- Research Overview
- Chemical Biology and Medicinal Chemistry
- Chemical Biology and Medicinal Chemistry Overview
- Discovering Enzyme Substrates and Functions
- Discovering Protein Ligands to Probe and Alter Function
- Discovering Enzyme Activators
- Analyzing Mechanisms of Drug Resistance via Chemical Biology
- Analyzing Enzyme Conformational Dynamics, Substrate Binding, and Catalysis
- Effective Drug Targeting of Pathogens via Medicinal Chemistry
- Computational Chemistry and Biology
- Computational Chemistry and Biology Overview
- Modeling protein regulation via allostery and post-translational modifications
- Visualizing and integrating bioinformatics and biomolecular data
- Modeling membrane permeation to optimize pharmacokinetics
- Determining enzyme function by predicting substrate specificity
- Physical Biology
- Protein and Cellular Engineering
- Protein and Cellular Engineering Overview
- Monitoring enzyme activity and disease biomarkers
- Generating human proteome antibodies via phage display and directed evolution
- Globally analyzing and dissecting apoptosis
- Proximity tagging of protein-protein interactions
- Investigating cellular interactions in tissues
- Creating fluorescent probes targeting the genome and key bio-pathways
- De novo design of catalytic and membrane proteins
- Probing and modulating membrane proteins
Physical biologists develop, improve, and apply techniques for determining the constantly changing chemical structures, shapes, locations, interactions, and quantities of molecules involved in vital biological processes.
Complex macromolecules (proteins, RNA, DNA) carry out the functions of life within and between our cells. In rational drug design, researchers seek to find and create small molecules that selectively bind to those macromolecules involved in disease processes to therapeutically alter their activity.
Characterizing shape-shifting, chemically modified targets
However, those molecular targets present multiple challenges to analysis that must be addressed by physical biology methods. Even beyond their sub-microscopic size (their chemical structures are determined only via indirect means, such as by how they diffract the beams of super-bright x-rays), such macromolecules are hardly static “locks” awaiting pharmaceutical “keys”:
Proteins are highly flexible molecules that may rapidly cycle through a variety of shapes (conformations) in tiny fractions of seconds, a process that regulates their function (or reflects dysregulation in disease). Only certain conformational states may be relevant for therapeutic intervention.
Also, the structures and functions of proteins are routinely altered by enzymes that cleave their peptide bonds or remove/add chemical groups and carbohydrates (post-translational modifications) amid biological processes.
By analyzing conformational changes and protein modifications, scientists can learn which form of a macromolecule to target, when, and where. They can also glean key insights from how nature itself precisely regulates macromolecular function and so discover key measures (biomarkers) at the molecular level to more rapidly diagnose disease or to determine if an intervention is proving effective.
Detecting interactions, tracing biological pathways
Beyond discovering specific molecular targets, scientists also seek to understand broader biological systems to determine the right nodes and stages at which to intervene in a sequential pathway of molecular interactions in order to have the most significant, precisely targeted, and enduring therapeutic effect.
Physical biology methods are thus applied to detecting and tracing the typically extremely rapid molecular interactions in biological pathways, as well as determining the timing and quantities of modifications to key molecular players in biological processes, including those to the DNA-protein complex in the cell nucleus that alter gene function (epigenetics).
Department scientists develop and apply a wide array of physical biology techniques that include among them:
- Mass spectrometry:
Uses mass-to-charge ratios to precisely detect, identify, and quantify shifting sub-sets of proteins (proteomics)—including the types and sites of their post-translational modifications in a given cell type over time, given different stimuli, disease states, or pharmaceutical treatments.
- Nuclear Magnetic Resonance (NMR) spectroscopy:
Uses shifts in the spins of key atomic nuclei placed in a magnetic field to sensitively determine changes in macromolecular conformation over time as well as to detect rapid interactions between molecules in transient complexes and biological pathways.
- Super-resolution microscopy (Stochastic Optical Reconstruction Microscopy):
Uses photo-switchable fluorescent labels and software that tracks their coordinates to compile 3D images of macromolecular complexes and sub-cellular structures smaller than the diffraction limit of conventional light microscopy. Such analysis is rapid enough to record videos of dynamic biological processes.