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(12) United States Patent (10) Patent No.: US 9,605,040 B2 Von Maltzahn Et Al

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(12) United States Patent (10) Patent No.: US 9,605,040 B2 Von Maltzahn Et Al USOO9605040B2 (12) United States Patent (10) Patent No.: US 9,605,040 B2 VOn MaltZahn et al. (45) Date of Patent: Mar. 28, 2017 (54) NUTRITIVE PROTEINS AND METHODS 5,866.338 A 2f1999 Hartwell et al. 6,004,930 A 12/1999 Hainline 6,291,245 B1 9/2001 Kopetzki et al. (71) Applicant: Pronutria, Inc., Cambridge, MA (US) 6,361,966 B1 3/2002 Walker et al. 6,495,344 B1 12/2002 Carr (72) Inventors: Geoffrey von Maltzahn, Boston, MA 6,630,320 B1 10/2003 Davis et al. (US); Michael J. Hamill, Wellesley, 7,211,431 B2 5/2007 Rao et al. MA (US); Rajeev Chillakuru, 7,214,786 B2 5/2007 Kovalic et al. 7,252,972 B2 8, 2007 Kikuchi et al. Cambridge, MA (US); John F. 7,314,974 B2 1/2008 Cao et al. Kramarczyk, Somerville, MA (US); 7,790,688 B2 9/2010 Wolfe et al. David Arthur Berry, Brookline, MA 8,071,122 B2 12/2011 Yamka et al. (US); Brett Adam Boghigian, Boston, 8,329,646 B2 12/2012 Tisdale et al. MA (US); Nathaniel W. Silver, 8,343,747 B2 1/2013 Burke et al. 8,409,840 B2 4/2013 Muller et al. Cambridge, MA (US) 8,426,184 B2 4/2013 Blum et al. (73) Assignee: Axcella Health Inc., Cambridge, MA 8,486,888 B2 7/2013 Greenberg (US) (Continued) FOREIGN PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this CN 101.886107 A 11 2010 patent is extended or adjusted under 35 EP O347890 B1 3, 1993 U.S.C. 154(b) by 0 days. (Continued) (21) Appl. No.: 14/387,675 OTHER PUBLICATIONS (22) PCT Filed: Mar. 15, 2013 Takio et al. Proc. Nati. Acad. Sci. USAVol. 84, pp. 4851-4855, Jul. 1987.* (86). PCT No.: PCT/US2O13/0322O6 Bolotin et al. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403, 11:731-753 (C) S 371 (c)(1), 2001 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/ (2) Date: Sep. 24, 2014 O1.* Broadbent et al. Applied and Environmental Microbiology, vol. 68, No. 4, Apr. 2002, p. 1778-1785.* (87) PCT Pub. No.: WO2013/148328 Barac, M. et al., “Profile and Functional Properties of Seed Proteins PCT Pub. Date: Oct. 3, 2013 from Six Pea (Pisum sativum) Genotypes.” Int. J. Mol. Sci., 2010, pp. 4973-4990, vol. 11. (65) Prior Publication Data Chinpongpanich, A. et al., "Biophysical Characterization of Calmodulin and Calmodulin-Like Proteins from Rice, Oryza sativa US 2015/OO876O2 A1 Mar. 26, 2015 L.” Acta Biochim. Biophys. Sin., 2011, pp. 867-876, vol. 43. (Continued) Related U.S. Application Data Primary Examiner — Jeanette Lieb (74) Attorney, Agent, or Firm — Fenwick & West LLP (60) Provisional application No. 61/615,791, filed on Mar. 26, 2012. (57) ABSTRACT Nutritive proteins are provided. In some embodiments the (51) Int. Cl. nutritive proteins comprise at least one of a level of a) a ratio C07K I4/435 (2006.01) of branch chain amino acid residues to total amino acid A6 IK 38/00 (2006.01) C07K I4/47 (2006.01) residues present in the nutritive protein equal to or greater A23. 3/04 (2006.01) than the ratio of branch chain amino acid residues to total C07K I4/45 (2006.01) amino acid residues present in whey protein; b) a ratio of A2.3L 33/75 (2016.01) leucine residues to total amino acid residues present in the (52) U.S. Cl. CPC ................. C07K 14/47 (2013.01); A23J 3/04 nutritive protein equal to or greater than the ratio of leucine (2013.01); A23L 33/175 (2016.08); C07K residues to total amino acid residues present in whey pro 14/415 (2013.01); A61 K 38/00 (2013.01) tein; and c) a ratio of essential amino acid residues to total (58) Field of Classification Search amino acid residues present in the nutritive protein equal to None See application file for complete search history. or greater than the ratio of essential amino acid residues to total amino acid residues present in whey protein. Also (56) References Cited provided are nucleic acids encoding the proteins, recombi U.S. PATENT DOCUMENTS nant microorganisms that make the proteins, methods of making the proteins using recombinant microorganisms, 3,870,801 A 3, 1975 Tombs 4,016,147 A 4/1977 Fujimaki et al. compositions that comprise the proteins, and methods of 4,601,980 A 7, 1986 Goededel et al. using the proteins, among other things. 4,687,782 A 8, 1987 Brantman 5,736,187 A 4, 1998 Tesmer et al. 16 Claims, 1 Drawing Sheet US 9,605,040 B2 Page 2 (56) References Cited (Thale Cress), Retrieved from EBI Accession No. EMBL:BX822075, Feb. 6, 2004, 2 pages. U.S. PATENT DOCUMENTS Database UniProt Accession No. 022287, “RecName: Full=Mannose-1-phosphate Guanylyltransferase 1: EC=2,7.7.13; 8,546,118 B2 10/2013 Weiner et al. AltName: Full=GDP-mannose Pyrophosphorylase 1: AltName: 8,618,047 B2 12/2013 Hofman et al. Full=Protein Embryo Defective 101: AltName: Full=Protein Hyper 8,735,107 B2 5, 2014 Weiner et al. sensitive to Ammonium Ion 1: AltName: Full=Protein Sensitive to 8,809,259 B2 8/2014 Berry et al. 8,815,806 B2 8/2014 Aluko et al. 0.” Retrieved from EBI Accession No. UNIPROT:022287, Sep. 21, 8,822,412 B2 9/2014 Berry et al. 2011, 3 pages. 8,877.281 B2 11/2014 Segall et al. European Extended Search Report, European Application No. 9,364463 B2 6, 2016 Ferrando et al. 13770153.8, Oct. 30, 2015, 11 pages. 2004f0071825 A1 4/2004 Lockwood Hughes, G.J. et al., “Protein Digestibility-Corrected Amino Acid 2004/O123343 A1 6/2004 La Rosa et al. Scores (PDCAAS) for Soy Protein Isolates and Concentrate: Cri 2004/0266689 A1 12/2004 McMichael et al. teria for Evaluation.” Journal of Agricultural and Food Chemistry, 2005/0010973 A1 1/2005 Rao et al. Dec. 14, 2011, pp. 12707-12712, vol. 59, No. 23. 2006, O150283 A1 7/2006 Alexandrov et al. Israel Office Action, Israel Patent Application No. 234617, Oct. 22. 2006, O159724 A1 7, 2006 Bell 2015, 3 pages (with concise explanation of relevance). 2007,0264688 A1 11/2007 Venter 2008, OO32000 A1 2/2008 Schnorr et al. Israel Office Action, Israel Patent Application No. 234621, Oct. 22. 2008/0206430 A1 8, 2008 Avila 2015, 3 pages (with concise explanation of relevance). 2008/0268038 A1 10, 2008 Wolfe Lee, J., “Soy Protein Hydrolysate; Solubility, Thermal Stability, 2008/0317725 A1 12/2008 Baum Bioactivity, and Sensory Acceptability in a Tea Beverage.” Master's 2009, O181903 A1 7, 2009 Wolfe et al. Thesis, University of Minnesota, Aug. 2011, 131 pages. 2009/O19782O A1 8, 2009 Wolfe et al. Sang, J. et al., “Cross-Talk Between Calcium-Calmodulin and Nitric 2009,0203606 A1 8, 2009 Wolfe et al. Oxide in Abscisic Acid Signaling in Leaves of Maize Plants.” Cell 2009,0252684 A1 10/2009 Wolfe et al. Research, 2008, pp. 577-588, vol. 18. 20090304901 A1 12/2009 Bobzin et al. Schaafsma, G., “Criteria and Significance of Dietary Protein 2010.0055246 A1 3/2010 Ahn Sources in Humans and the Protein Digestibility-Corrected Amino 2010/0179089 A1 7, 2010 Deutz et al. Acid Score 1,” J. Nutr., Jul. 31, 2000, pp. 1865S-1867S, Online 2010, O189864 A1 7, 2010 Marsland Retrieved on Oct. 15, 2015 Retrieved from the 2010, O189865 A1 7, 2010 Sweet Internet-URL:http://jn.nutrition.org/content/130/7/1865S.full. 2010/0267831 A1 10/2010 Kobayashi et al. 2010/0286023 A1 11/2010 Wolfe et al. pdf+html>. 2010/0317597 A1 12/2010 Ney et al. Singapore Office Action. Singapore Application No. 11201405842P, 2010.0330250 A1 12/2010 Segall et al. Nov. 17, 2015, 18 pages. 2011 0183052 A1 7/2011 Sherwood et al. Tsunoda, Y. et al., “Improving Expression and Solubility of Rice 2011 (0250310 A1 10/2011 Mateus et al. Proteins Produced as Fusion Proteins in Escherichia coli.' Protein 2011/0319596 A1 12/2011 De La Torre-Montemayor Expr. Purif. 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