Flagship Pioneering

Senior Scientist, Protein Engineering

Flagship Pioneering$126K — $181K *
Pharmaceuticals & Biotech
5 - 7 years of experience
Job Overview by Ladders

Qualifications

  • PhD in molecular biology, protein engineering, biochemistry, or a related field with 5+ years of industry or postdoctoral experience.
  • Deep practical expertise in molecular biology, particularly in construct design and troubleshooting.
  • Proven skills in membrane protein design across various architectures and topologies.
  • Experience in applying known methods and creating novel constructs.
  • Proficient in plasmid engineering and molecular cloning at a library scale.
  • Hands-on knowledge of lentiviral transduction and mammalian cell culture practices.
  • Strong initiative, leadership, organizational skills, and effective communication capabilities.

Responsibilities

  • Design and optimize membrane protein constructs leveraging existing methods and creating novel designs.
  • Troubleshoot design and expression issues using published methodologies and first-principles.
  • Conduct molecular biology and plasmid engineering, ensuring quality control and sequencing.
  • Run assays to evaluate construct performance and streamline design-build-test cycles.
  • Enhance workflows and establish best practices for experimental documentation.
  • Collaborate with screening and translational teams to prepare constructs for selection and analysis.
  • Translate experimental findings into actionable insights and contribute to scientific strategy.

Benefits

  • Opportunity to shape the scientific foundation of a novel platform company.
  • Custom role designed for professional growth and impactful contributions.
  • Weekly lunches, monthly social events, and access to a community lunchroom with snacks and coffee.
Full Job Description
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.

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.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

Similar Jobs

More Jobs at Flagship Pioneering

More Pharmaceuticals & Biotech Jobs

Find similar Senior Scientist, Protein Engineering jobs: