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US 2019/0155988 A2Published application
Computational Design of Self-Assembling Cyclic Protein Homo-oligomers
AssigneeUniversity of Washington
InventorsDavid Baker, Jorge Fallas, George Ueda, William H. Sheffler, Vanessa Nguyen
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Abstract
Described herein are polypeptides capable of self-assembling to form homo-oligomers, and methods for designing such polypeptides.
Claims20
A polypeptide comprising the general formula X1-X2-X3-X4-X5, wherein:
- (a) X1 comprises the amino acid sequence that is selected from the group consisting of:
- (i) the amino acid sequence at least 50% identical along its length to SEQ ID NO:1,
- (ii) the amino acid sequence at least 50% identical along its length to SEQ ID NO:
- 2;
- and
- (iii) the amino acid sequence at least 50% identical along its length to SEQ ID NO:3;
- (b) X2 comprises the amino acid sequence that is selected from the group consisting of:
- (i) the amino acid sequence at least 50% identical along its length to residues SEQ ID NO:
- 1, wherein X2 possesses changes from SEQ ID NO:
- 1 at least at residues 16, 20, and 24;
- (ii) the amino acid sequence at least 50% identical along its length to residues SEQ ID NO:2, wherein X2 possesses changes from SEQ ID NO:2 at least at residues 18, 22, and 26;
- and
- (iii) the amino acid sequence at least 50% identical along its length to residues SEQ ID NO:3, wherein X2 possesses changes from SEQ ID NO:3 at least at residues 18, 22, and 26;
- and
- (c) X3, X4, and X5 are independently absent, or comprise the amino acid sequence that is selected from the group consisting of:
- (i) the amino acid sequence at least 50% identical along its length to SEQ ID NO:1,
- (ii) the amino acid sequence at least 50% identical along its length to SEQ ID NO:2;
- and
- (iii) the amino acid sequence at least 50% identical along its length to residues SEQ ID NO:3;
- wherein the polypeptide does not comprise the amino acid sequence of SEQ ID NO:
- 5-7.
18 more elements
A polypeptide comprising the general formula X1-X2-X3-X4, wherein:
- X1 is at least 50% identical along its length to residues 1-34 of the amino acid sequence of SEQ ID NO:
- 8, wherein the amino acid sequence of X1 differs from the amino acid sequence of residues 1-34 of SEQ ID NO:
- 8 at least at residues 6, 8, 13, 21, 25, and 28;
- X2 is absent, or is at least 50% identical along its length to residues 36-68 of the amino acid sequence of SEQ ID NO:
- 8;
- X3 is absent, or is at least 50% identical along its length to residues 69-102 of the amino acid sequence of SEQ ID NO:
- 8;
- and
- X4 is absent, or is at least 50% identical along its length to residues 103-119 of the amino acid sequence of SEQ ID NO:
- 8.
7 more elements
A polypeptide comprising the amino acid sequence at least 50% identical to the amino acid sequence of SEQ ID NO:
- 10, wherein all oligomerizing positions in SEQ ID NO:
- 10 have the amino acid residue shown in SEQ ID NO:
- 10, or conservative substitutions thereof, and wherein the polypeptide does not comprise acid sequence of SEQ ID NO:9.
A polypeptide comprising the amino acid sequence at least 50% identical to SEQ ID NO:
- 11, wherein the polypeptide amino acid sequence differs from SEQ ID NO:
- 11 at least at residues 7, 8, 10, 14, 17, 118, 122, 146, 149, and 150.
A polypeptide comprising the amino acid sequence that is at least 50% identical over its length to the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOS:
- 10 and 12-40.
A method, comprising:
- determining a cycle of monomeric proteins using a computing device;
- determining a docking score for the cycle of monomeric proteins using the computing device, the docking score representing interaction between two or more monomeric proteins in the cycle of monomeric proteins with respect to a multi-dimensional rigid body transformation between one or more backbone atoms of the two or more monomeric proteins;
- determining whether the docking score for the cycle of monomeric proteins is a relatively-low docking score using the computing device;
- after determining that the docking score for the cycle of monomeric proteins is a relatively-low docking score, determining one or more interfaces between the two or more monomeric proteins in the cycle of monomeric proteins using the computing device;
- and
- generating an output related to the cycle of monomeric proteins.
3 more elements
Dependencies are inferred from the claim text.