Physical Biology

In a nutshell

“Seeing,” counting shape-shifting molecules in action

In the 17th century, the use of early microscopes led to the discovery of blood cells and bacteria. Viewing things invisible to the naked eye allowed scientists to understand the biology underlying health and disease. Eventually, based on the quantities and types of those cells and germs, physicians could more precisely diagnose and treat illness, while researchers could rapidly measure if a treatment being developed was effective.

Modern pharmaceutical research focuses on the forms and quantities of protein molecules that are thousands of times smaller than the cells in which they carry out the activities of life—and especially on parts of those molecules, crucial to understanding how they work or go awry, which are smaller still. These can be far more precise biomarkers for detecting and differentiating diseases and for determining a potential drug’s effectiveness.

Physical biologists have developed advanced techniques to find and count these needles in the biological haystacks of cells and tissues. They can also describe their complex chemical structures down to the positions of individual atoms, which crucially aids medicinal chemists designing drug molecules to selectively alter their activities to treat disease.

But that turns out to be only part of the challenge. Think of a molecule’s chemical structure as a human body, which adopts different positions to carry out different activities, from working to napping. To activate a protein or to put it to sleep, a scientist must know which positions optimize those states and which configurations to target. So physical biologists have developed sophisticated methods to determine the different shapes that biomolecules adopt for different types and levels of activity.

Beyond the biological yoga of individual molecules, proteins act on and physically change one another in rapid-fire biological sequences, or join together in complexes like team players taking their positions at game time. To follow this action, physical biologists must relinquish “close-ups” for the fast-moving bigger picture, while still tracking the roles of key players with labels that glow (fluorophores) or alter mass (isotopes). The goal is to understand the methods nature uses to regulate proteins and thus healthy biology so that medicinal chemists can harness them to treat disease.

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.

Challenges include

  • Proteomics, post-translational modifications, and epigenetics
  • Capturing conformational dynamics and transient interactions
  • Viewing the cell’s inner life via light microscopy