Instruments & Resources

All living systems rely on the tiniest of cellular functions to maintain health and vigor. When these functions break from disease or other stresses, the whole organism suffers. Structural biology allows us to study the relationships between cellular proteins, how they communicate, and their functions. With a better understanding of these cellular roles, we can look for ways to improve crops for food, biofuels, and bioproducts in a resource-constrained future.

The science

Our Structural Biology Integrated Research Platform focuses on examining the assembly, structure, and function of proteins and protein complexes at the nanoscale, down to ångströms, across space and time.

With high-resolution images, we can see details in the molecular organization of a biosystem in three dimensions. We can also map the chemical processes involved in micronutrient exchange both within and between cells and their environment, revealing links between proteins' structural and biochemical dynamics, protein complexes, and other biomolecules. These views help us understand how changes in morphology and composition affect biological systems.

How we do the science

EMSL’s structural biology expertise includes a breadth of cutting-edge capabilities.

• Using atom probe tomography, we can produce three-dimensional images of elements and molecular fragments—at the atomic scale—within soft biological materials.
• With high-resolution cryo-electron microscopy (EM), we can determine the atomic-scale structure of proteins and protein complexes greater than ~100 kilodalton (kDa). With this information, we can uncover and understand the molecular mechanisms regulating cellular processes. We also use cryo-EM to determine cellular ultrastructure in microbial systems—giving us clues into how organisms respond within a microbial consortium or to environmental stresses.
• Working with nuclear magnetic resonance spectroscopy, we can measure the distance between protons to determine the structure of small proteins less than ~50kDa.
• Employing mass spectrometry, we can study the organizational relationship between protein complex subunits—providing clues to the molecular mechanisms driving enzymatic reactions in these complexes.

Combined with mid-range scientific computing and complementary expertise in other areas, EMSL’s structural biology expertise is expanding to include correlative multi-modal imaging and analyses.

Research in action

Unearthing soil viruses 

Soil is rich with microbes—from fungi to viruses. The roles of these microbes are not fully understood. Researchers from EMSL, Stanford University, Lawrence Berkeley National Laboratory, Mammoth Biosciences, Oregon Health & Science University, and Washington State University found that soil viruses carry a set of genes called auxiliary metabolic genes that are not involved in viral replication. Instead, these genes appeared to help metabolize chitosan—a molecule closely related to chitin found in insect exoskeleton and fungal cell walls. The researchers cloned the genes and expressed the proteins to determine the protein structure using X-ray crystallography. Then they compared the structure to other enzymes responsible for chitosan metabolism to validate its function. Their study supports the hypothesis that soil viruses carry genes that can support host metabolism.

Characterizing wildfire smoke

Up to 20 percent of the phosphorus emitted annually worldwide comes from wildfires. With changes in climate and fuel availability, wildfires are predicted to increase in occurrence. The phosphorus from wildfires can end up in water systems and impact aquatic ecosystems—too much of the element can create harmful algal blooms that deplete oxygen in the water. Researchers from Michigan Technological University and EMSL used an ultrahigh resolution, custom-built 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer to characterize the organic aerosols in wildfire smoke for the first time.

Examining particles from wild grass 

Living organisms can release a variety of biological particles into the atmosphere—from cell debris to bacteria. A multi-institutional team of scientists led by EMSL researchers characterized the biological particles released from the wild grass Brachypodium distachyon. They collected particles from eight different developmental stages of the plant’s life cycle and analyzed the particle morphology, elemental composition, and abundance. Their studies revealed that fungal spores were most prevalent during the stage just before flowering, while bacteria were more abundant during flowering and fruit development.

Essential biological molecules—like proteins, lipids, RNA, and metabolites—create the language of gene expression and energy exchange that leads to healthy cells, organisms, and living systems. EMSL’s Biomolecular Pathways Integrated Research Platform connects these biomolecules to their communication signals, biological roles, and energy functions to better explain and understand the trillions of small interactions that make up the world as we know it. This essential knowledge provides an enhanced understanding of cellular communication to improve resource use and create a more resilient environment.

The science

The collective biomolecules in plants, fungi, and microbes determine an organism’s structure, function, and dynamics. EMSL has integrated capabilities to quantify the functional components of complex systems and probe biological molecules with unknown functions through increasing the rate, dynamic range, and resolution by which we analyze proteins and metabolites. Our accelerated throughput—with integrated metabolomics, proteomics, and lipidomics—provides ultrasensitive measurements that explain the molecular mechanisms behind biological processes. With this capability, our research community explores biological complexity and diversity in the quest for more efficient bioproduct synthesis and robust environmental nutrient cycling predictions.

How we do the science

EMSL’s Biomolecular Pathways expertise includes a breadth of cutting-edge capabilities.

We combine advanced mass spectrometers, nuclear magnetic resonance (NMR) spectrometers, and data processing and integration to conduct high-throughput proteomics, metabolomics, and lipidomics for biological discovery investigations. We provide comprehensive and integrated characterization of complex biological and environmental systems using a combination of protein, metabolite, and lipid analyses.

• Combining quantitative bottom-up proteomics and top-down proteomic approaches yields an expanded quantitative survey of the protein complement and understanding of molecular assemblies.
• We perform in-depth structure and function studies of intact proteins using high-resolution mass spectrometry (MS) and NMR spectroscopy.

• Our combined approach using NMR spectroscopy and liquid chromatography-MS, gas chromatography-MS, and ion mobility spectrometry-MS yields greater metabolome coverage and more accurate metabolite identifications than any one technique alone.
• Our MS imaging capabilities combine spatial, qualitative, and quantitative molecular information to study metabolites within specific locations.

• We use mid-range scientific computing-based advanced data analytics and visualization software to more effectively translate large amounts of molecular measurements and multiomics data to essential biological understanding.

Research in action

Elucidating the role of riverbank microbes in carbon and nitrogen cycling 

Sediment along the river’s edge—known as the hyporheic zone—contains numerous microbes that can transform pollutants and influence river health. Researchers from EMSL and Colorado State University used advanced instrumentation—such as nuclear magnetic resonance and mass spectrometers—to find out which microbes are involved in carbon and nitrogen cycling. Analyzing samples collected from the hyporheic zone of the Columbia River near Richland, Wash., the team identified specific genes within microbes that play a role in greenhouse gas emissions. The researchers then created a conceptual model detailing the roles of different microbes in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification.

Producing precursors to sustainable fuels 

Replacing fossil fuels with sustainable alternatives can reduce human-made greenhouse gas emissions. However, producing sustainable alternatives at an industrial scale is challenging. Researchers from the Agile BioFoundry—a consortium of Department of Energy national laboratories—identified a viable strategy for producing muconic acid, a precursor chemical for bioproducts and petrochemicals. They engineered a strain of bacteria to produce cellular machinery that converts plant sugars into muconic acid. They also found that overexpression of certain genes involved in membrane transport would increase muconic acid synthesis. They achieved up to 92 percent of the maximum theoretical yield of muconic acid—bringing this process one step closer to commercial reality.

Investigating underground interactions between plants 

The area immediately surrounding plant roots—the rhizosphere—is teeming with microorganisms. Plants influence the composition of this microbiome through root secretions. Research from Michigan State University and EMSL shows that neighboring plants of different species can also affect each other’s rhizospheres—especially when the plants compete for resources. Their study showed that changes in root secretions—known as exudates—and the surrounding rhizosphere were most significant when neighboring plants were highly competitive.

The interplay of geology, chemistry, and biology among Earth systems is critically important for keeping Earth’s air and water clean and plants healthy. Our biogeochemical transformations expertise crosses scientific boundaries to investigate how nutrients, contaminants, and other chemical compounds move and change in the environment. With new information on how these exchanges occur, we can develop and improve predictive models to anticipate and manage their effects on both human and natural systems.

The science

From Earth’s layers beneath our feet to the atmosphere overhead, biogeochemical transformations underlie the cycling of carbon, nitrogen, iron, and other elements that are essential to life. At EMSL, our Biogeochemical Transformations Integrated Research Platform helps researchers answer fundamental questions about chemical, physical, hydrologic, microbial, and atmospheric interactions that affect the transformation and mobility of critical nutrients, contaminants, aerosols, particles, and compounds within the environment.

We use the latest platforms and approaches to gain new insights into the physiochemical effects of nutrient cycling in the environment, the interactions between metabolic pathways, and the dynamics of microbial communities. From molecular structures and activity, to cellular and community-scale processes, we seek to improve scientific understanding of microbial metabolism and nutrient cycling in the environment.

How we do the science

EMSL’s biogeochemical expertise combines multiple scientific disciplines and data visualization approaches with multiscale modeling platforms.

• We have a suite of assaying methods related to sequencing, enzymatic activity probing, fractionation, aggregation, CO₂ respiration, and more for soil microbiology investigations.
• X-ray computed tomography is used to obtain three-dimensional microstructural information on plant/soil samples. A wide spatial resolution range can be covered, from centimeter-scale to nanoscale, using different instruments to visualize and volumetrically analyze the morphology and distribution of pores, soil moisture content, and organic matter.
• Helium ion microscopy and scanning electron microscopy are employed to investigate fungal-driven mineral weathering and carbon and other plant nutrient allocation in arid, semi-arid, sub-humid, and humid environments.
• Mass spectrometry and nuclear magnetic resonance are used to attain high-resolution chemical information about soil organic matter. Our mass spectrometry imaging capabilities are capable of encompassing a range of spatial scales to perform molecular and/or element mapping with high resolution and isotope sensitivity.
• Pore water chemistry is determined using analytical techniques including inductively coupled plasma mass spectrometry and ion chromatography. Soil mineralogy is investigated using X-ray diffraction.
• Mössbauer spectroscopy provides information on chemical speciation, e.g., ⁵⁷Fe compounds, and gives insight into their redox chemistry.
• X-ray photoelectron spectroscopy can provide elemental analysis and chemical-state information from the very top of sample surfaces for elements critical to geochemical cycling (C, N, O). N-depth compositional information is also available via Ar+ ion beam depth profiling.

We also steward the open-source NWChem computational chemistry code for quantum chemistry and electronic-structure calculations. Insights gained from these integrated capabilities help us develop and refine algorithms and models for predicting complex coupled systems.

Research in action

Heavy elements in sediments

Identifying chemical forms of uranium in sediments is key to understanding how the contaminant reacts and moves in the environment. A recent EMSL user project analyzed sediment samples with our high-spatial-resolution secondary ion mass spectrometer and found that uranium attached itself to organic matter, not inorganic minerals. This finding suggests that uranium may be more mobile and widespread than expected, and have implications for regulatory contamination limits, monitoring periods, and remediation strategies.

Microbes in sediments

Researchers involved with the WHONDRS and Subsurface Science Focus Area projects are also looking at microbial communities in hyporheic zones—the sediments beneath a waterway or along the water’s edge—for their potential to respire or fix nutrients during various environmental conditions. The combination of field data and EMSL statistical modeling approaches link fine-scale processes with larger-scale seasonal dynamics to infer ecological processes through space and time.

Nutrients in sediments

EMSL researchers are currently studying calcium and soil organic matter (SOM) interactions to better understand molecular-level processes that influence nutrient cycling in alkaline soils. Results from our field site in Warden, Washington, show that calcium-containing minerals play a critical role in SOM stabilization. In turn, SOM stabilization leads to nutrient availability. In the lab, the research team is investigating why this happens. The current thought is that larger molecules, with a greater number of nucleophilic functional groups, are stabilized when organic molecules aggregate in the soils through cation bridging. Through this process, greater quantities of nutrients are absorbed.