Engineered N-Terminal Peptide Binders for Metal-Chelation Sequencing
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Solution Overview
Problem
Current high-throughput protein sequencing methods, such as mass spectroscopy, face challenges with high instrument costs, require sophisticated users, and struggle with quantification across the dynamic range of the proteome, particularly for low abundance proteins, and lack sufficient amino acid specificity in binders.
Innovation Solution
Development of engineered N-terminal modifying reagents and binders, specifically metalloenzymes, that modify peptides to create high-affinity binding sites for metal ions, enabling accurate and sensitive peptide sequencing through metal chelation and enzymatic reactions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If mass spectroscopy is used for protein sequencing, then sequencing capability is provided, but instrument cost is high and user expertise is required
Solution Approach 1:
The patent replaces complex mass spectroscopy instrumentation with a biochemical system using engineered binders and metal ions. The sequencing process is transformed from physical measurement to chemical binding, eliminating the need for expensive instruments while maintaining sequencing capability through molecular recognition and affinity-based detection.
Solution Approach 2:
The patent employs synthetic, easily produced binder proteins and metal ion complexes as consumable reagents rather than requiring expensive, maintainable instrumentation. These biochemical components can be synthesized cost-effectively and discarded after use, replacing the need for high-cost instrument maintenance and operation.
2Measurement precision
If mass spectroscopy is used for protein analysis, then sequencing information is obtained, but quantification ability across dynamic range is poor
Solution Approach 1:
The patent utilizes variable metal ion concentrations and binder affinities to achieve quantification across different protein abundance levels. By adjusting metal ion concentration and utilizing binders with different dissociation constants, the system can accurately quantify proteins across a wide dynamic range, from abundant to trace abundance species.
Solution Approach 2:
The patent introduces metal ions as intermediary agents that bridge the gap between protein analysis and detection. Metal ions bind to specific amino acid sequences with varying affinities, serving as amplifiers that enable sensitive detection of low-abundance proteins while maintaining linearity across the dynamic range through controlled metal-protein interactions.
3Measurement precision
If conventional binders are used for peptide recognition, then binding occurs, but amino acid specificity and affinity are insufficient
Solution Approach 1:
The patent engineers binders with highly specific recognition motifs that focus on particular amino acid sequences and metal ion binding sites. The binder structure is optimized to interact specifically with certain amino acids (such as histidine, cysteine, or metal-coordinating residues) while maintaining high affinity through localized chemical interactions at the binding interface.
Solution Approach 2:
The patent creates composite binding systems combining engineered protein binders with metal ion cofactors. This composite approach integrates the specificity of protein recognition with the high-affinity binding capability of metal ion coordination, achieving both specific amino acid recognition and strong binding affinity through synergistic interactions between the binder and metal ion.
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
Facilitates high-throughput, accurate, and sensitive peptide sequencing by enhancing binder affinity and specificity, allowing for the analysis of a wide range of proteins, including low abundance species.
Implementation Method 1
each modified NTAA residue is capable of coordinating or chelating a metal cation
Implementation Method 2
an engineered binder that specifically binds to an N-terminally modified peptide modified by an N-terminal modifier agent... each modified NTAA residue is capable of coordinating or chelating a metal cation
Data Source
AI summary
The present disclosure relates to a metalloprotein binder that specifically binds to a N-terminally modified peptide. Also provided herein is methods and related kits for treating or analyzing a peptide using the metalloprotein binder. The methods and compositions provided herein are useful for high-throughput peptide analysis and/or sequencing.