De Novo Protein Switches for Conformational Control
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Solution Overview
Problem
Current technologies have not successfully designed proteins that can switch conformations in response to external inputs, as achieving multiple stable states with small free energy differences is challenging.
Innovation Solution
The development of non-naturally occurring polypeptides comprising a helical bundle with alpha-helices connected by amino acid linkers, which can undergo conformational switching upon binding with a key polypeptide, thereby activating bioactive peptides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If proteins are designed to fold into lowest free energy state, then structural stability is improved, but conformational switching capability deteriorates
Solution Approach 1:
The patent designs proteins with dynamic conformational switching capability by creating multiple stable states (folded and unfolded) that can be interconverted. The helical bundle structure with carefully designed linkers allows the protein to transition between conformations in response to external inputs, making the system dynamic rather than static.
Solution Approach 2:
The patent controls the free energy landscape by adjusting design parameters such as helix length (18-60 amino acids), linker length (2-10 amino acids), and number of helices (2-7). These parameter changes enable tuning of the energy difference between folded and unfolded states, allowing conformational switching while maintaining sufficient stability.
2Stability of the object's composition
If free energy gap between folded structure and other structures is maximized, then folding stability is improved, but conformational switching capability deteriorates
Solution Approach 1:
The patent optimizes the free energy gap by adjusting structural parameters: helix length (18-60 residues), linker length (2-10 residues), and helix count (2-7). These parameter changes create a controlled energy landscape where the folded state is stable but not so stable that switching becomes impossible, achieving a balance between folding stability and switching capability.
Solution Approach 2:
The design creates a dynamic system with multiple accessible states by controlling the energy landscape. The helical bundle with flexible linkers allows the protein to populate both folded and unfolded states, enabling conformational switching while maintaining adequate folding stability through optimized structural parameters.
3Adaptability or versatility
If free energy differences between states are made small, then conformational switching capability is improved, but structural stability deteriorates
Solution Approach 1:
The patent achieves the right balance by optimizing structural parameters: helix length (18-60 amino acids provides stability), linker length (2-10 amino acids provides flexibility), and number of helices (2-7). These parameter changes create small enough free energy differences for switching while maintaining sufficient structural stability through the helical bundle architecture.
4Adaptability or versatility
If de novo design of conformational switching proteins is attempted, then conformational switching capability is improved, but design reliability deteriorates
Solution Approach 1:
The patent segments the protein into distinct functional modules: stable helical bundles (2-7 helices with 18-60 residues each) and flexible linkers (2-10 residues). This segmentation allows independent optimization of stability (helices) and switching capability (linkers), improving design reliability while achieving conformational switching.
Solution Approach 2:
The patent establishes reliable design parameters through systematic optimization: helix length (18-60 residues), linker length (2-10 residues), and helix count (2-7). These parameter ranges have been validated to produce functional conformational switches, improving design reliability by providing proven design rules rather than trial-and-error approaches.
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 enables the creation of protein switches that can effectively toggle the activity of bioactive peptides, offering a modular and tunable mechanism for controlling biological functions.
Implementation Method 1
proteins that can switch conformations is more challenging
Implementation Method 2
proteins fold into their lowest free energy state
Implementation Method 3
amino acid linkers connecting each alpha helix
Implementation Method 4
bioactive peptides are capable of selectively binding to a defined target
Data Source
AI summary
Disclosed are protein switches that can sequester bioactive peptides and/or binding domains, holding them in an inactive (“off”) state, until combined with a second designed polypeptide called the key, which induces a conformational change that activates (“on”) the bioactive peptide or binding domain, components of such protein switches, and their use.