Areas of Research

Our department makes significant contributions to research in many areas of structural biology.

Our research informs the starting points for better drug design, identifying new classes of anti-tumor agents, ways to fight opportunistic infections in AIDS patients, combating inflammation in arthritis and cardiovascular disease, and preventing bronchial infections in cystic fibrosis patients.

Thomas Grant, PhD

  • AI in Structural Biology : We are developing tools to combine the latest AI-based structure prediction algorithms (e.g., AlphaFold) with experimental data. SWAXS is sensitive to protein conformations and can be performed in a wide variety of experimental conditions (e.g., pH, cofactors, temperature, etc.). We combine the local high accuracy of structure prediction tools with the global structural information from SWAXS data to predict highly accurate models of protein structures in solution.
  • Iterative phasing for solution scattering : We develop algorithms that solve the phase problem for solution scattering. This provides 3D electron density maps from the 1D solution scattering profiles, giving insights into particle shape at low-resolution.
  • Serial crystallography : Serial crystallography is a type of X-ray crystallography technique that uses X-rays to take diffraction snapshots of hundreds of thousands of microcrystals in succession to build up a complete 3D diffraction pattern. This technique is most often done with X-ray free electron lasers, but can also be done with synchrotrons. We often perform serial crystallography experiments for both soluble and membrane proteins. This is one of the few approaches that is capable of determining the high-resolution structures of membrane proteins and is amenable to time-resolved studies.
  • Solution Scattering : We use solution scattering to probe the low-resolution structure of macromolecules in aqueous solution. These data are highly complementary to other structural techniques that provide high-resolution data such as X-ray crystallography, NMR and cryoEM.
  • Time-resolved X-ray scattering : We use ultrafast time-resolved X-ray scattering with X-ray free electron lasers to probe the dynamic motions of biological macromolecules. Currently we study visual rhodopsin, the core light sensing protein triggering the process of vision in humans.
  • X-ray crystallography : We routinely employ X-ray crystallography for probing the atomic scale 3D structures of biological macromolecules. We use high-throughput crystallization screening, optimization and X-ray diffraction at synchrotrons and XFELs.
  • XFEL Data Reduction and Analysis : We develop algorithms for data reduction of large data sets (>100 TB) generated by X-ray free electron lasers for both serial crystallography and solution scattering. We regularly provide data analysis support to dozens of research groups (internal and external to BioXFEL), including data reduction, analysis, modeling and interpretation.

Andrew Gulick, PhD

  • Assay Development : We develop approaches to identify chemical probes that block enzyme reactions that can be used to improve our understanding of the role that proteins play in virulence.
  • Enzymology : We use biochemical and structural techniques to identify the mechanisms that proteins use to catalyze critical reactions.
  • Natural Product Biosynthesis : Many microbes use novel enzymes to produce small chemicals that are secreted into the environment and help the producing organism adapt to diverse environments. We use structural, chemical, and biological tools to identify natural products and the pathways for their biosynthesis.
  • Structural Biology : We use x-ray crystallography to determine the molecular structure of important macromolecules that carry out critical biological processes.

Michael Malkowski, PhD

  • Cyclooxygenase Catalysis and Inhibition : One of the most important groups of lipid second messengers is the eicosanoid class, derived from the oxygenation of arachidonic acid by the cyclooxygenase enzymes (COX-1 and COX-2). COX-1 and COX-2 are the targets of nonsteroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors. My laboratory is a leader within the field in utilizing X-ray crystallographic methods coupled with mutagenesis, functional and biophysical characterizations to understand the mechanistic basis of substrate and inhibitor binding in COX-1 and COX-2, as well as substrate selective oxygenation, inhibition, and allosteric regulation in COX-2.
  • Membrane Proteins : My lab has technical expertise in the expression, detergent solubilization, and purification of membrane-associated and integral membrane proteins for subsequent functional, biophysical, and structural characterization.
  • Protein Production : My lab has technical expertise in the expression of prokaryotic and eukaryotic proteins in bacterial, yeast, and insect cell expression hosts. We also have expertise in the purification of proteins using various modes of column chromatography.
  • Structural Biology
  • X-Ray Crystallography : My lab has technical expertise in all aspects of protein structure determination using X-ray crystallographic methods, including high-throughput crystallization screening and optimization, diffraction data collection, phasing (MIR and MAD), refinement, and model building.

Michael Martynowycz, PhD

  • Computational Algorithms for Electron Diffraction Data : We create and implement advanced computational algorithms to process and interpret electron diffraction data. These tools are essential for converting raw diffraction patterns into high-resolution structural models, aiding in the visualization of complex biological systems.
  • Cryo-Electron Microscopy (Cryo-EM) : Our research leverages cryo-EM to visualize biological macromolecules in their native states. By integrating MicroED with cryo-EM, we extend the capabilities of structural biology to study challenging targets such as membrane proteins, offering insights into their mechanisms at an atomic level.
  • Development of MicroED Techniques for Small Molecules : We are pioneering the use of MicroED for the structural determination of small molecules, including pharmaceuticals and novel compounds. This work expands the application of electron diffraction beyond macromolecules, providing valuable structural information for material science and drug discovery.
  • Electron Counting and Radiation Damage Mitigation : We develop and refine protocols for electron counting in MicroED, enhancing data quality while mitigating the effects of radiation damage. This allows for more accurate structure determination, even from extremely small or radiation-sensitive crystals.
  • Ion Beam Milling for CryoEM and MicroED : We develop advanced methods for thinning macromolecular and small molecular crystals at cryogenic temperatures using gallium and plasma ion beam sources. Our techniques enable the precise preparation of ideal samples for cryoEM and MicroED, facilitating high-resolution structural studies of membrane proteins and viral infection mechanisms in intact, frozen cells. By correlating light, electron, and ion beam images, we optimize sample quality, ensuring accurate and detailed structural analysis.
  • Microcrystal Electron Diffraction (MicroED) : We utilize MicroED to determine the atomic structures of macromolecules and small molecules from nanocrystals. By advancing techniques in sample preparation, such as focused ion beam (FIB) milling, and optimizing data acquisition methods, we achieve high-resolution structural data that is critical for understanding molecular function.
  • Structural Analysis of Membrane Proteins : Our lab specializes in the structural characterization of membrane proteins using MicroED and cryo-EM. Through innovative approaches in sample preparation and data collection, we provide detailed models that reveal the intricate workings of these crucial biological molecules
  • Structure-Based Drug Design : By elucidating the atomic structures of biological macromolecules, particularly those involved in disease pathways, we contribute to the rational design of therapeutic agents. Our structural insights inform the development of drugs with improved efficacy and specificity.

Aviv Paz, PhD

  • “Classical” structural biology : We routinely employ X-ray crystallography (using the excellent facilities at the HWI), cryogenic electron microscopy (in HWI and with other collaborators), protein modeling, and ligand docking to solve structures of membrane and soluble protein targets.
  • Biochemical/biophysical characterization : We perform numerous assays locally and at synchrotron facilities to tease out various biochemical and biophysical aspects important for the functions of our targets.
  • Cellular assays : We employ various functional assays such as uptakes of fluorescent ligands, cell-surface abundance, etc., to characterize the proteins in cells overexpressing our targets. Findings are compared to results of detergent solubilized proteins and reconstituted systems (that only contain our protein of interest) to gain insight into the influence of other cellular components on our targets.
  • Heterologous protein overexpression : My lab uses bacterial, yeast, and cell lines for the overexpression of our targets.
  • Membrane proteins : Due to the hydrophobic nature of membrane proteins special handling using detergents is required for the solubilization, purification, and characterization of these proteins. Furthermore, to biochemically/biophysically study these purified proteins in lipidic environments (which are much closer to the native environment than detergents) reconstitution of detergent-solubilized proteins in lipidic environments such as proteoliposomes, nanodiscs, bicelles, etc., are routinely performed in the lab.
  • Method development : My research style is very receptive for improving existing methods and developing new ideas related to structural biology and protein purification.
  • Protein purification : We utilize multiple affinity systems, ion-exchange, and size-exclusion chromatography utilizing gravity and FPLC systems.

Monica Pillon, PhD

  • Cell Biology : Using model human cell lines, we perturb discrete RNA processing signals to determine their importance in gene regulation and cell function.
  • Enzymology : We harness the power of enzyme studies to discover the mechanism of action of ribonucleases and the role of their regulatory partners.
  • Integrated Structural Biology : We combine structural approaches such as cryo Electron Microscopy (CryoEM), X-ray crystallography, and chemical crosslinking mass spectrometry to reveal the architecture of RNA processing machines in action.
  • Reconstitution of Ribonucleoprotein Assemblies : Our lab specializes in the production and assembly of historically refractory RNA processing molecular machines.

Alex Vecchio, PhD

  • Membrane Protein Structure and Function : Claudins, Occludin, Tricellulin, Tight Junctions, Paracellular Transport, Lipid-synthesizing Enzymes, Scaffolding Proteins, Clostridium perfringens Enterotoxin
  • Protein Biochemistry and Biophysics : Chromatography, Protein/Protein & Protein/Lipid Interactions, Binding Equilibria, Bio-layer Interferometry, Microscale Thermophoresis
  • Structural Biology : X-ray Crystallography, Cryogenic Electron Microscopy (Cryo-EM), Microcrystal Electron Diffraction (MicroED)