Intein-modified enzymes, their production and industrial applications
First Claim
Patent Images
1. A method of making an intein modified protein including:
- identifying a plurality of cysteine, serine or threonine sites within the protein, whether native or introduced;
analyzing the local sequence of each cysteine, serine or threonine site in the plurality of cysteine, serine or threonine sites with a support vector machine;
identifying an active site of the protein, wherein a respective distance separates the active site and each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites, and identifying the respective distance between the active site and each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites; and
identifying a secondary structure of the protein at each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites;
inserting an intein into the protein at a site immediately before one of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites that is ranked 0.75 or higher by the support vector machine, within ten angstroms of the active site, and within ten amino acids from a loop-β
-sheet junction or within ten amino acids from a loop-α
-helix junction; and
screening the intein modified protein to determine if the intein modified protein has a permissive or switching phenotype.
4 Assignments
0 Petitions
Accused Products
Abstract
A method of predicting an intein insertion site in a protein that will lead to a switching phenotype is provided. The method includes identifying a plurality of C/T/S sites within the protein; selecting from the plurality of C/T/S/ sites those that are ranked 0.75 or higher by a support vector machine, within ten angstroms of the active site of the protein, and at or near a loop-β-sheet junction or a loop-α-helix junction. A method of controlling protein activity and hosts including proteins with controlled activity are also provided. Also, intein modified proteins and plants containing intein modified proteins are provided.
-
Citations
3 Claims
-
1. A method of making an intein modified protein including:
-
identifying a plurality of cysteine, serine or threonine sites within the protein, whether native or introduced; analyzing the local sequence of each cysteine, serine or threonine site in the plurality of cysteine, serine or threonine sites with a support vector machine; identifying an active site of the protein, wherein a respective distance separates the active site and each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites, and identifying the respective distance between the active site and each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites; and identifying a secondary structure of the protein at each of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites; inserting an intein into the protein at a site immediately before one of the cysteine, serine or threonine sites in the plurality of cysteine, serine or threonine sites that is ranked 0.75 or higher by the support vector machine, within ten angstroms of the active site, and within ten amino acids from a loop-β
-sheet junction or within ten amino acids from a loop-α
-helix junction; andscreening the intein modified protein to determine if the intein modified protein has a permissive or switching phenotype. - View Dependent Claims (2, 3)
-
Specification
-
- Resources
Litigation Campaign Assessment
Thank you for your request. You will receive a custom alert email when the Litigation Campaign Assessment is available.
×
-
Current AssigneeAgrivida, Inc. (Nippon Soda Company Limited)
-
Original AssigneeAgrivida, Inc. (Nippon Soda Company Limited)
-
InventorsShen, Binzhang, Lazar, Gabor, de la Vega, Humberto, Apgar, James, Lessard, Philip, Raab, R. Michael
-
Primary Examiner(s)Page, Brent T
-
Application NumberUS12/590,444Publication NumberTime in Patent Office1,257 DaysField of SearchNoneUS Class Current435/320.1CPC Class CodesC12N 15/8216 Methods for controlling, re...C12N 15/8241 Phenotypically and genetica...C12N 15/8246 Non-starch polysaccharides,...C12N 9/2437 Cellulases (3.2.1.4; 3.2.1....C12N 9/248 XylanasesC12N 9/2482 Endo-1,4-beta-xylanase (3.2...C12Y 302/01004 Cellulase (3.2.1.4), i.e. e...C12Y 302/01008 Endo-1,4-beta-xylanase (3.2...
