Scientist - Protein Engineering

Overview

Alka Li Labs is developing engineered microbial systems that selectively recover valuable metals from low-grade and complex industrial streams. Our platform uses synthetic biology to program microbes to accumulate specific metal ions, enabling recovery of lithium, cobalt, rare earth elements, and other critical minerals from unconventional resources. We combine metabolic engineering, protein engineering, and bioprocess development to build scalable biological systems for mineral extraction and separation.

Alka Li Labs is seeking a Protein Engineer to lead high-throughput engineering of proteins involved in microbial metal accumulation. This is a full-time on-site role in San Francisco.

The role will focus on designing and executing large-scale protein engineering and screening campaigns to identify and optimize proteins that improve metal uptake, selectivity, and accumulation for target metals including rare earth elements and other critical minerals.

You will design variant libraries using mutagenesis and computational approaches, develop cloning strategies to generate pooled libraries, and implement high-throughput screening or selection strategies in microbial systems. This role will work closely with the broader strain engineering team to translate protein engineering insights into new microbial strains capable of improved metal uptake and selectivity.

• Design and execute high-throughput protein engineering campaigns targeting proteins involved in metal accumulation
• Generate and screen large variant libraries using mutagenesis, recombination, or AI-guided sequence design
• Develop cloning workflows and transformation strategies for efficient pooled library construction
• Design high-throughput screening or selection assays to identify improved protein variants
• Apply protein structure insights and computational tools (e.g., protein language models or structure prediction) to guide engineering strategies
• Collaborate with strain engineering teams to integrate improved protein variants into microbial hosts
• Analyze screening results and guide iterative engineering cycles
• Document experimental design, results, and workflows to support rapid iteration

• Experience with protein engineering or directed evolution
• Hands-on experience generating and screening protein variant libraries
• Strong molecular biology skills including cloning, mutagenesis, and library construction
• Experience designing high-throughput screens or selections
• Familiarity with protein structure analysis or computational protein design tools
• Experience working with microbial expression systems
• Strong experimental design, data analysis, and troubleshooting skills
• Ability to work in a fast-moving interdisciplinary environment

• Experience with large pooled library screens
• Familiarity with AI-guided protein engineering or protein language models
• Background in metabolic engineering or synthetic biology
• Experience developing screening assays linked to cellular phenotypes

• PhD in Bioengineering, Biochemistry, Molecular Biology, Chemical Engineering, or related discipline (or equivalent industry experience).