System and methods for increasing synthesized protein stability

Abstract

A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.

1 - 10 . (canceled) 
     
     
         11 . A blue fluorescent protein (BFP) variant comprising an amino acid sequence comprising one or more mutations at one more residues selected from: T18, S28, Y96, S114, V124, T127, D151, N173, and R198, relative to SEQ ID NO:1. 
     
     
         12 - 30 . (canceled) 
     
     
         31 . The BFP variant of  claim 11 , wherein the one or more mutations are substitutions. 
     
     
         32 . The BFP variant of  claim 11 , wherein the amino acid sequence comprises one or more mutations at one or more residues selected from: T18, S28, 5114, V124, T127, D151, N173, and R198, relative to SEQ ID NO: 1. 
     
     
         33 . The BFP variant of  claim 32 , wherein the one or more mutations are substitutions. 
     
     
         34 . The BFP variant of  claim 32 , wherein the one or more mutations at one or more residues are selected from: T18 W, S28A, S114V, V124T, T127P, D151G, N173T, and R198L, relative to SEQ ID NO: 1. 
     
     
         35 . The BFP variant of  claim 11 , wherein the amino acid sequence comprises substitution mutations of T18 W, S28A, S114V, V124T, T127P, D151G, N173T, and R198L, relative to SEQ ID NO: 1. 
     
     
         36 . The BFP variant of  claim 11 , wherein the amino acid sequence comprises any one of SEQ ID NOs: 2-28. 
     
     
         37 . The BFP variant of  claim 36 , wherein the amino acid sequence comprises SEQ ID NO: 23. 
     
     
         38 . The BFP variant of  claim 11 , wherein the amino acid sequence consists of any one of SEQ ID NOs: 2-28. 
     
     
         39 . The BRP variant of  claim 38 , wherein the amino acid sequence consists of SEQ ID NO: 23. 
     
     
         40 . A fusion protein, comprising an amino acid sequence comprising any one of SEQ ID NOs: 2-28. 
     
     
         41 . The fusion protein of  claim 40 , wherein the amino acid sequence comprises SEQ ID NO: 23. 
     
     
         42 . A protein fragment, comprising an amino acid sequence comprising any one of SEQ ID NOs: 2-28. 
     
     
         43 . The protein fragment of  claim 42 , wherein the amino acid sequence comprises SEQ ID NO: 23. 
     
     
         44 . A nucleic acid molecule, comprising a nucleotide sequence encoding the BFP variant of  claim 11 . 
     
     
         45 . The nucleic acid molecule of  claim 44 , wherein the molecule is a plasmid or an expression vector. 
     
     
         46 . A nucleic acid molecule, comprising a nucleotide sequence encoding the BFP variant of  claim 37 . 
     
     
         47 . The nucleic acid molecule of  claim 46 , wherein the molecule is a plasmid or an expression vector. 
     
     
         48 . A kit comprising the nucleic acid molecule of  claim 44 . 
     
     
         49 . A kit comprising the nucleic acid molecule of  claim 46 .