Principal Scientist, Structural Biology / Protein Biophysics

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 163,000 - 215,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Other benefits

Job summary

Flagship Pioneering seeks a Principal Scientist to build an amyloid research platform from the ground up in Cambridge, MA. This hands-on role spans protein biophysics, chemical biology, structural biology and drug discovery, producing assay-grade amyloid proteins and qualifying rigorous assays.

The candidate will lead experimental strategy, train a team, coordinate CROs, and translate data into actionable insights for advancing therapies in amyloid diseases.

Qualifications

• PhD with 8+ years of experience in structural biology, biophysics, or related field.
• Hands-on recombinant protein expression, purification and QC with aggregation-prone proteins.
• Experience with kinetic assays and global kinetic-fitting of data.
• Familiarity with amyloid aggregation mechanisms and seeding biology.

Responsibilities

• Contribute to scientific and technical direction with leadership.
• Establish in-house production and QC of recombinant amyloid proteins.
• Design and analyze amyloid aggregation experiments and kinetics.
• Characterize amyloid aggregates via MS, NMR, AFM or related methods.
• Support cell-based assays for toxicity, seeding and clearance.
• Evaluate inhibitors and translate findings to cellular models.
• Manage CROs and academic collaborations with robust documentation.
• Drive project goals and present insights at team meetings.

Education

PhD in structural biology, chemical biology, biochemistry, biophysics, physical chemistry, or related field

Tools

NMR

Mass spectrometry

Cryo-EM

AFM

Protein expression

Protein purification

Job description

Principal Scientist, Structural Biology / Protein Biophysics

Cambridge, MA USA

Company Summary

Flagship Labs 132 (FL132) is an early-stage biotechnology company founded to address unmet need for patients with amyloidogenic diseases. 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. This is a hands‑on role with significant responsibility for a scientist who is excited to set technical direction from day one and, over time, help build the team.

FL132 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 motivated, highly collaborative, and technically versatile Principal Scientist to help build FL132’s amyloid research platform from the ground up. This is a hands‑on role at the interface of protein biophysics, chemical biology, structural biology, and drug discovery: producing assay‑grade amyloid proteins, developing and qualifying rigorous aggregation and structural assays, and characterizing amyloid aggregates to advance therapies for amyloidogenic diseases. The successful candidate will have a strong track record of scientific and technical innovation, deep quantitative rigor, the drive to set technical direction from day one, and build company culture.

Key Responsibilities:

• Contribute to scientific and technical direction in collaboration with FSP leadership to shape company strategy. We are looking for someone who thinks critically and wants to lead the efforts to 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 measuring amyloid aggregation.
• Characterization of amyloid aggregates via mass spectrometry, NMR, AFM, or related methods.
• Support the build of cell‑based assays for evaluating 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 by establishing best experimental and documentation practices.
• Drive key project goals, ensure rapid, accurate turnaround of data and translate experimental results into insights presented at team meetings.

Required Qualifications

• PhD. in structural biology, chemical biology, biochemistry, biophysics, physical chemistry, or a related field, with 8+ years of relevant industry or postdoctoral experience.
• Hands‑on recombinant protein expression, purification, and QC ideally with intrinsically disordered or aggregation‑prone proteins.
• Deep expertise with kinetic assays of protein aggregation, familiarity with global kinetic‑fitting of resulting data.
• Familiarity with amyloid aggregation mechanisms and strain/seeding biology, and with cofactor/inducer systems.
• Motivated team‑player and effective independent contributor with strong organizational and written/verbal communication skills.

Preferred Qualifications:

• Experience with structural characterization of proteins and aggregates using mass spectrometry‑based approaches (e.g., LiP-MS, HDX-MS). Familiarity with cryo‑EM , atomic force microscopy (AFM) or NMR is a plus.
• Experience with statistical design of experiments (DoE) and the analysis of large, time‑resolved kinetic datasets.
• Experience managing contract research organizations (CROs).
• Familiarity with cell‑based assays (toxicity, seeding, clearance) and laboratory automation/liquid handling to support screening throughput.

If you have some of the experience listed but not all, please apply anyway. We welcome candidates from adjacent backgrounds, such as protein biophysics, NMR, cryo‑EM of non‑amyloid targets, or protein aggregation in biologics development, who are energized by applying their skills to a new problem.

What we can offer you:

• Opportunity to lay the scientific foundation of a transformative company as an early employee.
• Custom‑tailored role to maximize impactful contributions, professional growth, and scientific interests.
• Monthly social events, and community lunchroom with free snacks, 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 and cross‑functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

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.

The salary range for this role is $163,000 - $214,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL132 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL132's good faith estimate as of the date of publication and may be modified in the future.