Biophysics and Biophysical Chemistry
Seeing is belief: my lab is interested in visualizing and quantifying biological events as they happen in situ at real time. We use single molecule imaging and spectroscopy technology in live cells, combined with theoretical modeling to extract dynamic biological information. Currently, the lab is working on how cells regulate gene expression. Gene expression has to be tightly controlled both temporally and spatially for an organism to survive and prosper.
L. Mario Amzel
Structural Enzymology. Enzymes play a key role in all metabolic and cell-signaling processes. Characterization of an enzyme’s biological function must include the description of its mechanisms at an atomic level. Our laboratory is deciphering the catalytic mechanism of several enzyme families, using a combination of molecular biology, biochemistry and structural Biology. Systems under study fall into two classes: enzymes that recognize or process phosphates and redox enzymes.
Jungsan (Jay) Sohn
Research Interests: We are interested in understanding mechanisms that allow biological stress-sensors to detect danger signals and initiate highly coordinated coping-responses by assembling into higher order molecular assemblies.
Protein function is dynamically regulated in the cell by reversible posttranslational modifications. Lysine side chains are subject to a remarkably diverse array of modifications, ranging from acetylation to the attachment of polyubiquitin chains. Acetylation plays a central role in regulating transcription, whereas ubiquitination plays diverse roles, targeting substrates for degradation as well as non-degradative roles in a variety of signaling pathways.
Our research focuses on developing novel single-molecule imaging tools in live cells to probe the organization and dynamics of cellular processes, including gene regulation, chromosomal DNA conformation and cell division apparatus. Recently we expanded our horizons to map the spatial organization of a single cell’s genome and epigenetic markers, and to develop new single-molecule based technologies for sensitive early detection of cancer markers.
The emergence of structural genomics, proteomics, and the large-scale sequencing of many genomes provides experimental access to regions of protein sequence-structure-function landscapes which have not been explored through traditional biochemical methods. Indeed, protein structure-function relationships can now be examined rigorously through the characterization of protein ensembles, which display structurally convergent—divergent solutions to analogous or very similar functional properties.
James M. Berger
Research Interests: My laboratory's research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information. We are particularly interested in developing mechanistic models that explain how macromolecular machines transduce chemical energy into force and motion, and in determining how cells exploit these complexes and their activities for regulating the initiation of DNA replication, chromosome superstructure, and other essential nucleic acid transactions.
Our lab is focused on understanding the molecular mechanisms of how multisubunit protein assemblies function. We are particularly interested in elucidating the structural thermodynamics that govern ligand binding, subunit assembly, and allosteric control of neuroreceptors such as ionotropic glutamate receptors (iGluRs). iGluRs are ligand-gated ion channels that mediate the majority of excitatory synaptic transmission in the central nervous system.
My research is focused on pushing the limits of single-molecule detection methods to study complex biological systems. His group develops state-of-the-art biophysical techniques (e.g., multicolor fluorescence, super-resolution imaging, combined force and fluorescence spectroscopy, vesicular encapsulation, single-molecule pull-down) and applies them to study diverse protein–nucleic acid and protein-protein complexes, and mechanical perturbation and response of these systems both in vitro and in vivo.
<p><strong>Non-ribosomal peptide synthetases</strong> (NRPSs) are large enzymatic systems responsible for the biosynthesis of a wealth of secondary metabolites, many of which are used by pharmaceutical scientists to produce drugs such as antibiotics or anticancer agents. To synthesize all of these remarkably diverse compounds, bacteria and fungi use a surprisingly conserved strategy: NRPSs are organized in modules, made of conserved domains, that each incorporates a dedicated substrate.