Building Biomaterials Through Genetic Code Expansion

Republished By Plato

Followers: 0

Bischoff R.
Schlüter H.

Amino acids: chemistry, functionality and selected non-enzymatic post-translational modifications.

J. Proteome. 2012; 75: 2275-2296

Liu X.
et al.

Photo-cleavable purification/protection handle assisted synthesis of giant modified proteins with tandem repeats.

Chem. Sci. 2019; 10: 8694

Pena-Francesch A.
et al.

Mechanical properties of tandem-repeat proteins are governed by network defects.

ACS Biomater. Sci. Eng. 2018; 4: 884-891

Processing of collagen based biomaterials and the resulting materials properties.

Biomed. Eng. Online. 2019; 18: 24

Ilamaran M.
et al.

A self-assembly and higher order structure forming triple helical protein as a novel biomaterial for cell proliferation.

Biomater. Sci. 2019; 7: 2191-2199

Lajoie M.J.
et al.

Overcoming challenges in engineering the genetic code.

J. Mol. Biol. 2016; 428: 1004-1021

Zhao N.
et al.

A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo.

Nat. Commun. 2019; 10: 2947

Yang B.
et al.

In vivo residue-specific DOPA-incorporated engineered mussel bioglue with enhanced adhesion and water resistance.

Angew. Chem. Int. Ed. Engl. 2014; 53: 13360-13364

Hauf M.
et al.

Photoactivatable mussel-based underwater adhesive proteins by an expanded genetic code.

Chembiochem. 2017; 18: 1819-1823

Smolskaya S.
Andreev Y.A.

Site-specific incorporation of unnatural amino acids into Escherichia coli recombinant protein: methodology development and recent achievement.

Biomolecules. 2019; 9: 255

Expanding and reprogramming the genetic code.

Nature. 2017; 550: 53-60

Ros E.
et al.

Learning from nature to expand the genetic code.

Trends Biotechnol. 2021; 39: 460-473

Mukai T.
et al.

Rewriting the genetic code.

Annu. Rev. Microbiol. 2017; 71: 557-577

Merkel L.
Budisa N.

Organic fluorine as a polypeptide building element: In vivo expression of fluorinated peptides, proteins and proteomes.

Org. Biomol. Chem. 2012; 10: 7241-7261

Ta D.T.
et al.

Bioorthogonal elastin-like polypeptide scaffolds for immunoassay enhancement.

ACS Appl. Mater. Interfaces. 2018; 10: 30147-30154

Radhakrishnan J.
et al.

Gradient nano-engineered in situ forming composite hydrogel for osteochondral regeneration.

Biomaterials. 2018; 162: 82-98

Radhakrishnan J.
et al.

Injectable and 3D bioprinted polysaccharide hydrogels: from cartilage to osteochondral tissue engineering.

Biomacromolecules. 2017; 18: 1-26

Perret S.
et al.

Unhydroxylated triple helical collagen I produced in transgenic plants provides new clues on the role of hydroxyproline in collagen folding and fibril formation.

J. Biol. Chem. 2001; 276: 43693-43698

Wang Q.
et al.

Expanding the genetic code for biological studies.

Chem. Biol. 2009; 16: 323-336

Korendovych I.V.

Rational and semirational protein design.

Methods Mol. Biol. 2018; 1685: 15-23

Kim C.H.
et al.

Protein conjugation with genetically encoded unnatural amino acids.

Curr. Opin. Chem. Biol. 2013; 17: 412-419

Gubbens J.
et al.

In vitro incorporation of nonnatural amino acids into protein using tRNA(Cys)-derived opal, ochre, and amber suppressor tRNAs.

RNA. 2010; 16: 1660-1672

Hartman M.C.T.
et al.

Enzymatic aminoacylation of tRNA with unnatural amino acids.

Proc. Natl. Acad. Sci. U. S. A. 2006; 103: 4356-4361

Williams T.L.
et al.

Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency.

Amino Acids. 2021; 53: 89-96

Neumann H.
et al.

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome.

Nature. 2010; 464: 441-444

Wan W.
et al.

A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli.

Angew. Chem. Int. Ed. Engl. 2010; 49: 3211-3214

de la Torre D.
Chin J.W.

Reprogramming the genetic code.

Nat. Rev. Genet. 2021; 22: 169-184

Jewel D.
Chatterjee A.

Rewriting the genetic code.

Science. 2021; 372: 1040-1041

Lee J.
et al.

Expanding the limits of the second genetic code with ribozymes.

Nat. Commun. 2019; 10: 5097

Paulo Zambon J.
et al.

Methods to generate tissue-derived constructs for regenerative medicine applications.

Methods. 2020; 171: 3-10

Anju S.
et al.

Complicity of degradable polymers in health-care applications.

Mater. Today Chem. 2020; 16100236

Gaharwar A.K.
et al.

Engineered biomaterials for in situ tissue regeneration.

Nat. Rev. Mater. 2020; 5: 686-705

Brusatin G.
et al.

Biomaterials and engineered microenvironments to control YAP/TAZ-dependent cell behaviour.

Nat. Mater. 2018; 17: 1063-1075

Asadpour S.
et al.

Natural biomacromolecule based composite scaffolds from silk fibroin, gelatin and chitosan toward tissue engineering applications.

Int. J. Biol. Macromol. 2020; 154: 1285-1294

Sengupta D.
Heilshorn S.C.

Protein-engineered biomaterials: highly tunable tissue engineering scaffolds.

Tissue Eng. B Rev. 2010; 16: 285-293

Ayyadurai N.
et al.

Bioconjugation of L-3,4-dihydroxyphenylalanine containing protein with a polysaccharide.

Bioconjug. Chem. 2011; 22: 551-555

Pandurangan S.
et al.

Engineering of a skin-fiber-opening enzyme for sulfide-free leather beam house operation through xenobiology.

Green Chem. 2019; 21: 2070-2081

Tabisz B.
et al.

Site-directed immobilization of BMP-2: two approaches for the production of innovative osteoinductive scaffolds.

Biomacromolecules. 2017; 18: 695-708

Costa S.A.
et al.

Photo-crosslinkable unnatural amino acids enable facile synthesis of thermoresponsive nano- to microgels of intrinsically disordered polypeptides.

Adv. Mater. 2018; 30: 1704878

Xu Y.
et al.

Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.

J. Biol. Chem. 2002; 277: 27312-27318

Lukomski S.
et al.

Identification and characterization of a second extracellular collagen-like protein made by group A Streptococcus: control of production at the level of translation.

Infect. Immun. 2001; 69: 1729-1738

Yoshizumi A.
et al.

Self-association of Streptococcus pyogenes collagen-like constructs into higher order structures.

Protein Sci. 2009; 18: 1241-1251

Peng Y.Y.
et al.

Incorporation of hydroxyproline in bacterial collagen from Streptococcus pyogenes.

Acta Biomater. 2018; 80: 169-175

Ilamaran M.
et al.

Growth factor-mimicking 3,4-dihydroxyphenylalanine-encoded bioartificial extracellular matrix like protein promotes wound closure and angiogenesis.

Biomater. Sci. 2020; 8: 6773-6785

Almine J.F.
et al.

Elastin-based materials.

Chem. Soc. Rev. 2010; 39: 3371-3379

Bazewicz C.G.
et al.

Sensitive, site-specific, and stable vibrational probe of local protein environments: 4-azidomethyl-l-phenylalanine.

J. Phys. Chem. B. 2013; 117: 8987-8993

Amiram M.
et al.

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids.

Nat. Biotechnol. 2015; 33: 1272-1279

Martin R.W.
et al.

Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.

Nat. Commun. 2018; 9: 1203

Brennan M.J.
et al.

A bioinspired elastin-based protein for a cytocompatible underwater adhesive.

Biomaterials. 2017; 124: 116-125

Carrico I.S.
et al.

Lithographic patterning of photoreactive cell-adhesive proteins.

J. Am. Chem. Soc. 2007; 129: 4874-4875

Wu I.-L.
et al.

Multiple site-selective insertions of noncanonical amino acids into sequence-repetitive polypeptides.

Chembiochem. 2013; 14: 968-978

Wang Y.
et al.

Protein-engineered functional materials.

Adv. Healthc. Mater. 2019; 8e1801374

Sogawa H.
et al.

3,4-Dihydroxyphenylalanine (DOPA)-containing silk fibroin: its enzymatic synthesis and adhesion properties.

ACS Biomater. Sci. Eng. 2019; 5: 5644-5651

Teramoto H.
et al.

Genetic code expansion of the silkworm Bombyx mori to functionalize silk fiber.

ACS Synth. Biol. 2018; 7: 801-806

Harvey D.
et al.

Antibiotic spider silk: site-specific functionalization of recombinant spider silk using ‘click’ chemistry.

Adv. Mater. 2017; 29: 11604245

Kim S.
et al.

Salt triggers the simple coacervation of an underwater adhesive when cations meet aromatic π electrons in seawater.

ACS Nano. 2017; 11: 6764-6772

Wonderly W.R.
et al.

Dueling backbones: comparing peptoid and peptide analogues of a mussel adhesive protein.

Macromolecules. 2020; 53: 6767-6779

Kim H.J.
et al.

Mussel adhesion-employed water-immiscible fluid bioadhesive for urinary fistula sealing.

Biomaterials. 2015; 72: 104-111

Castillo J.J.
et al.

Comparison of natural extraction and recombinant mussel adhesive proteins approaches.

in: Puri M. Food Bioactives: Extraction and Biotechnology Applications. Springer International, 2017: 111-135

Jeong Y.S.
et al.

Enhanced production of DOPA-incorporated mussel adhesive protein using engineered translational machineries.

Biotechnol. Bioeng. 2020; 117: 1961-1969

Guo C.
et al.

Bio-orthogonal conjugation and enzymatically triggered release of proteins within multi-layered hydrogels.

Acta Biomater. 2017; 56: 80-90

Tamshen K.
et al.

Genetic code expansion enables site-specific pegylation of a human growth hormone receptor antagonist through click chemistry.

Bioconjug. Chem. 2020; 31: 2179-2190

Spieler V.
et al.

Targeting interleukin-4 to the arthritic joint.

J. Control. Release. 2020; 326: 172-180

Kim Y.
et al.

Specific labeling of zinc finger proteins using noncanonical amino acids and copper-free click chemistry.

Bioconjug. Chem. 2012; 23: 1891-1901

Deepankumar K.
et al.

Engineering transaminase for stability enhancement and site-specific immobilization through multiple noncanonical amino acids incorporation.

ChemCatChem. 2015; 7: 417-421

Davis B.G.
et al.

Site-selective glycosylation of proteins: creating synthetic glycoproteins.

Nat. Protoc. 2007; 2: 3185-3194

Lühmann T.
et al.

Bio-orthogonal immobilization of fibroblast growth factor 2 for spatial controlled cell proliferation.

ACS Biomater. Sci. Eng. 2015; 1: 740-746

Yamada T.
Takasu A.

Click grafting of alkyne-containing vinyl polymers onto biosynthesized extracellular matrix protein containing azide functionality and adhesion control of human umbilical vein endothelial cells.

RCS Adv. 2015; 5: 41445-41456

Takasu A.
et al.

Artificial extracellular matrix proteins containing phenylalanine analogues biosynthesized in bacteria using T7 expression system and the PEGylation.

Biomacromolecules. 2011; 12: 3444-3452

Xu R.
et al.

Site-specific incorporation of the mucin-type N-acetylgalactosamine-alpha-O-threonine into protein in Escherichia coli.

J. Am. Chem. Soc. 2004; 126: 15654-15655

Lepthien S.
et al.

In vivo double and triple labeling of proteins using synthetic amino acids.

Angew. Chem. Int. Ed. Engl. 2010; 49: 5446-5450

Wang F.
et al.

Genetic incorporation of unnatural amino acids into proteins in Mycobacterium tuberculosis.

PLoS One. 2010; 5e9354

Mukai T.
et al.

Codon reassignment in the Escherichia coli genetic code.

Nucleic Acids Res. 2010; 38: 8188-8195

Johnson D.B.F.
et al.

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites.

Nat. Chem. Biol. 2011; 7: 779-786

Johnson D.B.F.
et al.

Release factor one is nonessential in Escherichia coli.

ACS Chem. Biol. 2012; 7: 1337-1344

Lajoie M.J.
et al.

Genomically recoded organisms expand biological functions.

Science. 2013; 342: 357-360

Mukai T.
et al.

Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon.

Sci. Rep. 2015; 5: 9699

Mukai T.
et al.

Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli.

Nucleic Acids Res. 2015; 43: 8111-8122

Ayyadurai N.
et al.

A facile and efficient method for the incorporation of multiple unnatural amino acids into a single protein.

Chem. Commun. (Camb.). 2011; 47: 3430-3432

Hoesl M.G.
Budisa N.

In vivo incorporation of multiple noncanonical amino acids into proteins.

Angew. Chem. Int. Ed. Engl. 2011; 50: 2896-2902

Dunkelmann D.L.
et al.

A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design.

Nat. Chem. 2021; 13: 1110-1117

Liu C.C.
et al.

Toward an orthogonal central dogma.

Nat. Chem. Biol. 2018; 14: 103-106

Thyer R.
et al.

Directed evolution of an improved aminoacyl-tRNA synthetase for incorporation of L-3,4-dihydroxyphenylalanine (L-DOPA).

Angew. Chem. Int. Ed. Engl. 2021; 60: 14811-14816

Pandurangan S.
et al.

Enhanced cellular uptake and sustained transdermal delivery of collagen for skin regeneration.

ACS Appl. Bio Mater. 2020; 3: 7540-7549

Manandhar M.
et al.

Genetic code expansion: inception, development, commercialization.

J. Am. Chem. Soc. 2021; 143: 4859-4878

Lee S.
et al.

A facile strategy for selective incorporation of phosphoserine into histones.

Angew. Chem. Int. Ed. Engl. 2013; 52: 5771-5775

Hanson S.
et al.

Chemoenzymatic synthesis of oligosaccharides and glycoproteins.

Trends Biochem. Sci. 2004; 29: 656-663

Ayyadurai N.
et al.

Biosynthetic substitution of tyrosine in green fluorescent protein with its surrogate fluorotyrosine in Escherichia coli.

Biotechnol. Lett. 2011; 33: 2201-2207

Sisila V.
et al.

Esterification of polymeric carbohydrate through congener cutinase-like biocatalyst.

Appl. Biochem. Biotechnol. 2021; 193: 19-32

Augustine G.
et al.

Excited state electronic interconversion and structural transformation of engineered red-emitting green fluorescent protein mutant.

J. Phys. Chem. B. 2019; 123: 2316-2324

Ayyadurai N.
et al.

Evaluation and biosynthetic incorporation of chlorotyrosine into recombinant proteins.

Biotechnol. Bioprocess Eng. 2012; 17: 679

Cirino P.C.
et al.

Global incorporation of norleucine in place of methionine in cytochrome P450 BM-3 heme domain increases peroxygenase activity.

Biotechnol. Bioeng. 2003; 83: 729-734

Deepankumar K.
et al.

Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline.

Biochem. Biophys. Res. Commun. 2013; 440: 509-514

Jackson J.C.
et al.

Improving nature’s enzyme active site with genetically encoded unnatural amino acids.

J. Am. Chem. Soc. 2006; 128: 11124-11127

Qi H.
et al.

Novel mussel-inspired universal surface functionalization strategy: protein-based coating with residue-specific post-translational modification in vivo.

ACS Appl. Mater. Interfaces. 2019; 11: 12846-12853

Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications.

Curr. Protoc. Mol. Biol. 2014; 108: 16.30.1-11

Kunjapur A.M.
et al.

Engineering posttranslational proofreading to discriminate nonstandard amino acids.

Proc. Natl. Acad. Sci. U. S. A. 2018; 115: 619-624

Chin J.W.
et al.

An expanded eukaryotic genetic code.

Science. 2003; 301: 964-967

Ai H.-W.
et al.

Genetically encoded alkenes in yeast.

Angew. Chem. Int. Ed. Engl. 2010; 49: 935-937

Bacher J.M.
Ellington A.D.

Global incorporation of unnatural amino acids in Escherichia coli.

Methods Mol. Biol. 2007; 352: 23-34

Bezerra A.R.
et al.

Non-standard genetic codes define new concepts for protein engineering.

Life (Basel). 2015; 5: 1610-1628

Aleksashin N.A.
et al.

A fully orthogonal system for protein synthesis in bacterial cells.

Nat. Commun. 2020; 11: 1858

Fekner T.
Chan M.K.

The pyrrolysine translational machinery as a genetic-code expansion tool.

Curr. Opin. Chem. Biol. 2011; 15: 387-391

Expanding and reprogramming the genetic code of cells and animals.

Annu. Rev. Biochem. 2014; 83: 379-408

Cho C.-C.
et al.

The pyrrolysyl-tRNA synthetase activity can be improved by a P188 mutation that stabilizes the full-length enzyme.

J. Mol. Biol. 2022; 434167453

Bohlke N.
Budisa N.

Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion.

FEMS Microbiol. Lett. 2014; 351: 133-144