Sr. Scientist, Protein Engineering

Atlas Data Storage, Inc; South San Francisco (CA); On-site; USD 170,000 - 210,000; Full time

Job summary

AtlasBase, based in South San Francisco, seeks a Sr. Scientist, Protein Engineering to lead campaigns that improve enzyme activity, stability, and manufacturability within our molecular computing platform.

This role is an individual contributor, owning projects end-to-end at the bench, setting technical direction, and mentoring colleagues through collaboration with partners across biology, production, analytics, and engineering teams.

Qualifications

• Bachelor’s degree with 10+ years, Master’s 7+ years, or PhD with 3+ years of relevant industry or research experience.
• Degree in Biochemistry, Chemical Engineering, Molecular Biology, Protein Science, Biotechnology, or a related life sciences discipline.
• Hands-on experience in protein engineering and library design; High-throughput screening of protein variants; Assay development and optimization; Protein formulation and stability optimization; Protein expression and multi-step chromatographic purification
• Strong written and verbal communication skills, with the ability to present complex data clearly to both technical and cross-functional audiences.
• Proactive team-player mindset, strong attention to detail, and the ability to work independently and prioritize effectively in a fast-paced environment.
• Familiarity with laboratory safety protocols and experience maintaining rigorous scientific documentation.
• Laboratory automation and liquid handling experience applied to screening workflows.
• Proficiency in data analysis and scripting, or familiarity with machine-learning-guided protein design.
• Experience mentoring junior scientists or leading a project workstream as an individual contributor.

Responsibilities

• Design and execute protein engineering campaigns to improve enzyme activity, specificity, thermostability, expression, and manufacturability against defined project objectives.
• Design and construct mutagenesis and combinatorial libraries, selecting appropriate diversification and selection strategies for each engineering goal (e.g., site-saturation, combinatorial, error-prone PCR, or computationally guided design).
• Build and run high-throughput screening workflows, including plate-based assays, automation, and liquid handling, to evaluate large variant sets efficiently and reproducibly.
• Develop, optimize, and qualify biochemical and biophysical assays to support screening and candidate characterization; troubleshoot assay performance and drive assays from concept to routine use.
• Lead formulation optimization for engineered proteins: screen buffers, excipients, and stabilizers to maximize activity retention, solubility, and shelf life; run thermal, freeze-thaw, and accelerated stability studies; and define storage and handling conditions that meet platform and product requirements.
• Express and purify recombinant proteins using chromatography techniques (affinity, ion exchange, size exclusion, hydrophobic interaction) on ÄKTA and gravity column systems, and assess purity, identity, and quality using standard analytical methods.
• Analyze and interpret screening, characterization, and stability data; identify sequence-function and formulation-stability trends and feed them into subsequent design cycles.
• Maintain rigorous experimental documentation and adhere to SOPs and data integrity standards; contribute to protocol and SOP development as workflows mature.
• Communicate clearly in writing and verbally with cross-functional partners, present scientific findings at team meetings, and collaborate closely with molecular biology, protein production, analytical, engineering, and computational colleagues to keep projects aligned on timelines and deliverables.

Skills

Protein engineering

Library design

High-throughput screening

Protein expression & purification

Data analysis & scripting

Laboratory automation

Communication skills

Project leadership (IC)

Education

Bachelor’s degree in Biochemistry/related

Master’s degree in Biochemistry/related

PhD in relevant field

Tools

ÄKTA chromatography

Gravity column chromatography

Job description

AtlasBase is a fast-growing pioneer in Molecular Computing, bridging the gap between traditional IT and biotechnology. We are redefining global IT infrastructure by driving breakthroughs in both Molecular Compute and Molecular Data Storage. By commercializing synthetic DNA-based technologies at IT scale, AtlasBase delivers ultra-high-density, low-maintenance, and carbon-conscious solutions built for the explosive growth and value of the world's data. Leveraging nature's most durable medium, we provide a virtually permanent foundation that transforms how the world processes and secures its most critical information.

Originally spun out of Twist Bioscience, our team is an elite fusion of scientists, engineers, and operators dedicated to solving some of the most complex infrastructure challenges on Earth. While our work is grounded in deep science, our success depends on world-class talent across every discipline. We are seeking a Sr. Scientist, Protein Engineering who is ready to bring their expertise to a high-impact environment and help us build a brand-new category of technology.

About the role

To help drive this innovation, we are seeking a highly motivated Sr. Scientist to lead protein engineering efforts in support of our platform. The successful candidate will design and execute engineering campaigns to improve the activity, stability, and manufacturability of the enzymes at the core of our technology - from library design and high-throughput screening through purification, characterization, and formulation. This role requires deep hands-on technical expertise, sound experimental judgment, and the ability to translate screening data into the next round of design.

This is an individual contributor position with no direct reports. The successful candidate will own their projects end to end at the bench, set technical direction within their area, and influence the broader team through scientific leadership, collaboration, and informal mentorship rather than through people management.

Key Responsibilities

• Design and execute protein engineering campaigns to improve enzyme activity, specificity, thermostability, expression, and manufacturability against defined project objectives.
• Design and construct mutagenesis and combinatorial libraries, selecting appropriate diversification and selection strategies for each engineering goal (e.g., site-saturation, combinatorial, error-prone PCR, or computationally guided design).
• Build and run high-throughput screening workflows, including plate-based assays, automation, and liquid handling, to evaluate large variant sets efficiently and reproducibly.
• Develop, optimize, and qualify biochemical and biophysical assays to support screening and candidate characterization; troubleshoot assay performance and drive assays from concept to routine use.
• Lead formulation optimization for engineered proteins: screen buffers, excipients, and stabilizers to maximize activity retention, solubility, and shelf life; run thermal, freeze-thaw, and accelerated stability studies; and define storage and handling conditions that meet platform and product requirements.
• Express and purify recombinant proteins using chromatography techniques (affinity, ion exchange, size exclusion, hydrophobic interaction) on ÄKTA and gravity column systems, and assess purity, identity, and quality using standard analytical methods.
• Analyze and interpret screening, characterization, and stability data; identify sequence-function and formulation-stability trends and feed them into subsequent design cycles.
• Maintain rigorous experimental documentation and adhere to SOPs and data integrity standards; contribute to protocol and SOP development as workflows mature.
• Communicate clearly in writing and verbally with cross-functional partners, present scientific findings at team meetings, and collaborate closely with molecular biology, protein production, analytical, engineering, and computational colleagues to keep projects aligned on timelines and deliverables.

Qualifications

• Bachelor’s degree with 10+ years, Master’s degree with 7+ years, or PhD with 3+ years of relevant industry or research experience.
• Degree in Biochemistry, Chemical Engineering, Molecular Biology, Protein Science, Biotechnology, or a related life sciences discipline.
• Demonstrated hands‑on experience in: Protein engineering and library design; High-throughput screening of protein variants; Assay development and optimization; Protein formulation and stability optimization; Protein expression and multi-step chromatographic purification
• Strong written and verbal communication skills, with the ability to present complex data clearly to both technical and cross‑functional audiences.
• Proactive team‑player mindset, strong attention to detail, and the ability to work independently and prioritize effectively in a fast‑paced environment.
• Familiarity with laboratory safety protocols and experience maintaining rigorous scientific documentation.
• Laboratory automation and liquid handling experience applied to screening workflows.
• Proficiency in data analysis and scripting, or familiarity with machine‑learning‑guided protein design.
• Experience mentoring junior scientists or leading a project workstream as an individual contributor.

Physical Demands & Work Environment

• Work will be performed onsite in office and laboratory space located in South San Francisco.
• Mobility: Must be able to move about the laboratory and office environment regularly. This includes standing and walking for extended periods, often up to 6-8 hours per day.
• Manual Dexterity: Must have fine motor skills and steady hands to handle delicate instruments, operate laboratory equipment, pipette accurately, and perform repetitive benchwork with precision.
• Lifting/Carrying: Must be able to lift and carry up to 40 pounds occasionally, such as boxes of lab supplies or equipment.
• Visual Acuity: Must have sufficient visual acuity to read small print on labels, instrument displays, and computer monitors. Close vision, color vision, and the ability to adjust focus are required.
• Environmental Conditions: Frequently exposed to typical laboratory conditions, including biological samples, chemicals, and reagents. Must be able to wear appropriate personal protective equipment (PPE) such as lab coats, gloves, and safety goggles as required.