A Practical Guide to Phage- and Robotics-Assisted Near-Continuous Evolution
January 12th, 2024
Phage- and Robotics-assisted Near-continuous Evolution (PRANCE) is a technique for rapid, robust protein evolution. Robotics allows the parallelization of experiments, real-time monitoring, and feedback control.
We're trying to make the mysterious process of evolution predictable enough to use for engineering. PRANCE gives us the ability to bring evolution into the lab timescale with parallelization to understand it better. Lab automation is bringing in concepts from more general software engineering, including AI into developing control code.
People are also integrating manipulator arms and multi-directional conveyor systems into liquid handling platforms. Overall, automation is including more advanced instrumentation and workflows. Feedback control improves continuous evolution success by preventing common failure modes like extinction.
This is essential during multiplex evolutions where molecules have varying starting activities and dynamic evolution stringency is critical for desired results. New scientific questions include exploring how different conditions impact evolution, and looking at the effects on phage propagation and evolution circuit efficiency. With these improved protein engineering tools, we are looking to engineer more sophisticated proteins that are sensitive to their environment and dynamic in function.
Overview
Phage- and Robotics-assisted Near-continuous Evolution (PRANCE) is a novel technique designed for rapid and robust protein evolution. By leveraging robotics, this method allows for the parallelization of experiments, real-time monitoring, and feedback control, enhancing the predictability of evolutionary processes in a laboratory setting.
Key Study Components
Area of Science
- Protein engineering
- Evolutionary biology
- Laboratory automation
Background
- PRANCE integrates concepts from software engineering and AI into laboratory workflows.
- Automation includes advanced instrumentation such as manipulator arms and conveyor systems.
- Feedback control is crucial for preventing extinction during multiplex evolutions.
- Dynamic evolution stringency is essential for achieving desired results.
Purpose of Study
- To make the process of evolution predictable for engineering applications.
- To explore how different conditions impact evolution and phage propagation.
- To engineer sophisticated proteins that are sensitive to environmental changes.
Methods Used
- Robotics for parallelization of experiments.
- Real-time monitoring of evolutionary processes.
- Feedback control mechanisms to enhance continuous evolution.
- Integration of advanced liquid handling platforms.
Main Results
- Improved success rates in continuous evolution through feedback control.
- Insights into the effects of varying conditions on evolution efficiency.
- Development of proteins with dynamic functions and environmental sensitivity.
- Enhanced understanding of multiplex evolution challenges.
Conclusions
- PRANCE represents a significant advancement in protein engineering techniques.
- Automation and feedback control are key to successful evolutionary experiments.
- Future research will focus on optimizing conditions for protein evolution.
Frequently Asked Questions
Executive Industry Relevance
Phage- and Robotics-assisted Near-continuous Evolution (PRANCE) enables rapid, parallelized protein engineering with real-time feedback, addressing the unpredictability of evolutionary processes in R&D. By integrating robotics and feedback control, PRANCE supports scalable, multiplexed evolution experiments, reducing failure modes and enhancing experimental reliability. This capability is strategically positioned to accelerate early discovery and de-risk protein engineering portfolios.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables systematic interrogation of protein function and evolutionary pathways under controlled conditions.
- Supports biological de-risking by preventing extinction events during multiplexed evolution.
- Facilitates predictive confidence in engineered protein candidates through real-time feedback control.
Screening & Assay Development
- Prepares validated, feedback-controlled evolution systems for downstream screening workflows.
- Standardizes assay conditions across hundreds of parallel experiments, improving reproducibility.
- Enables scalable, high-throughput evaluation of protein variants for functional optimization.
Translational & Preclinical Research
- Aligns engineered protein outputs with dynamic, environment-sensitive functions relevant to disease models.
- Supports continuity from discovery through preclinical validation by enabling robust, multiplexed evolution.
- Provides mechanistic insights into phage propagation and evolution circuit efficiency for translational applications.
Pipeline & Workflow Integration
PRANCE is positioned at the intersection of early discovery, lead identification, and preclinical research, enabling continuous evolution and rapid iteration of protein candidates.
- Discovery Biology: Supports hypothesis testing and pathway clarification by enabling controlled, parallel evolution experiments.
- Screening: Delivers reproducible, quantitative outputs for reliable comparison of protein variants.
- Analytics: Provides real-time monitoring and feedback data to inform experimental adjustments and decision-making.
- Translational Research: Bridges discovery and preclinical stages by generating proteins with dynamic, disease-relevant properties.
- Enterprise Reuse: Establishes a scalable, reusable platform for ongoing protein engineering initiatives.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence and reduces mechanistic ambiguity in protein evolution.
- Operational Value: Delivers standardized, reproducible, and scalable evolution workflows.
- Strategic Value: Enables informed go/no-go decisions and capital-efficient portfolio advancement.
- Portfolio Impact: Supports risk-adjusted prioritization and advancement of engineered protein candidates.
Implementation Considerations
- Requires expertise in robotics, liquid handling, and feedback control systems.
- Demands integration of plate readers, pumps, heaters, and compatible software infrastructure.
- Necessitates cross-team standardization for multiplexed experiment setup and data analysis.
- Adaptation across different protein targets and evolution circuits may require protocol optimization.
- Practical limitations include initial equipment setup complexity and validation of system readiness.
