Apparatus for arbitrary peptide synthesis
View Patent ↗Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.
1. A peptide synthesis apparatus, comprising:
one or more peptide synthesizer units configured to sequentially provide two or more types of charged tRNA, one type of charged tRNA at a time, to one or more biological assemblers; and
one or more computing units operably coupled to the one or more peptide synthesizer units, the one or more computing units configured to direct the one or more peptide synthesizer units to sequentially provide the two or more types of charged tRNA to the one or more biological assemblers one type of charged tRNA at a time sequentially.
2. The peptide synthesis apparatus of claim 1 , wherein the one or more biological assemblers include one or more ribosome-based assemblers.
3. The peptide synthesis apparatus of claim 1 , wherein the one or more peptide synthesizer units include microfluidic-based peptide synthesizer units.
4. The peptide synthesis apparatus of claim 1 , wherein the one or more peptide synthesizer units include nanofluidic-based peptide synthesizer units.
5. The peptide synthesis apparatus of claim 1 , wherein the one or more computing units are configured to sequentially provide the two or more types of charged tRNA at least partially based on one or more of a predicted rate of incorporation of two or more amino acids into one or more peptides, a predicted rate of activity of one or more biological assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted rate of release of tRNA.
6. The peptide synthesis apparatus of claim 1 , further comprising one or more sources of the biological assemblers configured to provide the one or more biological assemblers.
7. The peptide synthesis apparatus of claim 1 , wherein the one or more computing units are configured to determine an order that the two or more types of charged tRNA are to be sequentially provided to the one or more biological assemblers and direct the one or more peptide synthesizer units to sequentially provide the two or more types of charged tRNA to the one or more biological assemblers one type of charged tRNA at a time sequentially according to the determined order.
8. The peptide synthesis apparatus of claim 1 , wherein the one or more computing units are configured to determine a timing that the two or more types of charged tRNA are to be sequentially provided to the one or more biological assemblers and direct the one or more peptide synthesizer units to sequentially provide the two or more types of charged tRNA to the one or more biological assemblers one type of charged tRNA at a time sequentially according to the determined timing.
9. The peptide synthesis apparatus of claim 1 , wherein two or more of the two or more types of charged tRNA have the same anti-codon and are charged with different amino acids.
10. The peptide synthesis apparatus of claim 1 , wherein two or more of the two or more types of charged tRNA have one or more of different anti-codons or different tRNA and are charged with the same amino acid.
11. The peptide synthesis apparatus of claim 1 , wherein the one or more computing units are configured to,
receive information representative of one or more target peptide structures;
determine one or more temporal-spatial parameters for synthesizing one or more peptides based at least partially on the information; and
direct the one or more peptide synthesizer units to sequentially provide the two or more types of charged tRNA to the one or more biological assemblers one type of charged tRNA at a time sequentially based at least partially on the temporal-spatial parameters.
12. The peptide synthesis apparatus of claim 1 , further comprising one or more fluid flows that connect and/or allow transfer of the two or more types of charged tRNA to the one or more biological assemblers.
13. The peptide synthesis apparatus of claim 1 , wherein the one or more computing units are configured to control one or more of an order or timing for providing the two or more types of charged tRNA to the one or more biological assemblers.
14. The peptide synthesis apparatus of claim 13 , wherein one or more of the order or the timing is at least partially based on one or more of a predicted rate of incorporation of two or more amino acids into one or more peptides, a predicted rate of activity of the one or more biological assemblers, a predicted rate of translocation of one or more nucleic acids, or a predicted rate of release of tRNA.
15. The peptide synthesis apparatus of claim 13 , wherein one or more of the order or the timing is at least partially based on monitoring of one or more of amino acid incorporation into one or more peptides, biological assembler activity, nucleic acid translocation, or tRNA release.
16. The peptide synthesis apparatus of claim 13 , wherein one or more of the order or the timing is at least partially based on one or more of availability of one or more nucleic acid codons, concentrations of one or more of the two or more types of charged tRNA, presence or absence of one or more of the two or more types of charged tRNA, or presence or absence of one or more anti-codons on one or more of the two or more types of charged tRNA.
17. The peptide synthesis apparatus of claim 1 , further comprising one or more tRNA charging units configured to charge one or more tRNA with amino acids to form the two or more types of charged tRNA.
18. The peptide synthesis apparatus of claim 1 , further comprising one or more monitoring units operably coupled to the one or more computing units, and wherein the one or more computing units are configured to direct the one or more peptide synthesizer units to sequentially provide the two or more types of charged tRNA to the one or more biological assemblers one type of charged tRNA at a time sequentially at least partially based on measurements taken by the one or more monitoring units.
19. The peptide synthesis apparatus of claim 18 , wherein the one or more monitoring units are configured to measure one or more of amino acid incorporation into one or more peptides, biological assembler activity, nucleic acid translocation, or tRNA release.
20. The peptide synthesis apparatus of claim 18 , wherein the one or more monitoring units are configured to measure one or more of presence or absence, concentration, or composition of one or more of the two or more charged tRNA or one or more tRNA.
21. The peptide synthesis apparatus of claim 1 , wherein the one or more peptide synthesizer units are configured to sequentially flow the two or more types of charged tRNA, one type of charged tRNA at a time, to the one or more biological assemblers.
22. The peptide synthesis apparatus of claim 1 , further comprising:
one or more sources of biological assemblers positioned to sequentially provide the one or more biological assemblers to two or more locations; and
wherein the one or more peptide synthesizer units include one or more sources of charged tRNA positioned to sequentially provide the two or more types of charged tRNA, one type of charged tRNA at a time, to the two or more locations.
23. The peptide synthesis apparatus of claim 1 , wherein the one or more peptide synthesizer units include two or more sources of charged tRNA, each of the two or more sources of charged tRNA positioned to sequentially provide the two or more types of charged tRNA, one type of charged tRNA at a time, to the one or more biological assemblers.