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Protein Engineering Scientist Jobs (NOW HIRING)

Systimmune

Director, Protein Engineering

Redmond, WA · On-site

$180K - $240K/yr

This is a hands-on scientific leadership role that combines team management, platform ownership ... Stay current on the protein engineering, display technology, and lab automation landscape; bring ...

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Protein Engineering Scientist information

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$40.5K

$98.8K

$156.5K

How much do protein engineering scientist jobs pay per year?

As of Jun 7, 2026, the average yearly pay for protein engineering scientist in the United States is $98,759.00, according to ZipRecruiter salary data. Most workers in this role earn between $78,000.00 and $116,000.00 per year, depending on experience, location, and employer.

What are the key skills and qualifications needed to thrive in the Protein Engineering Scientist position, and why are they important?

To thrive as a Protein Engineering Scientist, you need a strong background in molecular biology, biochemistry, and protein design, typically demonstrated through an advanced degree (MSc or PhD) in a life science field. Experience with techniques such as site-directed mutagenesis, protein expression and purification, and familiarity with analytical tools like HPLC, mass spectrometry, and relevant bioinformatics software is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills set top candidates apart. Mastery of these areas is crucial for efficiently designing, optimizing, and characterizing proteins that meet organizational and research goals.

What are some typical day-to-day responsibilities for a Protein Engineering Scientist?

As a Protein Engineering Scientist, your daily responsibilities often include designing and executing experiments to modify protein structures, analyzing biochemical data, and troubleshooting experimental results. You’ll regularly use both laboratory techniques and computational tools to optimize protein properties, document your findings, and present data to project teams. Collaboration is a key part of the role, so you’ll frequently interact with colleagues from molecular biology, bioinformatics, and downstream process development groups. This dynamic environment keeps the work intellectually stimulating and offers ongoing opportunities to learn from multidisciplinary teams.

What is a Protein Engineering Scientist job?

A Protein Engineering Scientist designs and optimizes proteins for specific applications using techniques like directed evolution and computational modeling. They work in biotechnology, pharmaceuticals, or academic research to develop enzymes, antibodies, or therapeutic proteins. Their role includes molecular biology, structural analysis, and laboratory experimentation to improve protein function, stability, or specificity.

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Protein Engineering Scientist jobs near you

Principal/ Senior Scientist - T Cell Engager & Multispecific Protein Engineering

PharmaEssentia U.S.A.

Bedford, MA • On-site

$150K - $200K/yr

Full-time

This job post has expired today. Applications are no longer accepted.

Job description

Principal/ Senior Scientist - T Cell Engager & Multispecific Protein Engineering
Position Overview
PharmaEssentia is a global biopharmaceutical company dedicated to developing innovative therapies for patients with unmet medical needs in oncology, hematology, and immunology. With strong capabilities in disease biology, biologics and translational science, we are expanding our research organization to drive the next generation of therapeutic breakthroughs.
The PharmaEssentia Innovation Research Center (PIRC) is seeking a highly motivated and collaborative Principal/ Senior Scientist to join our Biologics Platform team. This role will play a key role in the discovery, design, and optimization of T cell engager and multispecific protein therapeutics, advancing programs from early discovery through preclinical development.
The successful candidate will combine deep expertise in protein engineering, antibody and multispecific formats, and immuno-oncology biology with strong scientific leadership and hands-on execution. This position provides the opportunity to help shape next-generation biologics platforms and advance first-in-class or best-in-class therapeutic programs.
Key Responsibilities
  • Design, engineer, and optimize T cell engager modalities, including bispecific and multispecific antibodies and novel protein scaffolds, to improve potency, selectivity, safety profile, and developability.
  • Develop and execute protein engineering strategies to optimize affinity, stability, expression, pharmacokinetics/pharmacodynamics (PK/PD), and manufacturability.
  • Collaborate with internal teams and external partners/CROs on protein production, biophysical characterization, and cell-based functional assays.
  • Partner with biology and translational teams to evaluate T cell activation, immune synapse formation, cytokine release risk, and safety mitigation strategies
  • Provide scientific and technical leadership for biologics discovery programs, driving molecule design, screening strategies, and candidate selection.
  • Foster a culture of scientific rigor, transparency, collaboration, accountability, and inclusion within the research team.

Required Qualifications
  • PhD in Immunology, Protein Engineering, Biochemistry, Molecular Biology, or a related field, with 7+ years of relevant industry experience in biologics or protein therapeutics discovery (4+ years for Senior Scientist level).
  • Demonstrated expertise in protein and antibody engineering, including multispecific or immune-redirecting modalities (e.g., T cell engagers).
  • Strong understanding of T cell biology, immune synapse mechanisms, and CD3-based targeting strategies.
  • Experience leading or significantly contributing to biologics discovery programs from early discovery through lead optimization.
  • Track record of scientific contributions, including peer-reviewed publications, patents, or advancement of molecules into preclinical development.

Preferred Qualifications
  • Experience and knowledge in AI-driven protein foundation model for protein engineering is a plus.
  • Demonstrated experience providing project leadership in biologics discovery, including coordination of cross-functional teams and advancement of candidates toward IND-enabling studies.
  • Experience in T cell receptor (TCR) biology and engineering, including affinity tuning, specificity optimization, and/or TCR-based therapeutic modalities.
  • Experience with yeast display or other directed evolution platforms for high-throughput antibody or TCR screening.

EEO Statement:
At PharmaEssentia Innovation Research Center (PIRC), we are committed to providing an environment of mutual respect where equal employment opportunities are available to all applicants without regard to race, color, religion, sex, pregnancy (including childbirth and related medical conditions), national origin, age, physical and mental disability, marital status, sexual orientation, gender identity, gender expression, genetic information (including characteristics and testing), military and veteran status, and any other characteristic protected by applicable law. PIRC believes that diversity and inclusion among our team are critical to our success as a global company, and we seek to recruit, develop and retain the most talented people from a diverse candidate pool. PIRC does not accept unsolicited agency resumes. Staffing agencies should not send resumes to our HR team or to any PIRC employees. PIRC is not responsible for any fees related to unsolicited resumes from staffing agencies.
At PharmaEssentia, our goal is to treat as many people with cancer as possible. That means challenging the status quo with better science that leads to better lives. By joining our team, you will not only expand your own possibilities, but you will contribute to expanding options for people with cancer.
https://us.pharmaessentia.com/careers/

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