ZipRecruiter

Log In

1

Protein Engineer Jobs in Chicago, IL (NOW HIRING)

EVOZYNE INC

Applied AI Research Fellow

Chicago, IL · On-site

We are transforming how the industry approaches protein engineering. Our platform, EvoGen, is both generative and predictive. Rather than focusing on structure alone, we build models that learn how ...

fairlife LLC

Senior Data Engineer

Chicago, IL · On-site

$109K - $148K/yr

Core Power High Protein Shakes, a sports nutrition drink to support post-workout recovery; fairlife ... The Sr. Data Engineer will play a key role in deliveringfairlife'sambition of building a best-in ...

fairlife

Senior Data Engineer

Chicago, IL · On-site

$109K - $148K/yr

Core Power ® High Protein Shakes, a sports nutrition drink to support post-workout recovery ... The Sr. Data Engineer will play a key role in delivering fairlife's ambition of building a best-in ...

fairlife

Senior Data Engineer

Chicago, IL · On-site

$109K - $148K/yr

Core Power ® High Protein Shakes, a sports nutrition drink to support post-workout recovery ... The Sr. Data Engineer will play a key role in delivering fairlife's ambition of building a best-in ...

next page

Showing results 1-20

All JobsProtein Engineer JobsProtein Engineer Jobs in Chicago, IL

Protein Engineer information

See Chicago, IL salary details

$24.6K

$94.5K

$171.4K

How much do protein engineer jobs pay per year?

As of Aug 10, 2026, the average yearly pay for protein engineer in Chicago, IL is $94,451.00, according to ZipRecruiter salary data. Most workers in this role earn between $64,664.00 and $119,064.00 per year, depending on experience, location, and employer.

What are the key skills and qualifications needed to thrive as a protein engineer?

To thrive as a Protein Engineer, you need expertise in molecular biology, biochemistry, and protein structure-function analysis, often supported by an advanced degree in a relevant scientific field. Familiarity with tools such as protein modeling software, high-throughput screening systems, and genetic engineering techniques is commonly required. Attention to detail, strong analytical thinking, and effective teamwork are valuable soft skills in this role. These abilities are crucial for designing, optimizing, and testing proteins with desired properties, ensuring impactful contributions to research or product development.

What does a protein engineer do?

A Protein Engineer designs and modifies proteins for specific functions in fields like medicine, biotechnology, and bioengineering. They use computational modeling, molecular biology techniques, and biochemical assays to improve protein stability, activity, or binding properties. Their work is crucial for developing new therapeutics, enzymes, and biomaterials for various industries.

What are the most commonly searched types of Protein Engineer jobs in Chicago, IL? The most popular types of Protein Engineer jobs in Chicago, IL are:
What are popular job titles related to Protein Engineer jobs in Chicago, IL? For Protein Engineer jobs in Chicago, IL, the most frequently searched job titles are:
What job categories do people searching Protein Engineer jobs in Chicago, IL look for? The top searched job categories for Protein Engineer jobs in Chicago, IL are:
Protein Engineer jobs near you
Infographic showing various Protein Engineer job openings in Chicago, IL as of August 2026, with employment types broken down into 92% Full Time, 2% Part Time, and 6% Contract. Highlights an 87% Physical, 4% Hybrid, and 9% Remote job distribution, with an average salary of $94,451 per year, or $45.4 per hour.

Scientist / Senior Scientist, Protein Chemistry

The Fynder Group

Chicago, IL

$94K - $128K/yr

Full-time

Re-posted 13 days ago

Job description

We are seeking an innovative and driven Protein Chemist/Biochemist (Scientist / Senior Scientist) to join our dynamic R&D team. In this role, you will play a critical part in characterization of wild-type and genetically engineered fungal strains.  You will work at the intersection of protein biochemistry, proteomics, and molecular biology, with a focus on optimizing protein production and implementing different protein characterization methods, utilizing data-driven insights to solve complex technical challenges and accelerate relevant projects within the Fynder group. The ideal candidate thrives in a fast-paced, collaborative startup environment and possesses deep expertise in protein purification, advanced biophysical and bioanalytical characterization, and functional assay development.
Responsibilities

  • Protein Purification & Isolation: design, develop and optimize protein purification of native and heterologously expressed proteins from complex biological matrices. Execute purification workflows utilizing automated chromatography systems (e.g., affinity, ion exchange, size exclusion, hydrophobic interaction, ÄKTA FPLC chromatography platforms).

  • Advanced Characterization & Proteomics: Characterize the secretome and proteome of wild-type, engineered, and improved strains using biochemical, biophysical and analytical techniques, such as SDS-PAGE, western blotting, ELISA based assays, UV/vis spectroscopy, mass spectrometry, Bio-Layer Interferometry, flow cytometry, etc., to evaluate purity, structural integrity, post-translational modifications such as glycosylation, inter- and intra-molecular bonding, potency, stability, developability and functional activity.

  • Method & Assay Development: Independently design, develop, and optimize novel analytical methods and functional assays to determine structural and biophysical and biochemical attributes (e.g., molecular weight, aggregation, and stability).

  • High-Throughput Screening: Establish and execute high-throughput (HTP) micro-scale purification and screening workflows to rapidly evaluate large fungal variant libraries.

  • Cross-Functional Collaboration: Work within interdisciplinary teams and partner closely with molecular biology, strain engineering and fermentation teams to improve protein expression, yield, and product quality. 

  • Genotype-to-Phenotype Discovery: Partner closely with the molecular biology team to uncover connections between genotypes and key phenotypes of filamentous fungi, actively contributing to strain engineering and improvement strategies.

  • Execution & Data Analysis: Conduct hands-on, bench-top laboratory work, designing and troubleshooting independently, analyzing and interpreting data sets, and utilizing specialized software (e.g., Proteome Discoverer, UNIFI, PyMOL, or Prism) to deliver data-driven solutions to technical roadblocks.

  • Reporting & Presentation: Analyze and summarize results, maintaining meticulous experimental documentation, preparing SOPs, technical reports and presentations, and present scientific outcomes clearly and concisely to stakeholders.

  • Planning and Integration: Contribute to project planning, timelines and cross-functional scientific discussions.

Position Requirements & Qualifications
  • MS or Ph.D in Protein Chemistry, Biochemistry, or related field 
  • 2+ years of industrial experience
Technical Competencies: 

  • Deep knowledge of protein structure-function properties, advanced protein purification principles, structural characterization and understanding of protein chemistry, protein folding, aggregation and stability.

  • Experience with biologics characterization assays, including binding, blocking, competitive binding, functional activity using biochemical and cellular systems, etc

  • Proven hands-on expertise characterizing post-translational modifications, such as protein glycosylation profiles.

  • Experience with analytical instrumentation, including automated chromatography systems (FPLC/ÄKTA) and mass spectrometry (LC-MS/MS or MALDI-TOF), and analytical method development.

  • Experience working with microbial hosts and strain improvement programs focused on protein expression, metabolic engineering, or related applied research targets.

  • Familiarity with foundational computational software tools for structural visualization, data analytics, or proteomics pipelines (e.g., PyMOL, JMP, Prism, or equivalent).

Core Soft Skills & Attributes: 

  • Communication: Exceptional written, verbal, and interpersonal communication abilities required for cross-team coordination.

  • Teamwork & Mindset: An innovative mindset, a can-do attitude, and an intrinsic enthusiasm for engineering novel biological platforms for protein production.

  • Adaptability: Highly organized, detail-oriented, and perfectly comfortable navigating the fast-paced, shifting landscape of an early-to-mid stage biotech startup.

Preferred Qualifications:

  • Direct experience in quantifying and thoroughly structurally characterizing heterologously produced complex proteins.

  • Specific, hands-on scientific background working directly with filamentous fungi expression platforms.

  • Experience developing micro-scale high-throughput protein screening workflows or leveraging automated liquid handling systems.

  • Familiarity or basic working knowledge of industrial downstream processing (DSP) operations or engineering scale-up principles.

We may use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications, analyzing resumes, or assessing responses and identifying potential inconsistencies or verification signals in application materials based on available information. These tools assist our recruitment team but do not replace human judgment. Final hiring decisions are ultimately made by humans. If you would like more information about how your data is processed, please contact us.