Nutritive fragments, proteins and methods
Nutritive proteins are provided. In some embodiments the nutritive proteins comprise a first polypeptide sequence comprising a fragment of a naturally-occurring nutritive protein. In some embodiments the fragment comprises at least one of a) an enhanced ratio of branch chain amino acid residues to total amino acid residues present in the nutritive protein; b) an enhanced ratio of leucine residues to total amino acid residues present in the nutritive protein; and c) an enhanced ratio of essential amino acid residues to total amino acid residues present in the nutritive protein. In some embodiments, the fragment comprises at least one of a) a ratio of branch chain amino acid residues to total amino acid residues present in the nutritive protein; b) a ratio of leucine residues to total amino acid residues present in the nutritive protein; and c) a ratio of essential amino acid residues to total amino acid residues present in the nutritive protein, that is equal to or greater than the corresponding ratio present in a benchmark protein such as whey, egg or soy protein. Also provided are nucleic acids encoding the proteins, recombinant microorganisms that make the proteins, methods of making the proteins using recombinant microorganisms, compositions that comprise the proteins, and methods of using the proteins, among other things.
1. A method of maintaining or increasing at least one of muscle mass, muscle strength, and muscle functional performance in a subject, the method comprising providing to the subject a sufficient amount of a nutritive composition comprising an isolated nutritive protein fragment comprising a polypeptide sequence that is at least about 80% homologous to a fragment of a naturally-occurring protein sequence over the total length of the isolated nutritive protein fragment, wherein the isolated nutritive protein fragment is at least 25 amino acids in length, wherein the isolated nutritive protein fragment is less than or equal to 150 amino acids in length, wherein the polypeptide sequence comprises a ratio of essential amino acid residues to total amino acid residues of at least 40%, a ratio of branch chain amino acid residues to total amino acid residues of at least 18% and a ratio of Leu residues to total amino acid residues of at least 8%, wherein the isolated nutritive protein fragment has an aqueous solubility at pH 7 of at least 50 g/L, and wherein the isolated nutritive protein fragment is present in the composition in an amount of at least about 1 gram.
2. The method of claim 1 , wherein the isolated nutritive protein fragment has a simulated gastric digestion half-life of less than 10 minutes.
3. The method of claim 1 , wherein the polypeptide sequence comprises 0, 1, 2, or 3 cysteine residues, or wherein the isolated nutritive protein fragment comprises no disulfide bonds.
4. The method of claim 1 , wherein the isolated nutritive protein fragment does not comprise N-linked glycosylation and/or does not comprise O-linked glycosylation.
5. The method of claim 1 , wherein the polypeptide sequence has a calculated solvation score of −20 or less.
6. The method of claim 1 , wherein the polypeptide sequence comprises an amino acid sequence selected from:
i. an amino acid sequence selected from a SEQ ID;
ii. a modified derivative of an amino acid sequence selected from the SEQ ID list; and
iii. a mutein of an amino acid sequence selected from the SEQ ID list,
wherein the SEQ ID list is SEQ ID NOs 4-8, 12-13, 15-18, 20-27, 30, 32-37, 40-42, 45-51, 53, 56-57, 59, 63-69, 71, 74-77, 79, 81, 83, 85, 87, 90, 93-96, 98, 101-102, 106-108, 110-112, 114-115, 117-123, 128-130, 134-137, 139-141, 145-147, 151, 153, 155, 157-159, 161-162, 168-169, 174-175, 177-182, 188-189, 194, 196-197, 199-202, 204-205, 207, 209, 211-212, 214-215, 218-219, 221-222, 225-226, 228, 231-234, 237, 239, 241-247, 249-251, 255, 259-260, 268, 270-271, 274-278, 280, 282-285, 287-288, 290, 292-294, 299, 301, 304-306, 308-310, 313, 315-323, 326-329, 331, 333-338, 341, 348-349, 351, 354, 356, 359-360, 363-369, 372-375, 378-379, 381-386, 388, 393-398, 401, 404-405, 407-408, 410-411, 413-417, 420, 422, 426-429, 431-433, 436, 438-439, 441, 444, 446, 448-449, 451, 453-457, 459, 462-468, 471-473, 477, 479, 481-483, 485-489, 492-493, 495, 497, 499, 501-504, 508, 511, 515-516, 522-523, 527-528, 530, 533-537, 539-541, 543-549, 551-552, 554-557, 559-560, 565-566, 568, 570, 574-576, 578-580, 582-584, 586-591, 594, 597, 603-607, 610-612, 614-615, 617-618, 620-622, 624, 626-629, 634-635, 639, 641, 643, 645, 651-652, 654-655, 657, 659, 663-666, 675, 677-678, 680-681, 684-686, 688-689, 692, 694-696, 701, 706-708, 712-714, 717-718, 721-723, 725, 729-731, 733, 735-736, 738, 740-741, 744, 746-748, 750-751, 753, 755, 757-759, 762-764, 766-767, 775-776, 780-781, 784-785, 787, 800-807, 809, 812-820, 835, 838-839, 844, 847-848, 850-851, 854, 857, 862-863, 866, 868, 871-873, 875-876, 878-880, 882, 884-885, 887, 889, 891-892, 894, 898, 901-910, 912, 915-920, 924-928, 930, 935, 937-938, 941-943, 945-948, 950, 956-960, 964-967, 969-970, 972-973, 975, 977-978, 981-982, 985-988, 990, 992-997, 999-1011, 1014-1021, 1024-1025, 1027-1028, 1030, 1032-1050, 1052-1053, 1055-1077, 1079-1080, 1082-1096, 1098-1106, 1108-1112, 1114-1115, 1117-1121, 1123-1180, 1182-1190, 1192-1205, 1207-1232, 1234-1239, 1241-1244, 1246-1259, 1261-1274, 1276, 1278-1282, 1284-1285, 1287-1324, 1326-1342, 1344-1346, 1348-1360, 1362-1374, 1376-1414, 2519-2532, 2535-2556, 2559-2568, 2574-2596, 2598-2599, 2601-2609, and 2612-2613.
7. The method of claim 1 , wherein the polypeptide sequence further comprises a polypeptide tag, optionally wherein the tag comprises a polyhistidine-tag.
8. The method of claim 1 , wherein the polypeptide sequence comprises at least one of each essential amino acid.
9. The method of claim 1 , wherein the nutritive composition further comprises a protein, a polypeptide, a peptide, a free amino acid, a carbohydrate, a fat, a mineral or mineral source, a vitamin, a supplement, an organism, a pharmaceutical, and/or an excipient, optionally wherein the free amino acid is selected from the group consisting of essential amino acids, non-essential amino acids, branch chain amino acids, non-standard amino acids and modified amino acids.
10. The method of claim 1 further comprising providing a second isolated nutritive protein or fragment thereof comprising a second polypeptide sequence that is at least about 80% homologous to a fragment of a second naturally-occurring protein sequence over the total length of the fragment of the second isolated protein fragment, wherein the second polypeptide sequence comprises a ratio of essential amino acid residues to total amino acid residues of at least 40% and at least one of: a ratio of branch chain amino acid residues to total amino acid residues of at least 18% and a ratio of Leu residues to total amino acid residues of at least 8.
11. A method of treating at least one of cachexia, sarcopenia and frailty in a subject, the method comprising providing to the subject a sufficient amount of a nutritive composition comprising an isolated nutritive protein fragment comprising a polypeptide sequence that is at least about 80% homologous to a fragment of a naturally-occurring protein sequence over the total length of the isolated nutritive protein fragment, wherein the polypeptide sequence is at least 25 amino acids in length, wherein the isolated nutritive protein fragment is less than or equal to 150 amino acids in length, wherein the polypeptide sequence comprises a ratio of essential amino acid residues to total amino acid residues of at least 40% and at least one of: a ratio of branch chain amino acid residues to total amino acid residues of at least 18% and a ratio of Leu residues to total amino acid residues of at least 8%, wherein the isolated nutritive protein fragment has an aqueous solubility at pH 7 of at least 50 g/L, and wherein the isolated nutritive protein fragment is present in the composition in an amount of at least about 1 gram.
12. The method of claim 11 , wherein the isolated nutritive protein fragment has a simulated gastric digestion half-life of less than 10 minutes and/or wherein the polypeptide sequence has a calculated solvation score of −20 or less.
13. The method of claim 11 , wherein the polypeptide sequence comprises 0, 1, 2, or 3 cysteine residues, or wherein the isolated nutritive protein fragment comprises no disulfide bonds.
14. The method of claim 11 , wherein the isolated nutritive protein fragment does not comprise N-linked glycosylation and/or does not comprise 0-linked glycosylation.
15. The method of claim 11 , wherein the nutritive composition further comprises a protein, a polypeptide, a peptide, a free amino acid, a carbohydrate, a fat, a mineral or mineral source, a vitamin, a supplement, an organism, a pharmaceutical, and/or an excipient, optionally wherein the free amino acid is selected from the group consisting of essential amino acids, non-essential amino acids, branch chain amino acids, non-standard amino acids and modified amino acids.
16. The method of claim 11 , wherein the composition is provided to the subject orally.
17. The method of claim 11 , wherein the polypeptide sequence comprises a ratio of essential amino acid residues to total amino acid residues of greater than 49% and at least one of: a ratio of branch chain amino acid residues to total amino acid residues of greater than 24% and a ratio of Leu residues to total amino acid residues of greater than 11%.
18. The method of claim 1 , wherein the composition is provided to the subject orally.
19. The method of claim 1 , wherein the polypeptide sequence comprises a ratio of essential amino acid residues to total amino acid residues of greater than 49% and at least one of: a ratio of branch chain amino acid residues to total amino acid residues of greater than 24% and a ratio of Leu residues to total amino acid residues of greater than 11%.
20. The method of claim 1 , wherein the polypeptide sequence has less than 50% global homology to a known allergen.