Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent

Abstract

The VX nerve agent is one of the deadliest chemical warfare agents. Specific, sensitive, real-time detection methods for this neurotoxin have not been reported. The creation of proteins that use biological recognition to fulfill these requirements using directed evolution or library screening methods has been hampered because its toxicity makes laboratory experimentation extraordinarily expensive. A pair of VX-binding proteins were designed using a supercharged scaffold that couples a large-scale phase change from unstructured to folded upon ligand binding, enabling fully internal binding sites that present the maximum surface area possible for high affinity and specificity in target recognition. Binding site residues were chosen using a new distributed evolutionary algorithm implementation in protCAD. Both designs detect VX at parts per billion concentrations with high specificity. Computational design of fully buried molecular recognition sites, in combination with supercharged phase-changing chassis proteins, enables the ready development of a new generation of small-molecule biosensors.

Quantum Defect Sensitization via Phase-Changing Supercharged Antibody Fragments

“…While we present the first redesign of an antibody-derived scFv to form a supercharged ligand-induced folder, this approach can be extended to any natural or designed ligand binding protein that recognizes either other proteins, as described here, or small molecules for quantitative and mechanistic understanding of biochemical processes. , This approach opens a new dimension in biodevice development, combining the specificity inherent to biological recognition, the extraordinary electric field changes inherent to ligand-induced folding in supercharged proteins, and the NIR fluorescence of quantum defects to create robust, versatile, and sensitive biosensors.…”

Emerging Landscape of Supercharged Proteins and Peptides for Drug Delivery

“…This presents a novel approach for creating small molecule sensors. 83 Tang and colleagues devised a detection method based on ScGFP and cationic copolymers (CCP), mediating fluorescence resonance energy transfer between ScGFP and CCP in a complex. 84 This approach opens new directions for screening PARP-1 inhibitors and developing PARP-1-related anticancer drugs.…”

“…The scaffold’s capability to encapsulate all binding sites within the protein contributes to its high affinity and specificity, facilitating swift and precise detection of VX neurotoxins. This presents a novel approach for creating small molecule sensors . Tang and colleagues devised a detection method based on ScGFP and cationic copolymers (CCP), mediating fluorescence resonance energy transfer between ScGFP and CCP in a complex .…”

Modern Potentiometric Biosensing Based on Non‐Equilibrium Measurement Techniques

“…Nonetheless, expanding the repertoire of bioreceptors for potentiometric biosensing is a critical avenue for achieving the detection and analysis of diverse analytes. For example, rational design of peptides and screening of aptamers with high affinity and selectivity toward targets can facilitate potentiometric biosensing with unprecedented accuracy and sensitivity [39,40] …”

“…For example, rational design of peptides and screening of aptamers with high affinity and selectivity toward targets can facilitate potentiometric biosensing with unprecedented accuracy and sensitivity. [39,40] In addition, bioreceptors can be modified with lipophilic groups and immobilized onto or inside polymeric membranes by adsorption (Figure 2e). For example, oligonucleotides modified with a hydrophobic alkyl linker were immobilized onto the interface of the aqueous/organic phase as probes to detect target oligonucleotides via electrochemical methods.…”