Patent ID: 8855936

Claim:
A method for identifying a substitute amino acid at each of one or more amino acid residues of a reference protein or reference oligopeptide that increases the stability of the reference protein or reference oligopeptide in a custom computing apparatus, wherein the custom computing apparatus comprises at least one processor and a memory, and wherein the method comprises: receiving, in the memory, a plurality of parameters comprising an intrinsic pK a of each of the amino acids in the reference protein or the reference oligopeptide, a charge of each of the amino acids in the reference protein or the reference oligopeptide, distances between the amino acids in the reference protein or the reference oligopeptide, a dielectric constant for self-energy (∈′ p ) which is in a range of 35 to 40 and a dielectric constant for charge-charge interaction (∈′ eff ) which is in a range of 35 to 40; accessing, by the at least one processor, the plurality of parameters; calculating, by the at least one processor, a gradient of free energy over charges of a plurality of amino acid residues of a protein or oligopeptide wherein the protein is or oligopeptide initially the reference protein or oligopeptide respectively, and wherein the gradient of free energy over the charges is determined as: ∂ Δ ⁢ ⁢ G fold elec ∂ Q i ≈ - 2.3 ⁢ RT ⁡ ( pK i , int p ⁡ ( ɛ p ′ ) - pK i , w w ) + 332 ⁢ ∑ i ≠ j ⁢ ⁢ Q j ⁡ [ 1 r ij ⁡ ( ɛ eff ′ ) ij ] , wherein α is a scaling factor, (∈′ p ) is a dielectric constant for self-energy, (∈′ eff ) is a dielectric constant for charge-charge interaction, Q i and Q j are the charges of the i th and j th residues respectively, pK i,w w is the pK a of the i th residue in water, pK i,int p (∈′ p ) is the intrinsic pK a of the i th residue in its given protein state when all other residues are neutral, the notation ∈′ p indicating that this pKa is a function of ∈′ p ), j is the number of amino acid residues of the protein or oligopeptide, and r ij is the distance between residues i and j; determining, from the gradient, a change in charge (ΔQ,) of the protein that increases the stability of the reference protein or reference oligopeptide, wherein the plurality of amino acid residues of the protein or oligopeptide that increases the stability of the reference protein or oligopeptide comprise one or more substitute amino acids as compared to the reference protein or reference oligopeptide, respectively; repeating the determining the change in charge of the protein that increases the stability of the reference protein or reference oligopeptide to identify substitutions that further stabilize the protein or oligopeptide; and identifying a substitute amino acid at each of one or more amino acid residues of the reference protein or reference oligopeptide that increases the stability by changing the ΔQ i .