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Protein Engineering Scientist Jobs (NOW HIRING)

MSD

Sr. Scientist, Generative Protein Design

Cambridge, MA · On-site

$100K - $136K/yr

Ph.D. in Biochemistry, Computational Biology, Protein Engineering, Physics, Bioengineering ... Commitment to scientific excellence and rigor. * Excellent communication and collaboration skills.

Kaigene, Inc

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Scientist (Protein Expression and Purification)

Rockville, MD · On-site

$60K - $80K/yr

We are seeking a highly motivated and experienced scientist to join our protein engineering team ... Design and execute protein engineering experiments to optimize protein function, stability and ...

Kaigene, Inc

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Scientist (Protein Expression and Purification)

Rockville, MD · On-site

$60K - $80K/yr

We are seeking a highly motivated and experienced scientist to join our protein engineering team ... Design and execute protein engineering experiments to optimize protein function, stability and ...

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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 Aug 21, 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 is a protein engineering scientist?

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.

What are the typical day-to-day responsibilities of 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 are the key skills and qualifications needed to thrive as a protein engineering scientist?

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.

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Protein Engineering Scientist jobs near you
Infographic showing various Protein Engineering Scientist job openings in the United States as of August 2026, with employment types broken down into 92% Full Time, 4% Part Time, 3% Contract, and 1% Nights. Highlights an 85% Physical, 5% Hybrid, and 10% Remote job distribution, with an average salary of $98,759 per year, or $47.5 per hour.

Scientist/Sr Scientist, Protein Engineering

Earli, Inc.

Redwood City, CA • On-site

Full-time

Re-posted 21 days ago

Job description

Earli tackles the #1 problem in the $100B cancer drug market: systemic toxicity. On-target/off-tumor effects force suboptimal dosing, reduced efficacy and sidelining some of the most potent drug classes such as cytokines. Earli's BioAI approach flips this paradigm: Drugs are produced only where needed-in the tumor, by the tumor, against the tumor. Cancer cells become their own drug factories, enabling localized immune activation, even in cold tumors.
This was enabled by three core innovations:
  1. Extrahepatic lipid nanoparticles (LNPs) that reach tumors such as lung cancer
  2. AI-designed genetic switches that activate only in malignant cells by sensing transcription factor dysregulation
  3. Local production of immune therapies (TCEs, cytokines, multispecifics) at the tumor site - "produce locally, consume locally"

Together, these technologies create a new biological control layer, allowing tumors to self-identify and trigger their own targeted immune attack-achieving specificity beyond current targeted or IO therapies.
Earli plans to enter the clinic by mid-2027 with a Phase 1/2 lung cancer trial. The company is backed by a16z, Khosla, Perceptive, Alex Gorsky, Marc Benioff, Breyer, Emerson Collective, Sands Capital and others. The SAB includes Jim Allison (Nobel Laureate, MD Anderson), Bob Langer (Co-founder Moderna, MIT), Phil Greenberg (Co-founder Juno), Amy Abernethy (frm. Principal Deputy FDA Commissioner), Bill Hait (former J&J EVP Oncology R&D), and Alan Ashworth (President UCSF Cancer Center). The leadership team brings deep gene therapy, LNP, CMC and tech experience; CEO Cyriac Roeding previously led a $250M (11x return) exit.
Who You Are
  • You share our same sense of dedication, scientific passion and entrepreneurial spirit
  • You work well in a fast-paced and extremely focused startup environment
  • You are not only smart, but clever and constantly think outside the box
  • You are able to make logical decisions in an instant when there is little time to evaluate
  • You are a natural communicator and relationship builder
  • You stay calm under high pressure and stress
  • You have the ability to multi-task in a serious way, with an extreme attention to detail
  • You become a representative of the core DNA of the company through who you are

The Position
Earli is seeking a highly motivated and scientifically rigorous Scientist/Senior Scientist to join our Therapeutics Group. This is a hands-on, bench-based role in which you will drive the design, engineering, and functional characterization of novel protein-based therapeutic candidates targeting the tumor microenvironment and the immune system's response to cancer.
You will bring deep expertise in molecular/protein design and medium-throughput mammalian protein expression/purification systems, combined with a strong immunology or immuno-oncology foundation to design, express, and functionally characterize immune agonist payloads using primary immune cells. You will work at the intersection of protein science and translational immunology, partnering closely with the broader Therapeutics and Platform teams to advance Earli's pipeline from early-stage discovery through preclinical proof-of-concept.
This position reports to the Head of Therapeutics.
Your Primary Responsibilities
Molecular/Protein Design & Engineering
  • Design novel protein therapeutics-including cytokines, immune agonists, fusion proteins, bispecific constructs (multi-domain and 2A-based), leveraging structure-function knowledge and/or computational tools to guide engineering hypotheses.
  • Engineer protein variants to optimize potency, selectivity, half-life, manufacturability, or other developability attributes relevant to DNA encoded oncology applications.
  • Identify strategies to improve candidate properties based on experimental outcomes.
  • Stay current with the scientific literature on protein therapeutics, bispecific engager biology, cytokine engineering, and relevant tumor immunology to inform design decisions.
Mammalian Protein Expression & Production
  • Develop and execute medium-throughput transient mammalian expression workflows (HEK293, CHO, or equivalent) to produce protein candidates for functional evaluation.
  • Optimize expression constructs (signal sequences, tags, codon usage, linkers) to maximize yield, potency and solubility of challenging therapeutic formats.
  • Perform His or Fc based affinity purification; characterize proteins by SDS-PAGE, SEC, ELISA, and other relevant analytical methods.
  • Characterize efficiency of mRNA transcription and protein translation and address bottlenecks.
  • Establish quality criteria to prioritize candidates for to functional assays; maintain comprehensive records of expression and purification outcomes.
In Vitro Functional Assays
  • Design, develop, and execute functional assays in relevant cancer cell lines and primary human immune cells (PBMCs, T cells, NK cells, monocytes/macrophages) to evaluate candidate activity, potency, and selectivity.
  • Utilize flow cytometry, cytokine profiling (Luminex, CBA, ELISA), proliferation, cytotoxicity, and signaling assays to characterize potential candidates.
  • Design and execute tumor microenvironment (TME)-relevant in vitro model systems, including co-culture platforms, to assess immunological mechanism of action (MoA).
  • Contribute to development of high-content or medium-throughput screening platforms for candidate triage in collaboration with the broader team.
Collaboration & Scientific Leadership
    • Contribute original scientific thinking to project strategy, experimental design, and data interpretation; present findings to internal teams and leadership clearly and compellingly.
    • Collaborate cross-functionally with Platform Biology, Delivery, and Computational teams to integrate protein therapeutics within Earli's cancer-activated gene expression system.
    • Proactively identify scientific risks and propose mitigation strategies; drive projects forward with appropriate urgency in a fast-paced startup environment.
    • Author and maintain clear experimental records, SOPs, and internal research reports; contribute to external publications and patent disclosures as appropriate.
    • Mentor junior scientists and research associates where appropriate; model a culture of intellectual rigor, curiosity, and collaboration.
Your Required Experience, Knowledge and Skill
Required
  • Ph.D. in Immunology, Biochemistry, Molecular Biology, Protein Engineering, Cancer Biology, or a closely related field with 4+ years of postdoctoral or industry experience; OR M.S./B.S. with 8+ years of directly relevant industry experience.
  • Solid molecular biology skills: multi-component gene cloning, mammalian vector design, PCR/qPCR, and standard biochemical assays (Western blot, ELISA).
  • Hands-on expertise in recombinant protein expression in mammalian systems (HEK293, CHO) including transient transfection, construct design, and small-scale purification.
  • Strong background in cellular and molecular immunology, with deep understanding of the innate and adaptive immune response in the context of cancer.
  • Experience designing and executing in vitro functional assays in cancer cell lines and primary human immune cells; proficiency in multiparameter flow cytometry.
  • Track record of generating high-quality, reproducible data and clear scientific communication in presentations and written reports.
  • Ability to integrate and collaborate into a high achieving team environment.
  • Ability to handle multiple projects simultaneously and meet aggressive project timelines.
  • Exceptional verbal communication and scientific writing.
  • Desire to continue to continue in a laboratory focused role.
Preferred
  • Industry experience in biotherapeutics discovery, particularly in oncology.
  • Experience with cytokine engineering, immunocytokines, bispecific antibodies or T cell engagers, or other immunomodulatory therapeutic formats.
  • Familiarity with tumor microenvironment biology and ex vivo TME modeling approaches.
  • Experience with high-throughput or automated expression/assay platforms.
  • Structural biology intuition (PyMOL, AlphaFold) or familiarity with computational protein design tools to inform engineering decisions.
  • Experience with viral and non-viral gene delivery methods (lentivirus, AAV, mRNA, LNP) for cell line engineering or functional studies.
  • Track record of scientific publication and/or patent contributions.

The anticipated base salary for this position is $110,000-$145,000 per year.
If interested in applying, please attach a CV or have a well-developed LinkedIn profile for us to be able to assess your background.
We look forward to hearing from you!

Apply