Development of Modular Synthetic Sensors for Protein Biomarker Detection

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Project summary Protein detection and biomarker profiling have wide-ranging significance in many areas of disease prognostics, diagnostics, and therapeutics. For example, the progression and development of various cancers are accompanied by alterations in specific protein expressions. These variations in different biofluids are indicative of disease-like conditions. A long-standing difficulty of existing methods is the detection of multiple proteins in a complex biological sample with high sensitivity and a broad dynamic range. In addition, scalable protein identification and quantification techniques are usually created with sacrificed sensitivity, so their applicability in clinical settings remains limited. To overcome these fundamental and technical shortcomings, we will develop, optimize, and validate a next-generation class of sensing elements for targeted protein biomarker detection at single-recognition event precision. These proposed studies aim to engineer synthetic sensors made of a single-polypeptide chain protein nanostructure. This protein nanostructure encompasses a membrane protein pore and a programmable protein binder. The protein pore is a reporter that generates an output signature, which depends on the identity and quantity of the biomarker. A programmable binder is a small antibody- mimetic scaffold, such as a monobody or an affibody, sampling the targeted biomarker in solution. Hence, a generic binder can be modified for multiple protein analytes. This way, such a modular design significantly expands the utility of these sensing elements for numerous biomarkers while preserving their high sensitivity and specificity using the resistive-pulse technique. This critical benefit is facilitated by the genetically encoded nature of these sensors so that they can form combinatorial libraries of tethered binders. These manipulations of modular pore-based detectors equipped with antibody-mimetic binders have not been conducted previously. They are intended for use in challenging biofluids, where specific binder-biomarker interactions will be unambiguously distinguished from nonspecific interactions of the medium constituents. Further advantages of this real-time and label-free technology include maintaining an amplified signal-to-noise ratio in a wide dynamic range due to the superior bandwidth of time-resolved electrical recordings. The expected immediate outcomes of these proposed studies will be the following: (i) development, optimization, and validation of monobody- and affibody-based sensors for protein detection; (ii) protein biomarker detection in multiplexed and high- throughput formulations; (iii) protein biomarker detection in heterogeneous solutions. These results will represent a platform for fingerprinting panels of multiple protein targets in biofluids without impairing the sensitivity of these determinations. This proposed research will impact quantitative proteomics and biosensor technology by providing a fundamental basis and tools for ultrasensitive biomarker detection.