Circular dichroism is one of the major spectroscopic techniques for low resolution structural characterization of purified proteins, analysis of their conformational stability, and investigation of structural changes in proteins associated with their interactions with partners. This technique allows analyzing protein secondary and tertiary structure. The Jasco spectropolarimeter (Jasco-815) is used for these studies by Uversky.

Dynamic light scattering

Protein aggregation is accompanied by the formation of particles whose size increases over time that leads to the increase in light scattering. Dynamic light scattering provides an opportunity to determine the size (hydrodynamic radius) and size distribution of particles, polymers, and biopolymers from 0.5 nm 1000 nm. The corresponding analysis is conducted by automated DynaPro Plate Reader (Wyatt Technology) equipped with the DynaPro Plate Reader Temperature Control unit (Wyatt Technology), which permits the Peltier-driven temperature regulation for the plate reader from 4°C - 70°C with an ambient temperature of 24°C. These studies are conducted by Uversky. 

Fluorescence spectroscopy

Fluorescence spectroscopy is used for the analysis of the fluorescent properties of biological molecules. Since fluorescent properties of the fluorophore depend on its environment, fluorescence can be used for low resolution structural characterization of purified proteins, analysis of their conformational stability, investigation of structural changes in proteins associated with their interactions with partners, as well as it represents a unique tool to follow formation of amyloid fibrils. The JascoSpectrofluorometer (FP-8300) is used for these studies by Uversky.

Confocal microscopy, the ‘bread and butter’ of virtually all research investigations, is an optical imaging technique that offers shallow depth of field, elimination of out-of-focus glare, and ability to collect serial optical sections from thick specimens. The Byrd Microscopy Core houses 3 laser-scanning confocal units including Olympus FV10i, ZeissLSM 880, and NikonC2+ Ti-E.

Drosophila melanogaster, commonly known as the fruit fly, is a powerful genetic model system to study neurodegeneration, neurogenesis, axonal guidance and brain development. The Bhat lab specializes in the use of drosophila model systems.

Fluorescence reporter proteins/probes are coupled with live-cell confocal imaging to study many biological processes, including protein trafficking, axonal transport, mitochondrial membrane potential, mitochondrial fusion, calcium levels, protein turnover, etc. Techniques such as photoactivation, fluorescence resonance transfer (FRET), and ratiometric imaging are employed for a variety of different applications. These studies are conducted using sophisticated instruments at the Byrd Microscopy Core. These studies are conducted by multiple labs, including Thinakaran, Blair, Parent, Heckmann, and Dharap.

X-ray crystallography is the main experimental technique used to determined three-dimensional structures of proteins, using X-ray diffraction by protein crystals.  The high resolution structural information provided by X-ray crystallography is used to understand protein function and to engineer novel inhibitors.  USF is a member of the SER-CAT beamline at the Advanced Photon Source (APS) of Argonne National Laboratory, a national synchrotron-radiation light source.  This gives us regular access to one of the best X-ray facilities in the world and allows us to do data collection remotely through robotic systems. These studies are conducted by the Chen lab.  

Molecular docking  

Molecular docking uses computational programs to simulate molecular interactions between proteins and small molecule ligands.  These calculations provide valuable insights into how proteins bind to their substrates and regulators, and offer an effective tool to screen compound libraries in silico and to design new small molecule inhibitors.  Using the high performance scientific computing server at USF, we can virtually screen millions of commercially available compounds against proteins of interest and identify potential inhibitors. Subsequently, molecular docking can also be employed to evaluate modifications of lead compounds to enhance their activities. These studies are conducted by the Chen lab.