Protein Sequencing With Terminal Amino Acid Recognition Signals
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Solution Overview
Problem
The complexity surrounding protein structure, composition, and modification presents challenges in determining large-scale protein sequencing information for a biological sample.
Innovation Solution
The application provides methods and compositions for determining amino acid sequence information from polypeptides by using terminal amino acid recognition molecules that differentially associate with different types of amino acids to produce detectable characteristic signatures, allowing for real-time sequencing without iterative reagent cycling and harsh chemical reagents.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional protein sequencing methods are used, then amino acid sequence information can be determined, but the process requires laborious labeling and harsh chemicals, reducing productivity and increasing complexity
Solution Approach 1:
The patent extracts and eliminates the need for traditional laborious labeling steps and harsh chemicals by using affinity reagents that directly bind to terminal amino acids. The sequencing process is simplified to rely on natural amino acid recognition rather than artificial labeling, thereby improving productivity while reducing process complexity.
Solution Approach 2:
The affinity reagents self-recognize and bind to specific terminal amino acids without requiring external labeling or complex preparation. The system uses the inherent properties of amino acids (their side chains) for recognition, allowing the process to serve itself and eliminating the need for additional labeling reagents and harsh chemical treatments.
2Measurement precision
If traditional sequencing methods with iterative reagent cycling are used, then complete sequence information can be obtained, but the process is time-consuming and reduces productivity
Solution Approach 1:
The patent implements continuous sequencing by eliminating iterative reagent cycling. The affinity reagents continuously bind to exposed terminal amino acids as the polypeptide is degraded, allowing real-time detection without stopping for reagent changes. This continuous action maintains measurement precision while dramatically improving sequencing throughput.
Solution Approach 2:
The polypeptide is pre-immobilized on a surface before sequencing begins, and the degradation process is initiated in advance. This preliminary preparation allows the sequencing reaction to proceed continuously without interruption for sample handling or reagent cycling, thereby maintaining accuracy while enhancing productivity.
3Loss of information
If polypeptides are degraded sequentially to expose amino acids, then sequence information can be determined, but the process requires complex reagent cycling and reduces productivity
Solution Approach 1:
The patent introduces an intermediary detection system that continuously monitors the degradation process. Affinity reagents act as intermediaries between the degrading polypeptide and the detection system, binding to exposed terminal amino acids in real-time and transmitting sequence information without requiring iterative reagent cycling, thus preventing information loss while improving throughput.
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
This approach increases the throughput and accuracy of protein sequencing by enabling real-time analysis of polypeptides using existing instruments without significant modifications, allowing for both genomic and proteomic analyses to be performed using the same sequencing instrument.
Implementation Method 1
obtaining data during a degradation process of a polypeptide... data is indicative of a signal produced by one or more amino acid recognition molecules binding to different types of terminal amino acids at the terminus during the degradation process
Implementation Method 2
analyzing the data to determine portions of the data corresponding to amino acids that are sequentially exposed at a terminus of the polypeptide during the degradation process
Data Source
AI summary
Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.