Could a Computer-designed Protein Protect Soldiers?

New work could lead to developing the easier production of therapeutics and improved detection and diagnostics against chemical and biological agents.

Model of a full-sized antibody (IgG) bound to two molecules of the designed binder (FcB6.1) at its Fc-domain. Close-up inset shows the interactions between the normally surface-exposed histidine residue (His433) of the IgG with the binder.  (Image courtesy of Dr. David Baker, University of Washington/Released)

Model of a full-sized antibody (IgG) bound to two molecules of the designed binder (FcB6.1) at its Fc-domain. Close-up inset shows the interactions between the normally surface-exposed histidine residue (His433) of the IgG with the binder. (Image courtesy of Dr. David Baker, University of Washington/Released)

DTRA CB/JSTO basic research-funded scientists, managed by DTRA CB’s Dr. Ilya Elashvili and led by Dr. David Baker from the University of Washington, recently reported successful computational designs to generate a switchable binding molecule to an immunoglobulin G (IgG) domain, the main antibody isotype found in blood that serves as a critical component in certain therapeutic and biosensor applications.

This finding could save the lives of warfighters and first responders exposed to chemical and biological threats by improving biosensors to detect those agents and making cheaper therapeutics for after-exposure applications.

In a recent Proceedings of the National Academy of Sciences USA article, “Computational design of a pH-sensitive IgG binding protein,” researchers described the computational design used to generate a pH-dependent binding protein that binds to the IgG Fc Domain.

The switchable IgG binding takes place in a mild pH range: with a high affinity (Kd ~4 nM) binding at pH 8.2 and greater than 500-fold reduced affinity at pH 5.5.

The authors report that the designed protein is highly expressed in bacteria and extremely stable both to heat and denaturants (withstanding repeated heating-cooling cycles of up to 80 degrees Celcius, 3 M urea or 1.5 M guanidine).

As the authors point out, the heat and denaturant stability is an attractive feature for an antibody capturing reagent for chip- or bead-based assays and diagnostics; surfaces coated with the designed binder for antibody immobilization could be regenerated for reuse with different antibodies by a simple heating procedure, denaturant wash, or pH change.

The article also discusses the utility of this binder protein for production of purified recombinant monoclonal antibodies and Fc-fusion proteins, which are an important class of biological pharmaceuticals, and are widely used as research reagents.

Even though their production technology has been significantly enhanced, the critical purification steps remain expensive with reduced productivity.

This is due to the fact that the current technology uses an antibody affinity capture on a Protein A column, the elution from which is typically achieved by lowering the pH to 3. Such a low pH frequently results in aggregation and denaturation of the antibody and of Fc-fusion proteins.

Replacing Protein A with the designed binder would make all processes of the affinity chromatography (i.e., both the binding and elution) able to proceed in a mild pH range, resulting in a much better yield of the product.

As the authors pointed out, the successful outcome of this design was made possible by an earlier DTRA CB/JSTO-funded basic research effort that developed general strategy for computational design of custom binders, which were the subject of the earlier publications in Science and Journal of Molecular Biology.

The science article reported how that basic research effort enabled the same team of researchers to design custom binders for proteins. Also, we had recently reported (“Custom- Designed Binders for Small Molecules Could Counter Chem-Bio Threats” in the October 2013 JSTO in the News) how that same basic research enabled the same team to successfully design custom-binders not only for large bio-macromolecules, but also for any small molecule of interest.

This first ever computationally designed pH-controllable binder presented here could benefit both Department of Defense and civilian applications by making therapeutics production easier and improve detection and diagnostics against chemical and biological agents to protect warfighters and first responders.

Story by John Davis
Defense Threat Reduction Agency’s Chemical and Biological Technologies Department

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Could a Computer-designed Protein Protect Soldiers?