Synthetic binding proteins
AssigneeNew England Biolabs, Inc.
InventorRichard D. Morgan
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Abstract
Methods and compositions are provided for creating a binding protein that recognizes a rationally chosen recognition sequence in which a first amino acid has been substituted for a second amino acid using site-directed mutagenesis of a member protein of a set of proteins at an identified position or positions correlated with recognition of a chosen specified target module in the recognition sequence. A system is provided for automating the storage and manipulation of the correlations between positions and types of amino acid residues in the binding protein with specific modules at specified positions in the target recognition sequence and for designing and creating proteins with novel specificities.
Claims3
A system comprising:
- a memory for storing
- instructions and a computer programmed to execute the instructions stored in memory, such that the computer is programmed to perform the steps of:
- (a) using an initial restriction endonuclease or methyltransferase to query a database in a BLAST search, thereby creating a set of binding proteins wherein each binding protein has a defined amino acid sequence, the amino acid sequences sharing an expectation value (E) of less than e-20 for sequences of more than 200 amino acids or less than e-10 for sequences of less than 200 amino acids;
- the binding proteins binding to specific target recognition sequences in a substrate;
- (b) aligning the target recognition sequences recognized by the binding proteins in the set;
- (c) aligning the amino acid sequences of the binding proteins of the set;
- and
- (d) identifying correlations between single nucleotides the aligned recognition sequences and one or more position-specific amino acids in the aligned amino acid sequences of the binding proteins.
Dependencies are inferred from the claim text.