Amino Acid Binding Proteins for Sensitive Protein Sequencing
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Solution Overview
Problem
Current methods for sequencing proteins face challenges in achieving sensitivity, throughput, and cost efficiency comparable to DNA sequencing technologies, particularly in detecting post-translational modifications and low-abundance proteoforms.
Innovation Solution
Development of recombinant amino acid binding proteins that recognize specific amino acids in peptide ligands, such as aspartate, glutamate, glutamine, arginine, histidine, lysine, glycine, and serine, with tailored amino acid sequences for enhanced binding and sequencing capabilities.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional protein sequencing methods are used, then sequencing capability is achieved, but sensitivity and detection of low-abundance proteoforms are insufficient
Solution Approach 1:
The patent segments the protein sequencing process into distinct functional modules: amino acid recognizers for specific binding, cleaving reagents for sequential release, and detection systems for signal generation. This modular segmentation enables parallel processing of multiple peptide bonds simultaneously, improving throughput while maintaining high detection sensitivity through specialized recognizer designs for each amino acid type.
Solution Approach 2:
The patent introduces amino acid recognizers as intermediary molecules that mediate between the target protein and the detection system. These recognizers bind specifically to individual amino acids with high affinity and specificity, converting the chemical information of amino acid sequences into detectable binding events. This intermediary layer amplifies the detection signal and enables sensitive detection of low-abundance proteoforms while maintaining high throughput through parallel recognizer-protein interactions.
2Measurement precision
If protein sequencing sensitivity is improved, then detection of post-translational modifications is enhanced, but cost and complexity increase
Solution Approach 1:
The patent employs universal amino acid recognizers that can detect multiple amino acid types and post-translational modifications through a single platform. The recognizers are designed with universal binding motifs that recognize common amino acid structures while accommodating variations due to PTMs. This universal approach allows detection of diverse proteoforms using the same methodological framework, reducing overall system complexity while maintaining high detection sensitivity across different modification types.
Solution Approach 2:
The patent utilizes parameter changes in the recognizers' binding characteristics to distinguish different amino acids and PTMs. By tuning binding affinity, specificity, and kinetic parameters of the recognizers, the system can detect subtle differences in amino acid structures and modifications. This parameter-based discrimination enables sensitive detection of PTMs without requiring completely separate detection methods for each modification type, thereby controlling method complexity.
3Adaptability or versatility
If conventional sequencing methods are used, then basic sequencing is achieved, but digital quantification and single-cell analysis are not feasible
Solution Approach 1:
The patent replaces traditional mechanical and chemical sequencing approaches with a biomolecular recognition-based system. Instead of relying on complex mechanical sequencing devices or expensive mass spectrometry instrumentation, the invention uses naturally occurring or engineered amino acid recognizers that bind to target proteins through specific molecular interactions. This substitution enables digital quantification through counting of binding events and facilitates single-cell analysis by requiring minimal protein input, while maintaining cost efficiency through the use of recombinant protein technology and simplified detection workflows.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The amino acid binding proteins enable sensitive, high-throughput protein sequencing with improved detection of post-translational modifications and low-abundance proteoforms, facilitating single-cell analysis and cost-effective digital quantification.
Implementation Method 1
amino acid binding proteins that recognize specific amino acids in peptide ligands during protein sequencing reactions
Data Source
AI summary
Provided herein are novel amino acid binding proteins that recognize aspartate and/or glutamate in protein sequencing reactions; novel amino acid binding proteins that recognize arginine in protein sequencing reactions; and novel amino acid binding proteins that recognize glycine, alanine, and/or serine in protein sequencing reactions.