A Platform for Constructing, Evaluating, and Screening Bioconjugates on the Yeast Surface

Overview

Journal Protein Eng Des Sel

Publisher Oxford University Press

Specialties Biochemistry
Biotechnology

Date 2016 Aug 13

PMID 27515702

Citations 17

Authors

James A Van Deventer

Doris N Le

Jessie Zhao

Haixing P Kehoe

Ryan L Kelly

Affiliations

Soon will be listed here.

Abstract

The combination of protein display technologies and noncanonical amino acids (ncAAs) offers unprecedented opportunities for the high throughput discovery and characterization of molecules suitable for addressing fundamental and applied problems in biological systems. Here we demonstrate that ncAA-compatible yeast display facilitates evaluations of conjugation chemistry and stability that would be challenging or impossible to perform with existing mRNA, phage, or E. coli platforms. Our approach enables site-specific introduction of ncAAs into displayed proteins, robust modification at azide-containing residues, and quantitative evaluation of conjugates directly on the yeast surface. Moreover, screening allows for the selective enrichment of chemically modified constructs while maintaining a genotype-phenotype linkage with encoded azide functionalities. Thus, this platform is suitable for the high throughput characterization and screening of libraries of chemically modified polypeptides for therapeutic lead discovery and other biological applications.

Citing Articles

Reaching New Heights in Genetic Code Manipulation with High Throughput Screening.

Lino B, Williams S, Castor M, Van Deventer J Chem Rev. 2024; 124(21):12145-12175.

PMID: 39418482 PMC: 11879460. DOI: 10.1021/acs.chemrev.4c00329.

Protein Engineering and High-Throughput Screening by Yeast Surface Display: Survey of Current Methods.

Lopez-Morales J, Vanella R, Appelt E, Whillock S, Paulk A, Shusta E Small Sci. 2024; 3(12).

PMID: 39071103 PMC: 11271970. DOI: 10.1002/smsc.202300095.

Systematic Evaluation of Protein-Small Molecule Hybrids on the Yeast Surface.

Huang M, Rueda-Garcia M, Harthorn A, Hackel B, Van Deventer J ACS Chem Biol. 2024; 19(2):325-335.

PMID: 38230650 PMC: 11146673. DOI: 10.1021/acschembio.3c00524.

Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display.

Cribari M, Unger M, Unarta I, Ogorek A, Huang X, Martell J J Am Chem Soc. 2023; 145(50):27380-27389.

PMID: 38051911 PMC: 11058326. DOI: 10.1021/jacs.3c08291.

Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast.

Lahiri P, Martin M, Lino B, Scheck R, Van Deventer J Biochemistry. 2023; 62(14):2098-2114.

PMID: 37377426 PMC: 11146674. DOI: 10.1021/acs.biochem.2c00711.

References

Traxlmayr M, Lobner E, Antes B, Kainer M, Wiederkum S, Hasenhindl C . Directed evolution of Her2/neu-binding IgG1-Fc for improved stability and resistance to aggregation by using yeast surface display. Protein Eng Des Sel. 2012; 26(4):255-65. DOI: 10.1093/protein/gzs102. View

Wiltschi B, Wenger W, Nehring S, Budisa N . Expanding the genetic code of Saccharomyces cerevisiae with methionine analogues. Yeast. 2008; 25(11):775-86. DOI: 10.1002/yea.1632. View

Des Soye B, Patel J, Isaacs F, Jewett M . Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol. 2015; 28:83-90. PMC: 5113029. DOI: 10.1016/j.cbpa.2015.06.008. View

Chari R, Miller M, Widdison W . Antibody-drug conjugates: an emerging concept in cancer therapy. Angew Chem Int Ed Engl. 2014; 53(15):3796-827. DOI: 10.1002/anie.201307628. View

Ng S, Jafari M, Derda R . Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry. ACS Chem Biol. 2011; 7(1):123-38. DOI: 10.1021/cb200342h. View

Wang Q, Wang L . New methods enabling efficient incorporation of unnatural amino acids in yeast. J Am Chem Soc. 2008; 130(19):6066-7. DOI: 10.1021/ja800894n. View

Traxlmayr M, Hasenhindl C, Hackl M, Stadlmayr G, Rybka J, Borth N . Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing. J Mol Biol. 2012; 423(3):397-412. PMC: 3469823. DOI: 10.1016/j.jmb.2012.07.017. View

Link A, Vink M, Tirrell D . Presentation and detection of azide functionality in bacterial cell surface proteins. J Am Chem Soc. 2004; 126(34):10598-602. DOI: 10.1021/ja047629c. View

Kwon O, Yoo T, Othon C, Van Deventer J, Tirrell D, Zewail A . Hydration dynamics at fluorinated protein surfaces. Proc Natl Acad Sci U S A. 2010; 107(40):17101-6. PMC: 2951393. DOI: 10.1073/pnas.1011569107. View

10.

Van Deventer J, Kelly R, Rajan S, Wittrup K, Sidhu S . A switchable yeast display/secretion system. Protein Eng Des Sel. 2015; 28(10):317-25. PMC: 4596280. DOI: 10.1093/protein/gzv043. View

11.

Horiya S, Bailey J, Temme J, Guillen Schlippe Y, Krauss I . Directed evolution of multivalent glycopeptides tightly recognized by HIV antibody 2G12. J Am Chem Soc. 2014; 136(14):5407-15. PMC: 4004241. DOI: 10.1021/ja500678v. View

12.

Lim K, Madabhushi S, Mann J, Neelamegham S, Park S . Disulfide trapping of protein complexes on the yeast surface. Biotechnol Bioeng. 2010; 106(1):27-41. DOI: 10.1002/bit.22651. View

13.

Dirksen A, Madsen M, Dello Iacono G, Matin M, Bacica M, Stankovic N . Parallel synthesis and screening of peptide conjugates. Bioconjug Chem. 2014; 25(6):1052-60. DOI: 10.1021/bc500129w. View

14.

Ye S, Zaitseva E, Caltabiano G, Schertler G, Sakmar T, Deupi X . Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature. 2010; 464(7293):1386-9. DOI: 10.1038/nature08948. View

15.

VanAntwerp J, Wittrup K . Fine affinity discrimination by yeast surface display and flow cytometry. Biotechnol Prog. 2000; 16(1):31-7. DOI: 10.1021/bp990133s. View

16.

Sun S, Schultz P, Kim C . Therapeutic applications of an expanded genetic code. Chembiochem. 2014; 15(12):1721-9. PMC: 4472442. DOI: 10.1002/cbic.201402154. View

17.

ODonoghue P, Ling J, Wang Y, Soll D . Upgrading protein synthesis for synthetic biology. Nat Chem Biol. 2013; 9(10):594-8. PMC: 3975081. DOI: 10.1038/nchembio.1339. View

18.

Ng S, Jafari M, Matochko W, Derda R . Quantitative synthesis of genetically encoded glycopeptide libraries displayed on M13 phage. ACS Chem Biol. 2012; 7(9):1482-7. DOI: 10.1021/cb300187t. View

19.

Johnson J, Lu Y, Van Deventer J, Tirrell D . Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications. Curr Opin Chem Biol. 2010; 14(6):774-80. PMC: 3008400. DOI: 10.1016/j.cbpa.2010.09.013. View

20.

Hasenhindl C, Traxlmayr M, Wozniak-Knopp G, Jones P, Stadlmayr G, Ruker F . Stability assessment on a library scale: a rapid method for the evaluation of the commutability and insertion of residues in C-terminal loops of the CH3 domains of IgG1-Fc. Protein Eng Des Sel. 2013; 26(10):675-82. PMC: 3785252. DOI: 10.1093/protein/gzt041. View