Compositions and methods for protein design
First Claim
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1. A method for producing a protein having a desired characteristic comprising vi) applying an algorithm to a protein scaffold to generate a plurality of possible variants;
- vii) screening the plurality of variants in silico to produce a rank ordered list of variants;
viii) generating nucleic acid molecules having predefined sequences that encode at least 10 of the variants wherein the nucleic acid molecules are generated by a method comprising;
a) providing a pool of oligonucleotides comprising partially overlapping sequences that define the sequence of each of said nucleic acid molecules that encode said variants;
b) incubating said pool of oligonucleotides under hybridization conditions and at least one of the following conditions;
(i) ligation conditions, (2) chain extension conditions, or (iii) chain extension and ligation conditions, thereby forming nucleic acid constructs; and
c) separating constructs having said predefined sequences from constructs not having said predefined sequences, thereby forming the nucleic acid molecules that encode said variants; and
ix) causing expression of said nucleic acid molecules to produce said protein variants; and
x) screening the variants to identify variants having the desired characteristic.
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Abstract
In certain aspects the present invention provides methods and compositions related to rational protein design.
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Citations
20 Claims
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1. A method for producing a protein having a desired characteristic comprising vi) applying an algorithm to a protein scaffold to generate a plurality of possible variants;
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vii) screening the plurality of variants in silico to produce a rank ordered list of variants;
viii) generating nucleic acid molecules having predefined sequences that encode at least 10 of the variants wherein the nucleic acid molecules are generated by a method comprising;
a) providing a pool of oligonucleotides comprising partially overlapping sequences that define the sequence of each of said nucleic acid molecules that encode said variants;
b) incubating said pool of oligonucleotides under hybridization conditions and at least one of the following conditions;
(i) ligation conditions, (2) chain extension conditions, or (iii) chain extension and ligation conditions, thereby forming nucleic acid constructs; and
c) separating constructs having said predefined sequences from constructs not having said predefined sequences, thereby forming the nucleic acid molecules that encode said variants; and
ix) causing expression of said nucleic acid molecules to produce said protein variants; and
x) screening the variants to identify variants having the desired characteristic. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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17. A biosynthetic library comprising a plurality of synthetic DNAs encoding a plurality of candidate proteins which can be selected or screened for species having a predetermined property or set of properties, the library comprising plural DNAs comprising regions of sequence homology and being assembled from chemically synthesized oligonucleotides.
- 18. A biosynthetic library comprising a plurality of synthetic DNAs encoding a plurality of candidate proteins which can be selected or screened for species having a predetermined property or set of properties, the library comprising plural DNAs chemically synthesized or assembled from chemically synthesized oligonucleotides and comprising reading frames of multiple said DNAs exploiting consistent codon usage patterns so as to promote similar expression levels in a selected expression system.
Specification