Senior Protein Engineer: Enzyme Design & HTS Leader

Atlas Data Storage, Inc

South San Francisco (CA)

On-site

USD 170,000 - 210,000

Full time

2 days ago

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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.