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Protein Engineering Jobs (NOW HIRING)

SystImmune, Inc

Director, Protein Engineering

Redmond, WA · On-site

$180K - $240K/yr

SystImmune is seeking a Director of Protein Engineering to lead the FUSE team. This is a hands-on scientific leadership role that combines team management, platform ownership, and program-level ...

Systimmune

Director, Protein Engineering

Redmond, WA · On-site

$180K - $240K/yr

SystImmune is seeking a Director of Protein Engineering to lead the FUSE team. This is a hands-on scientific leadership role that combines team management, platform ownership, and program-level ...

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Protein Engineering information

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$32.5K

$63K

$95.5K

How much do protein engineering jobs pay per year?

As of Jul 21, 2026, the average yearly pay for protein engineering in the United States is $62,977.00, according to ZipRecruiter salary data. Most workers in this role earn between $47,000.00 and $72,000.00 per year, depending on experience, location, and employer.

What is a Protein Engineering job?

A Protein Engineering job involves designing, modifying, and optimizing proteins for specific applications in medicine, biotechnology, and industry. Scientists in this field use computational modeling, directed evolution, and genetic engineering to enhance protein functions. Roles may include developing enzymes for drug production, improving therapeutic proteins, or creating biomaterials. This work often requires expertise in molecular biology, biochemistry, and structural biology.

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

To thrive in Protein Engineering, you need a solid background in biochemistry, molecular biology, and genetic engineering, typically supported by a relevant advanced degree. Experience with laboratory techniques such as PCR, site-directed mutagenesis, protein expression/purification, and analytical tools like mass spectrometry or chromatography is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills help you stand out in this role. These competencies are crucial for designing novel proteins, collaborating in multidisciplinary teams, and ensuring successful project outcomes in biotech or pharmaceutical environments.

What are typical daily responsibilities for someone working in Protein Engineering?

A typical day in Protein Engineering involves designing and conducting experiments to modify protein sequences, expressing and purifying proteins, and analyzing their structure or function using techniques like chromatography and spectroscopy. You will often document your results, troubleshoot unexpected findings, and present data to colleagues or project teams. Collaboration with scientists in molecular biology, bioinformatics, and structural biology is common to ensure robust experimental design and data interpretation. The role may also include literature reviews to stay updated with the latest research and participating in team meetings to plan next steps or project timelines.

More about Protein Engineering jobs
What cities are hiring for Protein Engineering jobs? Cities with the most Protein Engineering job openings:
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Protein Engineering jobs near you
Infographic showing various Protein Engineering job openings in the United States as of July 2026, with employment types broken down into 94% Full Time, 4% Part Time, and 2% Contract. Highlights an 87% Physical, 3% Hybrid, and 10% Remote job distribution, with an average salary of $62,977 per year, or $30.3 per hour.

Scientist - Protein Engineering

Merge Labs

San Francisco, CA • On-site

$120K - $215K/yr

Full-time

Posted 29 days ago

Job description

Merge Labs is a frontier research lab with the mission of bridging biological and artificial intelligence to maximize human ability, agency and experience. We're pursuing this goal by developingfundamentally new approaches to brain-computer interfaces that interact with the brain at high bandwidth, integrate with advanced AI, and are ultimately safe and accessible for anyone to use.
About the team:
Our Bio team designs, builds, and characterizes the biotechnologies that form the foundation of next-generation brain-computer interfaces. We combine molecular engineering, synthetic biology, neuroscience, and advanced physical methods such as ultrasound to establish less invasive, high-bandwidth connections with neurons. The Bio team develops our core molecular technologies, validates their performance in vitro and in vivo, and demonstrates their advanced capabilities in animal models. We build custom experimental setups and pipelines and collaborate closely with engineers and data scientists. We work across disciplines to come up with creative ideas and solve some of the most challenging problems in biotechnology.
About the role
As a Protein Engineer in a BCI company, you will design, build, and optimize the key biomolecules that translate between the languages of cells and machines - turning neuronal activity at the molecular scale into interpretable signals and enabling precise modulation.
You'll work with unconventional proteins - from atypical biosensors and membrane proteins to complex, multi-component assemblies - and use your biophysical insights, high-throughput experimental methods, and close collaboration with our computational team to push the boundaries of what these molecules can do. Your work will set the molecular foundation for next-generation brain-computer interfaces.
In this role, you will:
  • Design and implement diverse protein engineering strategies - from rational design and computational modeling to directed evolution and combinatorial library - to build dynamic molecular systems with desirable properties.
  • Build and characterize protein variants at high throughput to test and iterate hypotheses rapidly and rigorously: implement and optimize scalable workflows from library generation, expression in various in vitro systems, to standard and custom assays.
  • Collaborate with our computational team to establish models linking sequences and structures to function, guide the generation of future constructs, and augment our intuition.
  • Explore the mechanisms behind complex biomolecules and translate that understanding into creative, out-of-the-box designswith the support of our biochemists, structural biologists, and computational teams.
  • Develop novel screening and validation methods to further accelerate the entire design-build-iterate loop and ensure a smooth transition toward in vivo applications.

You might thrive in this role if you:
  • Have a PhD in Bioengineering, Biophysics, Biochemistry, or a related field, or have equivalent experience leading research projects end-to-end.
  • Are proficient in library construction, protein expression in mammalian cells, and standard characterization.
  • Are comfortable using computational approaches for protein engineering and understand the fundamental principles involved.
  • Think mechanistically: you are motivated by understanding how things work, not just that they work.
  • Enjoy working with dynamic, multi-state proteins and/or complex protein assemblies.
  • Feel joy in collaboration and communicate naturally with experts across disciplines.
  • Are energized by 0->1 innovations and always on the lookout for creative ways to do better.
  • Want to be part of a fast-paced team working on frontier scientific and technical problems.

Nice to have
  • Experience with engineering multi-state proteins, membrane proteins, and multi-component protein assemblies.
  • Experience with protein expression in primary neurons, brain organoids, or brain tissues.
  • Experience with large-scale screening.
  • Experience with creative assay development.
  • Familiarity with machine learning or data-driven design approaches.

If you're excited about this role but don't meet every qualification, please apply. As we build, we're hiring for complementary strengths to form a high-impact team.
For more information about hiring at Merge, please visit our Hiring FAQ
Merge Labs does not discriminate on the basis of race, color, religion, national origin, age, sex, sexual orientation, gender, gender identity, gender expression, marital status, physical or mental disability, medical condition, genetic information, family status, ancestry, citizenship, U.S. military (state and federal) and veteran status, or any other legally protected status. It is our intention that all applicants be given equal opportunity and that selection decisions are based on job related factors. We are an equal opportunity employer.
Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.
We are committed to providing reasonable accommodations to applicants with disabilities, and requests can be made by emailing accommodations@merge.io.

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