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Biophysical characterization

Understanding the physical integrity of your material is critical for the downstream successes. Whether it be investigating aggregation state or binding activity,  these properties are extensively studied for both the protein target and your numerous ligands. This guarantees the highest quality of the material for every step of the project from confirmation of binding to crystallization and complex formation.

Aggregation state

Dynamic light scattering (DLS) is a critical biophysical method in our toolbox.  It is used to determine the size distribution profile of particles in solution, providing important hindsight in the aggregation state of the sample under study. This method relies on the autocorrelation function that is dependent on particle size.  We use it systematically for the protein targets as well as the compounds under study.

Protein target: The aggregation state of the protein target is assessed at two different stages: during the last step of purification, and after protein concentration.  DLS is done to test different buffers and additives to study their effect on the size distribution of the protein particles. This guides us in the choice of buffers and additives to add to the protein target to guarantee a stable monodispersed solution. DLS is also used during the concentration step and after a freeze-thaw cycle to follow the aggregation behavior of the protein. Whether optimizing conditions for a well behaved, crystallization-friendly target, or looking for the optimal formulation for biologics, DLS is a powerful tool that can provide critical information when manipulated by expert hands.

Small molecules: Intermolecular interaction is an intrinsic property of any molecule dissolved in a solvent and is the root cause of aggregation. These interactions are the basis for the structure and properties of everything we use and own in this world. They can be ordered, to form crystals, or random to form disordered aggregates that can be soluble or precipitated. The latter, that we refer to as small molecule aggregation, is a major concern in drug discovery. It causes all sorts of problems going from false positives in high throughput screening to the inability to form protein crystal complexes. At IniXium, we systematically evaluate the aggregation state of the ligands by using static and dynamic light scattering. This is done prior to crystal soaking or co-crystallization to evaluate the solubility of the compounds and the presence of soluble aggregates. Using this method, we are able to screen for conditions that minimize the formation of soluble aggregates of the ligands. 

Protein stability

Upon heating, most proteins will denature, and the thermal denaturation profile of each will be influenced by various conditions. In a Thermal shift assay (TSA) assay, we use the shift in this thermal denaturation profile to monitor the stability of the targets and find the ideal stabilization condition by screening conditions such as pH, small molecule ligands, additives, ions, sugar, etc.  A shift in the denaturation profile upon any ligand binding is also a powerful tool to examine binding interactions of ligands. Therefore, every compound dedicated to crystallization is tested in this assay to help us prioritize the crystal soaking experiments. 

We use the Tycho NT.6 instrument to rapidly evaluate protein quality and ligand binding. This instrument uses a label free method to analyze thermal denaturation. It is rapid, consumes negligible amount of protein, and allows for a rigorous interrogation of protein quality and stability.

Thermodynamics of binding

For a complete thermodynamic profile of the interactions, we use Isothermal titration calorimetry (ITC), a label-free in solution method to obtain thermodynamic parameters of binding such as Kd, stoichiometry, enthalpy and entropy.  This extremely sensitive method provides all the data in a single experiment by measuring the heat change upon interaction. At IniXium we use the automated version of the iTC200 which allows for unattended measurements of up to 75 binding interactions per day.