Senior Scientist, Protein Engineering — Enzyme Design Leader

Mammoth DS, Inc; South San Francisco (CA); On-site; USD 125,000 - 150,000; Full time

Job summary

AtlasBase is seeking a Senior Scientist, Protein Engineering in South San Francisco to lead production‑level enzyme design and optimization. You will own end‑to‑end projects, drive library design, screening workflows, and formulation optimization while collaborating with molecular biology, analytical, and engineering teams.

This on‑site role requires hands‑on experimentation, data interpretation, and mentorship rather than people management.

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.

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.
• Build and run high‑throughput screening workflows, including plate‑based assays, automation, and liquid handling, to evaluate large variant sets efficiently.
• 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

Assay development

Protein expression

Data analysis

SOP compliance

Lab automation

Communication skills

Education

Bachelor’s degree

Master’s degree

PhD

Tools

AKTA chromatography

HPLC

Job description

AtlasBase is seeking a Senior Scientist, Protein Engineering in South San Francisco to lead production‑level enzyme design and optimization. You will own end‑to‑end projects, drive library design, screening workflows, and formulation optimization while collaborating with molecular biology, analytical, and engineering teams.

This on‑site role requires hands‑on experimentation, data interpretation, and mentorship rather than people management.