Patent ID: 7139665

Claim:
A method for designing amino acid sequence change(s) in an aminoacyl tRNA synthetase (AARS), wherein said change could enable said AARS to incorporate an amino acid analog of a natural amino acid substrate of said AARS into a protein in vivo, comprising: (a) providing a three-dimensional structure model of said AARS with said natural amino acid substrate; (b) providing a rotamer library for said amino acid analog; (c) identifying, based on said three-dimensional structure model, anchor residues of said AARS interacting with the backbone of said natural amino acid substrate; (d) identifying, in the binding pocket of said AARS, amino acid position(s) involved in interaction with the side chain of said natural amino acid substrate as candidate variable residue position(s); (e) providing an AARS-analog backbone structure by substituting said natural amino acid substrate with said amino acid analog in said three-dimensional structure model, wherein the geometric orientation of the backbone of said amino acid analog is specified by the orientation of the backbone of said natural amino acid substrate, and wherein the backbone of said amino acid analog and all anchor residues identified in (c) are fixed in identity and rotameric conformation in relation to said AARS-analog backbone structure; (f) providing a group of potential rotamers for each of the candidate variable residue position(s) identified in (d), wherein the group of potential rotamers for at least one of said variable residue position(s) has a rotamer selected from each of at least two different amino acid side chains; and (g) analyzing the interaction of each of the rotamers for said amino acid analog and rotamers for said variable residue position(s) with all or part of the remainder of said AARS-analog backbone structure to generate a set of optimized protein sequences; wherein steps (b)–(d) are carried out in any order, and wherein said set of optimized protein sequences contain said amino acid sequence change(s) in the AARS, which change could enable the AARS to incorporate the amino acid analog into the protein in vivo.