Senior Scientist 1, Protein Engineering

Who We Are: At Bio Marin, we are driven by a singular mission: to transform lives through bold science. As a global biotechnology leader, we specialize in translating genetic discoveries into groundbreaking therapies that redefine the future of human health. Since 1997, we’ve leveraged our deep expertise in genetics and molecular biology to develop innovative treatments for rare and serious genetic conditions. Our approach is rooted in scientific rigor, a passion for solving complex problems, and a commitment to delivering meaningful advances for patients with unmet medical needs. We bring together top-tier talent—scientists, innovators, and problem-solvers—and foster a collaborative environment where bold ideas thrive. This has enabled us to build a diverse pipeline of commercial, clinical, and preclinical candidates with the potential to be first-in-class or best-in-class therapies. About Worldwide Research and Development (WWRD) WWRD spans the full spectrum of drug development—from early discovery through post-market clinical research. Our integrated teams work across disciplines to develop transformative therapies that make a real difference in the lives of patients with genetic diseases. Position: Senior Scientist 1, Protein Engineering

Location: San Rafael, CA

Department: Research & Early Development

Reports To: Director, Therapeutics Process Development and Characterization Research and Early Development is seeking a Senior Scientist in Protein Engineering to join our Therapeutic Modality group. This is an exciting opportunity for a creative and technically rigorous scientist who thrives at the intersection of synthetic biology, molecular design, and translational research. In this role, you will lead the design and development of next-generation therapeutic proteins—including enzymes, antibodies, and multi-specific modalities—for genetic diseases with high unmet need. Building on Bio Marin’s legacy of five FDA-approved protein-based therapies, your work will help shape the future of our biologics innovation and directly impact the development of transformative medicines.

Key Responsibilities: Protein Engineering & Innovation: Design and optimize therapeutic proteins using rational and computational approaches to enhance stability, solubility, and reduce immunogenicity. Construct Design & Molecular Biology: Collaborate with molecular biology teams to design expression constructs and troubleshoot cloning strategies. Computational & Structural Modeling: Use tools like PyMOL, Alpha Fold, Rosetta, and FoldX to guide design and predict structure-function relationships. Protein Expression & Characterization: Analyze expression, QC, and target engagement data to refine candidates and inform design iterations. Cross-Functional Collaboration: Serve as the protein engineering lead on cross-functional teams, aligning strategies with discovery and development goals. Scientific Innovation & External Engagement: Stay current with emerging technologies and engage with academic and industry collaborators. Data Analysis & Communication: Interpret complex datasets, generate reports, and present findings to internal and external stakeholders. Scientific Leadership & Mentorship: Contribute to publications, patents, and conferences; mentor junior scientists and foster a culture of innovation.

Education: Ph. D. in Protein Engineering, Structural Biology, Biochemistry, or related field Exceptional M.S. or B.S. candidates will also be considered

Experience: Ph. D. with 6+ years, M.S. with 10+ years, or B.S. with 12+ years of relevant industry experience Proven track record of independently leading protein engineering campaigns

Core Competencies: Strong problem-solving and critical thinking Excellent communication skills Effective leadership in cross-functional, matrixed environments High attention to detail and scientific rigor Self-motivated and collaborative Passion for innovation and scientific excellence

Preferred Qualifications: Experience with complex biologics (e.g., bispecific Abs, ADCs, oligomeric enzymes) Familiarity with antibody discovery platforms and display technologies Deep understanding of protein structure-function relationships Expertise in enhancing protein properties (e.g., affinity, solubility, stability) Strong publication and/or patent record Background in rare disease therapeutic development Experience with automation, high-throughput screening, or data analytics

Additional Information: This job description is intended to convey essential responsibilities and qualifications. It is not an exhaustive list of all duties or expectations.

Equal Opportunity Employer: Bio Marin is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability. Seniority level Seniority level Mid-Senior level Employment type Employment type Full-time Job function Job function Research and Science Industries Biotechnology Research and Pharmaceutical Manufacturing Referrals increase your chances of interviewing at Bio Marin Pharmaceutical Inc. by 2x Get notified about new Engineering Scientist jobs in San Rafael, CA. Oakland, CA $68,990.00-$104,230.00 2 days ago South San Francisco, CA $140,000.00-$150,000.00 4 days ago Scientist I-III/Senior/Lead - Polymer Formulation & Materials Characterization Alameda, CA $110,000.00-$160,000.00 5 days ago Scientist 1/2/Senior Scientist, Analytical Development Emeryville, CA $150,000.00-$170,000.00 1 day ago Scientist, Analytical Development (I, II, III)Scientists - Mathematicians, Neural Networking (full time, part time, consulting)Principal Scientist, Large Molecule CMC Analytical Development South San Francisco, CA $158,000.00-$206,780.00 1 day ago Scientist, Analytical Development and Quality Control Senior Scientist, Quantum Sensing (Control)San Francisco, CA $123,000.00-$190,000.00 1 month ago Brisbane, CA $166,175.00-$252,500.00 2 weeks ago Principal Research Scientist I/II, CMC Purification Development Technical Development Principal Scientist Scientist II, Analytical Development (Protein Chemistry)Senior Scientist/Principal Scientist, Biochemist and Cellular Neurobiologist South San Francisco, CA $163,000.00-$201,000.00 3 days ago Hercules, CA $80,000.00-$100,000.00 3 weeks ago South San Francisco, CA $82,500.00-$157,500.00 5 days ago Brisbane, CA $166,175.00-$252,500.00 1 week ago San Francisco, CA $136,000.00-$212,800.00 14 hours ago Principal Scientist – Biomarker Development and Translational Research Brisbane, CA $166,175.00-$252,500.00 1 week ago Scientist 1 Bioconjugation Chemistry (TEMPORARY)Principal Research Scientist I/II, CMC Purification Development South San Francisco, CA $121,000.00-$230,000.00 2 weeks ago Quantum Research Scientist, Device Team, AWS Center for Quantum Computing Senior Consultant or Principal-level Coastal Scientist/Engineer San Francisco, CA $125,000.00-$210,000.00 2 weeks ago San Francisco, CA $128,100.00-$192,200.00 5 hours ago Software Engineering Manager, Weather Platform We’re unlocking community knowledge in a new way. Experts add insights directly into each article, started with the help of AI.