Principal Scientist, Structural Biology / Protein Biophysics

Flagship Pioneering • Cambridge, MA

1d

About The Position

Flagship Labs 132 (FL132), an early-stage biotechnology company addressing unmet needs for patients with amyloidogenic diseases, is seeking a Principal Scientist to help build its amyloid research platform. This is a hands-on role at the intersection of protein biophysics, chemical biology, structural biology, and drug discovery. The scientist will produce assay-grade amyloid proteins, develop and qualify aggregation and structural assays, and characterize amyloid aggregates to advance therapies for amyloidogenic diseases.

As one of the company’s early employees, the successful candidate will help set technical direction, contribute to company strategy and culture, and may help build the team over time. The role involves close collaboration with Flagship Pioneering leadership and a growing, cross-functional team. The position level will be commensurate with the candidate’s education and years of experience.

Requirements

• PhD in structural biology, chemical biology, biochemistry, biophysics, physical chemistry, or a related field.
• At least 8 years of relevant industry or postdoctoral experience.
• Hands-on experience with recombinant protein expression, purification, and quality control, ideally involving intrinsically disordered or aggregation-prone proteins.
• Deep expertise in kinetic assays of protein aggregation and familiarity with global kinetic fitting of resulting data.
• Familiarity with amyloid aggregation mechanisms, strain and seeding biology, and cofactor or inducer systems.
• Motivated team player and effective independent contributor with strong organizational, written, and verbal communication skills.
• Entrepreneurial spirit and comfort working in and contributing to a dynamic, cross-functional team environment.

Nice To Haves

• Experience with structural characterization of proteins and aggregates using mass spectrometry-based approaches, such as LiP-MS or HDX-MS.
• Familiarity with cryo-EM, atomic force microscopy (AFM), or NMR.
• Experience with statistical design of experiments (DoE) and analysis of large, time-resolved kinetic datasets.
• Experience managing contract research organizations (CROs).
• Familiarity with cell-based assays for toxicity, seeding, or clearance.
• Familiarity with laboratory automation or liquid handling to support screening throughput.
• Relevant experience in adjacent fields, such as protein biophysics, NMR, cryo-EM of non-amyloid targets, or protein aggregation in biologics development.

Responsibilities

• Contribute to scientific and technical direction with Flagship Pioneering leadership to shape company strategy.
• Help build experimental methods and train the growing team.
• Establish in-house production and quality control of assay-grade recombinant amyloid proteins, including seed-free monomer preparation and characterization.
• Design and analyze amyloid aggregation experiments, including kinetic measurements.
• Characterize amyloid aggregates using mass spectrometry, NMR, AFM, or related methods.
• Support the development of cell-based assays to evaluate amyloid toxicity, seeding, and clearance.
• Evaluate inhibitors of amyloid aggregation and translate findings from biochemical systems into cellular models.
• Scope, contract, and manage CROs and academic collaborations, establishing best practices for experiments and documentation.
• Drive key project goals, ensure rapid and accurate data turnaround, and present experimental results and insights at team meetings.

Benefits

• Healthcare coverage.
• Annual incentive program.
• Retirement benefits.
• A broad range of other benefits.
• Opportunity to lay the scientific foundation of a transformative company as an early employee.
• Custom-tailored role intended to maximize impactful contributions, professional growth, and scientific interests.
• Monthly social events.
• Community lunchroom with free snacks and coffee.
• Access to a community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.

What This Job Offers

• Job Type: Full-time
• Career Level: Principal
• Education Level: Ph.D. or professional degree