
The performance of instrumentation for the precise biochemical characterization of proteins has increased dramitically in recent years, primarily as a result of improvements in computer hardware. This is particularly obvious in the field of mass spectrometry, where newer instruments show increases in resolution and sensitivty of more than 1000-fold over instruments dating from the year 2000, and in robotics, where sophisticated as well as dedicated instruments have become affordable and usable, even for small groups of users.