--- title: 'Principal Scientist, Structural Biology / Protein Biophysics at Flagship Pioneering, Inc.' canonical: 'https://feeny.ai/job/principal-scientist-structural-biology-protein-biophysics-flagship-pioneering-hmdq4s5y31f7' type: 'job' last_seen: '2026-11-06' --- # Principal Scientist, Structural Biology / Protein Biophysics at Flagship Pioneering, Inc. - **Company:** Flagship Pioneering, Inc. - **Location:** Cambridge, MA - **Posted:** 2026-11-04 - **Last confirmed live:** 2026-11-06 - **Apply:** https://boards.greenhouse.io/flagshippioneeringinc/jobs/8928133002?gh_jid=8928133002 ## Job description 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. 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 $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. 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. ## About Flagship Pioneering, Inc. ## Company Overview - **One-liner**: Flagship Pioneering is a life sciences venture creation firm that conceives, creates, and capitalizes breakthrough bioplatform companies in biotechnology, health, and sustainability. - **Entity Type**: Private (Venture Creation Firm) - **Headquarters**: Cambridge, Massachusetts, United States - **Founded**: 2000 - **Founders**: Noubar Afeyan (Co-Founder & CEO) ## Core Business - **Primary industry/industries**: Biotechnology Research, Life Sciences Venture Creation, Company Incubation - **Target customers**: B2B / B2G – partners with academic institutions, pharma companies, and investors; also acts as an employer for scientists, entrepreneurs, and corporate builders - **Mission or purpose statement**: “To harness the 21st century's most powerful technological forces for good to deliver a better future for all.” ## Products & Services Flagship does not sell products directly; its offerings are the companies it creates and the innovation platform it operates. - **Innovation Platform**: A systematic, institutionalized process to identify “unreasonable” scientific questions, test them rigorously, and spin out independent companies that develop therapeutics, diagnostics, agricultural technologies, and more. - **Portfolio Companies**: Over 120 companies founded, including Moderna, Generate:Biomedicines, Inari Agriculture, Tessera Therapeutics, Lila Sciences, and others. Each is a separate enterprise with its own products (e.g., mRNA vaccines, gene-editing tools, AI-driven drug discovery). ## Market Standing - **Valuation/Market Cap**: Not publicly disclosed (privately held) - **Key Metric**: Annual revenue of approximately $800 million (2025/2026 estimate) and 620 employees (+9.7% YoY growth) - **Notable Investors/Partners**: Flagship is itself an investor and partner; key collaborations include AWS (to accelerate drug discovery), Harvard Medical School, Broad Institute, and multiple top-tier biopharma companies. Portfolio company Moderna is a publicly traded giant. - **Growth Signals**: 78 active job postings (+50% quarterly), recent formation of Terion (digital agriculture infrastructure) and Serif Biomedicines (modified DNA platform), and expanded presence in Europe and Asia. ## Competitive Advantages - **Unique Model**: Combines scientific exploration, company creation, and capital investment under one roof – “a way that is largely without precedent” - **Deep Talent Pool**: Exceptional network of scientist-entrepreneurs and company builders; top hires from MIT, Harvard, Biogen, Novartis, and Pfizer - **Track Record**: Over two decades of founding transformational companies (e.g., Moderna’s COVID‑19 vaccine), demonstrating repeatable innovation - **Process-Driven**: Systematic methodology for turning “what‑if” questions into patentable bioplatforms, reducing risk compared to ad‑hoc startup creation ## Strategic Focus - **Current priorities**: Expanding AI/machine learning integration across drug discovery and life sciences (highlighted by AWS collaboration); entering preemptive health and medicine; advancing sustainable agriculture and climate solutions; growing international operations (UK, Singapore, Canada, Switzerland, Japan) - **Direction for growth**: Launching new platform companies at a steady cadence (e.g., Terion, Serif in 2026); deepening expertise in computational protein design, modified DNA, and gene editing ## Why Work Here - **Culture**: “Brave and bold organization of creative-thinkers with insurgent mindsets” – emphasis on fearlessness, mentorship, and teamwork across science and business - **Work Environment**: Headquarters in Cambridge, MA with 5 US offices; roles span research, strategy, finance, and operations; hybrid/remote flexibility varies by role - **Notable Perks**: Opportunity to work on world-changing science (e.g., COVID‑19 vaccine, gene editing) alongside top scientists and company builders; strong compensation (salary range example: Sr. Associate ~$68K, ML Engineer ~$122K; overall comp rating 3.7/5) - **Engineering/Science Culture**: Heavy investment in R&D (15% of workforce in research), cutting-edge tools (Cryo‑EM, AI/ML), and a process that encourages bold leaps ## Sources 1. [flagshippioneering.com](https://www.flagshippioneering.com/) 2. [flagshippioneering.com/about](https://www.flagshippioneering.com/about) 3. [flagshippioneering.com/join](https://www.flagshippioneering.com/join) 4. [flagshippioneering.com/join/roles](https://www.flagshippioneering.com/join/roles) 5. [linkedin.com/company/flagship-pioneering](https://www.linkedin.com/company/flagship-pioneering) ## Other roles at Flagship Pioneering, Inc. - [Senior Research Associate / Associate Scientist, Nonclinical](https://feeny.ai/job/senior-research-associate-associate-scientist-nonclinical-flagship-pioneering-kpyk97evc5j0) — Cambridge, MA - [Senior Analog/Mixed-Signal Hardware Engineer, Single-Molecule Sensing Instrumentation](https://feeny.ai/job/senior-analog-mixed-signal-hardware-engineer-single-molecule-sensing-jngdq7cygjxb) — Cambridge, MA - [FL114: Senior Research Associate, Genomics](https://feeny.ai/job/fl114-senior-research-associate-genomics-flagship-pioneering-inc-cambridge-0q5q7ej897wv) — Cambridge, MA - [FL114: Scientist, Genomics](https://feeny.ai/job/fl114-scientist-genomics-flagship-pioneering-inc-cambridge-7y7dcef63454) — Cambridge, MA - [Sr. Scientist, Protein & Cell Sciences](https://feeny.ai/job/sr-scientist-protein-cell-sciences-flagship-pioneering-inc-somerville-ma-qpeg3dfcafh3) — Somerville MA, United States - [Senior Director, Platform Experience](https://feeny.ai/job/senior-director-platform-experience-flagship-pioneering-inc-cambridge-cqx7ym4352dv) — Cambridge, MA - [Senior Scientist, LNP Formulations](https://feeny.ai/job/senior-scientist-lnp-formulations-flagship-pioneering-inc-cambridge-ztwykh5vnq98) — Cambridge, MA - [Flagship Pioneering ML Internship](https://feeny.ai/job/flagship-pioneering-ml-internship-flagship-pioneering-inc-cambridge-dsf2d8q572m7) — Cambridge, MA - [Research Associate II/Senior Research Associate, LNP Production](https://feeny.ai/job/research-associate-ii-senior-research-associate-lnp-production-flagship-bwk9zn8pyhy8) — Cambridge, MA - [Senior ML Engineer](https://feeny.ai/job/senior-ml-engineer-flagship-pioneering-inc-cambridge-aexf2nmm2e1x) — Cambridge, MA