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Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure.

<div class='caption-title'>Mapping Deletion Mutations with Respect to EGFP Primary, Secondary, and Tertiary Structure</div>
<div class='caption-title'>Relationship between EGFP and SASA</div>
<div class='caption-title'>Fluorescence Properties of EGFPG4Δ</div>
Arpino JA, Reddington SC, Halliwell LM, Rizkallah PJ, Jones DD
OpenAccess logo Structure 22 889-98 (2014)
Cited: 30 times
EuropePMC logo PMID: 24856363

Abstract

Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFP(G4Δ)) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFP(G4Δ) retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFP(G4Δ) structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone.

Articles - 4ka9 mentioned but not cited (3)

  1. Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Arpino JA, Reddington SC, Halliwell LM, Rizkallah PJ, Jones DD. Structure 22 889-898 (2014)
  2. A Biosensor Platform for Metal Detection Based on Enhanced Green Fluorescent Protein. Lee W, Kim H, Kang Y, Lee Y, Yoon Y. Sensors (Basel) 19 E1846 (2019)
  3. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. Arpino JA, Rizkallah PJ, Jones DD. Acta Crystallogr D Biol Crystallogr 70 2152-2162 (2014)


Reviews citing this publication (1)

  1. A review of visualisations of protein fold networks and their relationship with sequence and function. Sykes J, Holland BR, Charleston MA. Biol Rev Camb Philos Soc 98 243-262 (2023)

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  2. GFP to BFP Conversion: A Versatile Assay for the Quantification of CRISPR/Cas9-mediated Genome Editing. Glaser A, McColl B, Vadolas J. Mol Ther Nucleic Acids 5 e334 (2016)
  3. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Hollfelder F. Nat Commun 11 3469 (2020)
  4. Structure-guided engineering of adenine base editor with minimized RNA off-targeting activity. Li J, Yu W, Huang S, Wu S, Li L, Zhou J, Cao Y, Huang X, Qiao Y. Nat Commun 12 2287 (2021)
  5. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Nat Commun 12 5664 (2021)
  6. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Macdonald CB, Nedrud D, Grimes PR, Trinidad D, Fraser JS, Coyote-Maestas W. Genome Biol 24 36 (2023)
  7. Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase. Gonzalez CE, Roberts P, Ostermeier M. J Mol Biol 431 2320-2330 (2019)
  8. Production and purification of homogenous recombinant human selenoproteins reveals a unique codon skipping event in E. coli and GPX4-specific affinity to bromosulfophthalein. Cheng Q, Roveri A, Cozza G, Bordin L, Rohn I, Schwerdtle T, Kipp A, Ursini F, Maiorino M, Miotto G, Arnér ESJ. Redox Biol 46 102070 (2021)
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  10. Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature. Maddamsetti R, Johnson DT, Spielman SJ, Petrie KL, Marks DS, Meyer JR. Evolution 72 2234-2243 (2018)
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  12. Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation. Clausen L, Stein A, Grønbæk-Thygesen M, Nygaard L, Søltoft CL, Nielsen SV, Lisby M, Ravid T, Lindorff-Larsen K, Hartmann-Petersen R. PLoS Genet 16 e1009187 (2020)
  13. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification. Arpino JA, Baldwin AJ, McGarrity AR, Tippmann EM, Jones DD. PLoS One 10 e0127504 (2015)
  14. Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. Jackson EL, Spielman SJ, Wilke CO. PLoS One 12 e0164905 (2017)
  15. mCherry contains a fluorescent protein isoform that interferes with its reporter function. Fages-Lartaud M, Tietze L, Elie F, Lale R, Hohmann-Marriott MF. Front Bioeng Biotechnol 10 892138 (2022)
  16. A facile and efficient transposon mutagenesis method for generation of multi-codon deletions in protein sequences. Liu SS, Wei X, Ji Q, Xin X, Jiang B, Liu J. J Biotechnol 227 27-34 (2016)
  17. Hopeful (protein InDel) monsters? Tóth-Petróczy A, Tawfik DS. Structure 22 803-804 (2014)
  18. Structural plasticity of green fluorescent protein to amino acid deletions and fluorescence rescue by folding-enhancing mutations. Liu SS, Wei X, Dong X, Xu L, Liu J, Jiang B. BMC Biochem 16 17 (2015)
  19. Using the Evolutionary History of Proteins to Engineer Insertion-Deletion Mutants from Robust, Ancestral Templates Using Graphical Representation of Ancestral Sequence Predictions (GRASP). Ross CM, Foley G, Boden M, Gillam EMJ. Methods Mol Biol 2397 85-110 (2022)
  20. ΔFlucs: Brighter Photinus pyralis firefly luciferases identified by surveying consecutive single amino acid deletion mutations in a thermostable variant. Halliwell LM, Jathoul AP, Bate JP, Worthy HL, Anderson JC, Jones DD, Murray JAH. Biotechnol Bioeng 115 50-59 (2018)
  21. Computational modeling and prediction of deletion mutants. Woods H, Schiano DL, Aguirre JI, Ledwitch KV, McDonald EF, Voehler M, Meiler J, Schoeder CT. Structure 31 713-723.e3 (2023)
  22. A novel framework for engineering protein loops exploring length and compositional variation. Tizei PAG, Harris E, Withanage S, Renders M, Pinheiro VB. Sci Rep 11 9134 (2021)
  23. Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States. Vill AC, Delesalle VA, Tomko BE, Lichty KB, Strine MS, Guffey AA, Burton EA, Tanke NT, Krukonis GP. Phage (New Rochelle) 3 171-178 (2022)
  24. Considerations of AOX Functionality Revealed by Critical Motifs and Unique Domains. Brew-Appiah RAT, Sanguinet KA. Int J Mol Sci 19 E2972 (2018)
  25. Evaluation of GFP reporter utility for analysis of transcriptional slippage during gene expression. Wons E, Koscielniak D, Szadkowska M, Sektas M. Microb Cell Fact 17 150 (2018)
  26. Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure. Yang Y, Braga MV, Dean MD. Genome Biol Evol 16 evae093 (2024)


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