Protein Engineering Jobs in Boston, MA (NOW HIRING)

Company Summary
FL130 (Flagship Labs 130) is an early-stage biotechnology startup aiming to answer an ambitious and exciting question: What if... we could systematically identify bioactive peptides to inspire next-generation therapies and uncover novel targets? To answer this question, FL130 is pioneering a novel approach to peptide screening, and is recruiting a team of top-tier scientists to help build it. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering.
FL130 is backed by Flagship Pioneering, a company that invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since 2000, Flagship has originated and fostered the development of more than 100 scientific ventures advancing human health and sustainability, including Moderna, Generate Biomedicines, and Alltrna.
Position Summary
We are seeking a highly innovative Senior Scientist with deep molecular biology expertise and a strong track record in membrane protein engineering and surface display technology to help build a novel platform technology. This role is among the first hires, affording the opportunity to shape and influence the company's scientific direction. The successful candidate will design, build, troubleshoot, and test novel membrane protein constructs, both applying established scaffolds, structures, and methods from literature and designing and testing their own, across a range of membrane protein architectures and topologies. They will design and build the DNA and oligo libraries that power our high-throughput pooled screens and validate construct expression in mammalian cells. We're looking for a rigorous scientist who works proactively and is energized by the opportunity to help shape both FL130's scientific direction and team culture.
Key Responsibilities

• Design, engineer, and iteratively optimize novel membrane protein constructs across a range of membrane protein architectures and topologies, both leveraging established scaffolds, structures, and published methods and creating novel designs of your own.
• Troubleshoot construct design, expression, and folding for challenging membrane proteins, drawing on published structures and methods as well as first-principles design.
• Perform molecular biology and plasmid engineering at scale including construct design, ordering, and QC, as well as sequence verification.
• Design and run assays to characterize construct expression and performance, and drive design-build-test cycles.
• Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
• Partner closely with screening and translational colleagues to ensure constructs are fit for downstream pooled selection and functional readouts.
• Translate experimental data into meaningful insights and present results at team meetings; help shape scientific strategy; build and evolve the protein-engineering function.

Must-have Qualifications

• PhD. in molecular biology, protein engineering, biochemistry, bioengineering, or a similar field with 5+ years of industry or postdoctoral experience.
• Deep hands-on molecular biology expertise, including construct design and the practical experience of ordering, building, and troubleshooting many constructs in parallel.
• Demonstrated expertise in membrane protein construct design and engineering across diverse membrane protein architectures and topologies.
• A track record of both applying established methods, scaffolds, and structures and designing, building, and testing novel constructs of your own.
• Proficiency in plasmid engineering and molecular cloning, including library-scale assembly.
• Hands-on experience with lentiviral transduction and mammalian cell culture.
• Understanding of the secretory pathway, folding, and post-translational modifications.
• A motivated team-player with strong organizational skills, leadership instincts, and written and verbal communication skills who takes initiative and drives creative scientific direction proactively.

Preferred Experience

• Proficiency with computational protein design tools (e.g., Rosetta, AlphaFold-Multimer, RFdiffusion, ProteinMPNN)
• Experience with flow cytometry panel design, execution and analysis (FlowJo)
• Experience with synthetic gene / oligo-pool vendors and codon optimization
• Experience with high-throughput screening experimental design, execution and readout analysis
• Experience with electronic lab notebooks (e.g., Benchling)
• Prior experience as an early hire in a startup

What We Can Offer You

• The opportunity to lay the scientific foundation of a transformative platform company as an early employee.
• A custom-tailored role designed to maximize impactful contributions, professional growth, and your scientific interests.
• Weekly lunches, monthly social events, and a community lunchroom with free snacks and coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic, cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidate.
Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.
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.
Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.
The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. FL130 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL130's good faith estimate as of the date of publication and may be modified in the future.
Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.