Research

Interplay between Protein Vibrations and Photosynthesis Proteins

Photosynthesis proteins include photoharvesting proteins, energy transfer proteins, reaction center proteins and photo protective proteins. For all these systems, energy dissipation is critical. A key mechanism of energy dissipation is through the energy transfer to the vibrations within the macromolecules. These vibrations are in the terahertz frequency range. In addition, for some photo protective proteins, large scale conformational change occurs as they transition from the resting state to the photo protective state, and this transition may be facilitated by the directed sampling of atomic displacements biased by the protein structure and intramolecular interactions. We are using ATM to characterize the vibrations of photosynthesis proteins to examine the overlap of the energies with energy differences for electronic states between the chromophores, as well as the structural motions associated with the vibrations that enable efficient conformational transitions

 Orange State

 

 

Impact of Crystal Contacts on Protein Dynamics

Protein crystals are fascinating materials that provide 80% of known protein structures. These crystals form due to weak intermolecular interactions and often include 50% by volume water, including mobile water. These ordered array of biomacromolecules provide the needed orientational alignment to determine protein structure and characterize underlying protein dynamics using time resolved protein crystallography and anisotropic terahertz microspectroscopy. However, the specific intermolecular interactions perturb the measured dynamics from those in vivo.  We use ATM to characterize these perturbations by comparing the measured spectra with calculated spectra for different crystal symmetry groups. These studies include protein expression, purification and crystallization. Crystal unit cell and face indexing with X-ray diffraction. Protein collective vibration spectroscopy using Anisotropic Terahertz Microspectroscopy (ATM).

 Animation of rotating protein crystal on a harvesting tool.

Protein Dynamical Transition

Protein dynamics are intertwined with the solvent dynamics. A minimum hydration is necessary for proteins to function. The nature of the protein-solvent interaction has been exemplified by the observation of a turn on in protein dynamics at a temperature that appears largely dictated by the hydration. This turn on can be characterized using terahertz absorption measurements of solutions. Using THz time domain spectroscopy we explore how the protein-solvent interactions change with protein conformation and functional state. For example we have found that the turn on temperature shifts with inhibitor binding for enzymes and with photo bleaching for fluorescent proteins. We examine how these shifts may provide a characterization of the average protein-solvent interaction energy.

 

 

Finite Element Modeling of Near Field Optics

In many THz microspectroscopy configurations, detection of a transmitted THz beam is performed in the far-field. This is often done to facilitate environmental control of the sample, such as the humidity needed for protein crystals or vacuum conditions needed to isolate properties of semiconductor materials. Sample sizes of only 100 - 300 μm are typically used to measure the structural dynamics in fingerprinting protein dynamics, for example. This presents a need to use a subwavelength aperture to filter out the components of the beam that do not pass through the sample is paramount. Post-measurement corrections of artifacts arising in the detected absorbance spectrum account for known mechanisms such as etalon or signal drift. However, a loss of spectral fidelity is observed in the far field whose mechanisms remain largely unknown.

 

Computational Analysis of Picosecond Protein Motions

It is critical to complement our measurements with calculations to understand the results. First we need to calculate the specific dynamics that contribute to the measurement and then formulate those calculations into the measured quantity to directly compare to the experimental results. Ideally one would exactly model the measured system, for example, 1 mM protein solutions or protein crystals. These can be massive calculations. We simplify these calculations by doing single molecule calculations within a hydrated box with periodic boundary conditions. Our methods for determining the terahertz absorption then use either dipole autocorrelation or normal mode ensemble analysis. 

 Analysis of Protein Motions

 

 

Near Field Terahertz Anisotropic Microspectroscopy

Many important excitations on emerging solid state materials and biomacromolecules occur in the terahertz, or extreme infrared, range. Often these novel materials are only available in microscopic samples, with dimensions far below the diffraction limited focus for optical measurements using terahertz light. In order to overcome this diffraction limit we develop near field spectroscopic methods that include polarization sensitivity that provides a contrast mechanism to distinguish specific excitations from a large background. 

 Anisotropic Terahertz Spectroscopy Instrument Diagram