Protein engineering

Protein Engineering is the process of developing useful or valuable proteins by designing and producing non-natural polypeptides, usually by altering the sequence of amino acids found in nature.

We offer multiple ways to generate diversity within a protein or enzyme, which is the first step for protein engineering.

Site Saturation Mutagenesis (or SSM)

• A random mutagenesis technique used in protein engineering, in which single sequence positions are substituted with all possible amino acids. The exploration is done using the degenerate codon 'NNK' which efficiently introduces all 20 amino acids at specified positions in the protein or enzyme sequence.

• Doing SSM at every single position in a protein is a great first step when starting to engineer a protein or enzyme. It can uncover hot spots that can be combined later using 'Combi' engineering, which is explained below.

Combinatorial engineering (or Combi for short)

• Combi is a mutagenesis technique used in protein engineering, in which sets of sequence positions are substituted with defined codons.

• We can recombine a high number of mutations (usually discovered with SSM). Up to 12 positions can be simultaneously explored anywhere in the protein or enzyme sequence (with a few buildability restrictions). We're most confident in library sizes with 10,000-100,000 members.

Error-Prone PCR

• This library type is a common way to introduce multiple random mutations in a template.

DNA Shuffling

• This library type is a common way to recombine of beneficial mutations from multiple templates.

Custom bespoke libraries for AI applicaitons

• There is a revolution brewing in Protein AI. The algorithms and models need lots of training data to improve. Demand for genotype-phenotype datasets is rising. Researches working on AI methods for protein engineering sometimes prefer to have total control of sequence space. For efficiency, such libraries are usually constructed entirely from small oligonucleotides. This provides unparalleled flexibility in sequence design. We welcome the opportunity to be challenged by complex and demanding projects, especially for customers that have long lists of highly similar sequences they want us to build. This capability is currently in its beta phase, meaning it is still being tested and refined. Contact us to talk more about custom bespoke libraries!