Scientist, Responsive Protein Engineering and Screening

FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to redefine how critical research, diagnostic, and therapeutic molecules are designed and built. We are seeking passionate problem solvers ready to make a profound impact on biotechnology and therapeutic innovation.

Position Summary

We are seeking a creative, motivated, and technically exceptional scientist to join our Protein Science team. This role will focus on engineering and characterizing stimulus-responsive proteins, with an emphasis on light-responsive domains and allosteric control mechanisms.

The scientist will contribute to the design, expression, and screening of engineered protein variants, building scalable assay systems and workflows to evaluate activity and responsiveness across diverse conditions. This role is ideal for a hands-on experimentalist excited to work at the intersection of protein engineering, high-throughput screening, and platform development in a fast-paced, highly collaborative startup environment.

Key Responsibilities

• Design, express, and characterize engineered protein variants incorporating stimulus-responsive domains (e.g., light, voltage, temperature).

• Execute high-throughput protein expression workflows in bacterial and/or cell-free systems to support rapid screening of variant libraries.

• Develop and optimize functional assays to measure protein activity and responsiveness to external stimuli using plate-based and automated platforms.

• Build and refine scalable experimental workflows integrating protein production, screening, and data capture.

• Analyze and interpret experimental data to generate actionable insights and inform iterative design cycles.

• Collaborate closely with cross-functional teams, including Assay Development and Machine Learning, to integrate experimental outputs into broader platform efforts.

• Document experimental procedures and results rigorously; communicate findings clearly to internal stakeholders.

• Contribute to the growth of the Protein Science function, including lab infrastructure, best practices, and experimental strategy.

Qualifications

• Ph.D. in Biochemistry, Protein Engineering, Molecular Biology, Synthetic Biology, or a related discipline.

• 0–3 years of relevant experience in industry, biotechnology, or startup environments.

• Demonstrated expertise in protein engineering, including design and characterization of engineered or chimeric proteins.

• Hands-on experience with stimulus-responsive or allosterically regulated protein systems, particularly light-responsive domains.

• Proven experience developing and executing high-throughput protein expression and screening workflows.

• Strong background in assay development for protein activity and function.

• Experience with bacterial expression systems; familiarity with cell-free and/or cell-based systems is a plus.

• Ability to analyze and interpret complex biological datasets.

• Excellent organizational, communication, and problem-solving skills, with the ability to thrive in a dynamic, fast-paced environment.

Who You Are

Innovative Pioneer: You are excited to push the boundaries of protein engineering and develop novel approaches to controlling protein function.

Collaborative Contributor: You work effectively across disciplines, partnering closely with scientists in assay development, machine learning, and beyond.

Inventive Problem Solver: You proactively identify challenges and rapidly develop creative, practical solutions.

Mission-Driven Individual: You are motivated by the opportunity to fundamentally transform how biomolecules are designed and synthesized, with meaningful impact on human health and biotechnology.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, generating billions in value. Flagship companies are known for addressing humanity’s most pressing challenges and advancing innovative solutions with global impact.

We are an equal opportunity employer and are dedicated to building diverse and inclusive teams. If you have some of the qualifications listed above but not all, we still encourage you to apply. We value passion, experience in many forms, and unique backgrounds.

Come pioneer the future with us.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $100,000 - $143,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL116 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL116's good faith estimate as of the date of publication and may be modified in the future.