General method for designing self-assembling protein nanomaterials

Patent metadata

Field	Value
Publication number	US-8969521-B2
Application number	US-201313802464-A
Country	US
Kind code	B2
Filing date	Mar 13, 2013
Priority date	Apr 11, 2012
Publication date	Mar 3, 2015
Grant date	Mar 3, 2015

Abstract

Methods and systems for computationally designing self-assembling polypeptides are disclosed. A representation of a docked configuration of a symmetric protein architecture can be determined by a computing device configured to computationally symmetrically dock representations of protein building blocks within a representation of a symmetric protein architecture, where symmetrically docking a representation of a particular protein building block can include determining a configuration of the protein building blocks in three-dimensional space within the symmetric protein architecture configured to generate interfaces between building blocks suitable for computational protein interface design. The amino acid sequence of the docked protein building blocks can be computationally modified to specify protein-protein interfaces between the plurality of protein building blocks that are energetically favorable to drive self-assembly of a protein that includes the modified amino acid sequence.

First claim

What is claimed:

1. An isolated polypeptide, comprising the amino acid sequence of SEQ ID NO: 1 capable of forming a multimeric assembly.

2. The isolated polypeptide of claim 1 , consisting of the amino acid sequence of SEQ ID NO: 1.

3. The isolated polypeptide of claim 1 , comprising the amino acid sequence of SEQ ID NO: 2.

4. A multimeric assembly, comprising a plurality of polypeptides of claim 1 .

5. An isolated nucleic acid molecule encoding the isolated polypeptide of claim 1 .

6. A nucleic acid expression vector comprising the isolated nucleic acid molecule of claim 5 .

7. An isolated recombinant host cell, comprising the nucleic acid expression vector of claim 6 .

8. The isolated polypeptide of claim 1 , consisting of the amino acid sequence of SEQ ID NO: 2.

9. A multimeric assembly, comprising a plurality of polypeptides of claim 3 .

10. An isolated nucleic acid molecule encoding the isolated polypeptide of claim 3 .

11. A nucleic acid expression vector comprising the isolated nucleic acid molecule of claim 10 .

12. An isolated recombinant host cell, comprising the nucleic acid expression vector of claim 11 .

13. A multimeric assembly, comprising a plurality of polypeptides of claim 2 .

14. An isolated nucleic acid molecule encoding the isolated polypeptide of claim 2 .

15. A nucleic acid expression vector comprising the isolated nucleic acid molecule of claim 14 .

16. An isolated recombinant host cell, comprising the nucleic acid expression vector of claim 15 .

17. A multimeric assembly, comprising a plurality of polypeptides of claim 8 .

18. An isolated nucleic acid molecule encoding the isolated polypeptide of claim 8 .

19. A nucleic acid expression vector comprising the isolated nucleic acid molecule of claim 18 .

20. An isolated recombinant host cell, comprising the nucleic acid expression vector of claim 19 .

Assignees

• Univ Washington Ct Commerciali
• Univ California

Inventors

• Baker David
• King Neil
• Sheffler William
• Yeates Todd

Classifications

• G06F19/16

  Physics · mapped topic

• G06F19/12 Primary

  Physics · mapped topic

• G16B15/20

  Protein or domain folding · CPC title

• G16B5/00 Primary

  ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks · CPC title

• G16B15/00

  ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment · CPC title