How to Uncover Weak and Transient Protein Interactions Effectively
Over the last decade, the techniques used for researching biomolecules and developing new treatments based on synthetic biology underwent considerable advances. Today, researchers have an array of refined methods available to help isolate target proteins with high specificity and discover weak protein interactions. Understanding biological processes that govern and influence behaviors like cell signaling, growth, and morphology is rapidly revolutionizing medicine development.
In 2020, quickly understanding the rare cell populations and weak protein interactions of the SARS-CoV-2 virus became essential for dealing with the pandemic. To help define and characterize these interactions, many labs needed to rethink the efficacy workflows used in the specifying and isolating of target proteins.
Purification and Identification of Weak Protein Interactions
During the process of rapidly developing new medicines, labs need to have an efficient and effective workflow for uncovering transient or weak protein interactions. Therapeutic strategies now include the repurposing of existing agents according to specific interactions identified during the isolation and modification of proteins, which allows them to control and modulate specific biological processes.
Previous workflows used for the rapid isolation and purification of protein-protein interactions such as high-yield, high-purity, and high-activity (HHH) aren’t ideal for transient or low-affinity bindings. Due to these challenges, new methods like exclusion-based sample preparation (ESP™) using affinity purification is an effective method for isolating target proteins with weaker affinities.
Challenges with Isolating Weak and Transient Protein Interactions
For more than a century now, researchers continue to expend massive amounts of effort into understanding different protein interactions and the biological processes of the human genome. However, identifying the specific interactions of weak or transient proteins remains a challenge. Proteins interact with a variety of targets, including other proteins, metabolites, carbohydrates, lipids, metals, and molecules, where every interaction could have an impact on the subcellular compartment.
Conventional isolation methods of assays aren’t efficient when working with weak or very weak protein interactions. Additionally, a bias existed among researchers that these interactions were of little consequence due to the low concentrations compared to other mean proteins in the subcellular compartments. With newer methods, it is now apparent that ultra-weak protein-ligand interactions are biologically important. In these situations, using a method that can help uncover and isolate weak protein interactions becomes essential for understanding the internal dynamics of the subcellular compartments and low-affinity complexes.
New Methods for Uncovering Weak and Transient Protein Interactions
Recently, finding new methods to overcome the challenges with studying low-affinity protein interactions received intense focus from researchers. Techniques like magnetic bead extraction have the potential to help researchers develop new compounds, matrices, and protein complexes in an attempt to support and improve human health.
With newer methods, it is now apparent that ultra-weak protein-ligand interactions are biologically important. In these situations, using a method that can help uncover and isolate weak protein interactions becomes essential for understanding the internal dynamics of the subcellular compartments and low-affinity complexes.
Today, many labs are working to quickly identify new variants of the SARS-CoV-2 (or other acute respiratory distress syndromes) and develop neutralizing antibodies suitable for passive transfers to host cells. With affinity-based exclusion techniques, labs can ensure precise results by eliminating human error and automating many of the sample preparation steps required.
Magnetic Bead Extraction for Exclusion-Based Sample Preparation
For isolating nucleic acids, proteins, viruses, or protein complexes, ESP (Exclusion-Based Sample Preparation) uses surface tension and hydrophobicity when targeting analytes-of-interest. With an ESP workflow, researchers and drug developers can overcome the challenges of isolating and purifying weak protein interactions when compared to using conventional “bind-wash-elute” magnetic bead techniques which often promote dissociation of protein complexes
ESP works by passing paramagnetic particles (PMPs) bound through air and aqueous interfaces to purify proteins. The multiple “add and remove” steps in other magnetic bead extraction methods for liquid transfer increases the risk of contamination of samples. To overcome this issue, ESP moves the PMPs instead of the fluid, helping to enrich biomolecules and leave behind contaminants while conserving samples.
With ESP, lab technicians and researchers can:
- Minimize carryover by leveraging surface tension and minimizing surface contact
- Leave behind contaminants by moving PMPs instead of fluids
- Conserve samples that can be re-interrogated in fewer steps than conventional methods
Attaching a magnetic head with a hydrophobic surface to transfer PMP-bound analytes requires only one-step. The subsequent purification then uses magnets beneath the reagent wells to mediate the PMP release in a SLIDE process with multiple release processes running sequentially.
Using EXTRACTMAN® for Weak and Transient Protein Isolation
With EXTRACTMAN® slide ESP method, laboratories can rapidly and efficiently isolate and purify DNA, mRNA, and other protein complexes with weak affinity. Companies can choose from a completely automated solution (for higher accuracy and reduced error) or a manual magnetic bead extraction platform.
EXTRACTMAN – A Novel Platform for Target Protein Isolation
Using the innovative EXTRACTMAN magnetic bead extraction method, laboratories can implement a faster and gentler approach to isolate their target proteins. Compared to other conventional methods, EXTRACTMAN offers similar or higher yields and purity of mRNA samples. By using paired magnets in sample extraction with ESP technology, labs can solve many of the challenges involved in affinity purification. Labs can also save time while detecting weak protein-protein interactions by processing samples in parallel. To overcome the limitations of immunoprecipitation techniques in other methods, the EXTRACTMAN magnetic bead extraction and exclusion-based sample preparation is helping researchers develop new medicines and diagnostic techniques daily.
A simple slide allows you to move samples through the loading and isolation process, while the ESP™ technology preserves the remaining samples for further research. The manual platform allows researchers to process up to four samples in parallel, helping to speed up your weak protein isolation workflow. EXTRACTMAN is a universal platform that can work with a variety of commercially available magnetic bead kits.
Gilson Instruments for Sample Extraction Solutions
Gilson continues to provide innovative and efficient extraction and purification systems to support research, drug development, and processing of samples. Our EXTRACTMAN is capable of detecting new weak protein interactions when compared to conventional, tube-based capture methods.
Additionally, the added automation capabilities can help labs to set up a walkaway workflow that requires minimal supervision and intervention. For researchers that need a smart and efficient platform to uncover weak protein interactions in today’s labs, EXTRACTMAN is ideal. You can uncover cell signaling processes, protein mechanisms, post-translational modifications, and identify drug targets rapidly and efficiently.
Identifying Weak Proteins Interactions
EXTRACTMAN®, an innovative magnetic bead extraction platform, offers a faster and gentler approach to isolating target proteins from a variety of samples.Learn More