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PreprintCited by 3Protein Structure and DynamicsEvolution and Genetic DynamicsBacterial Genetics and Biotechnology

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Evolutionary engineering a larger porin using a loop-to-hairpin mechanism

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Dhar, Rik, Bowman, Alexander M., Hatungimana, Brunojoel, Slusky, Joanna SG·2023·Journal of Molecular Biology
DOI 10.1101/2023.06.14.544993PMC PMC11215794

Preprint — published as 10.1016/j.jmb.2023.168292 · Paper page

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Abstract

In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition. Highlights: We find evidence supporting a novel diversification mechanism in membrane β-barrels The mechanism is the conversion of an extracellular loop to transmembrane β-hairpin A chimeric protein modeling this mechanism folds stably in the membrane The chimera has more β-structure and a larger pore, consistent with a loop-to-hairpin transition

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Research works printed but not linked: 68

  1. 2020, Landscape of Eukaryotic Transmembrane Beta Barrel Proteins, J Proteome Res, 19, 1209, 10.1021/acs.jproteome.9b00740 · DOI
  2. 10.1038/nature02208 · DOI
  3. 10.1046/j.1365-2958.2000.01983.x · DOI
  4. 10.1016/S0005-2736(02)00577-1 · DOI
  5. 10.1016/j.jmb.2018.06.013 · DOI
  6. 10.1016/j.bbamem.2012.08.021 · DOI
  7. 10.1093/protein/10.6.699 · DOI
  8. 10.1093/protein/11.9.797 · DOI
  9. 10.1046/j.1432-1327.2000.01073.x · DOI
  10. 10.1128/JB.00825-12 · DOI
  11. 10.1021/bi981215c · DOI
  12. 2021, OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins, Front Bioinform, 1, 646581, 10.3389/fbinf.2021.646581 · DOI
  13. 10.1074/jbc.REV120.011473 · DOI
  14. 10.1016/0022-2836(72)90508-6 · DOI
  15. 10.1007/BF01734217 · DOI
  16. McLachlan A . Gene duplication and the origin of repetitive protein structures. Cold Spring Harbor symposia on quantitative biology: Cold Spring Harbor Laboratory Press; 1987. p. 411–20. · DOI
  17. Stephens S . Possible significance of duplication in evolution. Advances in genetics: Elsevier; 1951. p. 247–65. · DOI
  18. 2003, Evolution by gene duplication: an update, Trends in Ecology & Evolution, 18, 292, 10.1016/S0169-5347(03)00033-8 · DOI · Paper page
  19. 10.1016/j.jmb.2006.12.029 · DOI
  20. 10.1007/s12041-013-0212-8 · DOI
  21. Franklin MW , Nepomnyachyi S , Feehan R , Ben-Tal N , Kolodny R , Slusky JS . Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. Elife. 2018;7. · DOI
  22. 2021, Outer membrane protein evolution, Curr Opin Struct Biol, 68, 122, 10.1016/j.sbi.2021.01.002 · DOI
  23. 2015, A vocabulary of ancient peptides at the origin of folded proteins, Elife, 4, e09410, 10.7554/eLife.09410 · DOI
  24. 10.1002/pro.5560040820 · DOI
  25. 10.1093/molbev/msq017 · DOI
  26. Reddy BL , Saier Jr MH . Properties and phylogeny of 76 families of bacterial and eukaryotic organellar outer membrane pore-forming proteins. PloS one. 2016;11. · DOI
  27. 10.1002/bies.10321 · DOI · Paper page
  28. 2021, Membrane barrels are taller, fatter, inside-out soluble barrels, The Journal of Physical Chemistry B, 125, 3622, 10.1021/acs.jpcb.1c00878 · DOI
  29. 2011, Engineering of an E. coli outer membrane protein FhuA with increased channel diameter, J Nanobiotechnology, 9, 33, 10.1186/1477-3155-9-33 · DOI
  30. 2017, Engineering enhanced pore sizes using FhuA Δ1-160 from E. coli outer membrane as template, ACS sensors, 2, 1619, 10.1021/acssensors.7b00481 · DOI
  31. 10.1074/jbc.RA120.014366 · DOI
  32. 10.1046/j.1365-2958.2000.01748.x · DOI
  33. 2015, IR-spectroscopic characterization of an elongated OmpG mutant, Arch Biochem Biophys, 576, 73, 10.1016/j.abb.2015.04.010 · DOI
  34. 2017, Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif, Biochim Biophys Acta Biomembr, 1859, 1180, 10.1016/j.bbamem.2017.03.012 · DOI
  35. 10.1021/acs.biochem.8b00012 · DOI
  36. 10.1042/BJ20100371 · DOI
  37. 10.1016/j.jmb.2005.09.094 · DOI
  38. 10.1073/pnas.1501836112 · DOI
  39. 10.1042/BJ20121025 · DOI
  40. 10.1016/j.jmb.2016.09.021 · DOI
  41. 10.1128/jb.169.1.66-71.1987 · DOI
  42. 1988, An Artificial Hydrophobic Sequence Functions as Either an Anchor or a Signal Sequence at Only One of 2 Positions within the Escherichia-Coli Outer-Membrane Protein-Ompa, Journal of Biological Chemistry, 263, 19053, 10.1016/S0021-9258(18)37388-5 · DOI
  43. 1991, The class 3 outer membrane protein (PorB) of Neisseria meningitidis: gene sequence and homology to the gonococcal porin PIA, FEMS Microbiol Lett, 67, 179
  44. 10.1073/pnas.84.24.9084 · DOI
  45. 2015, High-level production of membrane proteins in E. coli BL21(DE3) by omitting the inducer IPTG, Microb Cell Fact, 14, 142, 10.1186/s12934-015-0328-z · DOI
  46. 10.1016/j.jmb.2016.09.021 · DOI
  47. Franklin MW . Drawing Insight from Structure to Guide Design [Doctoral Dissertation]. Ann Arbor: University of Kansas; 2019.
  48. 10.1111/j.1432-1033.1974.tb03671.x · DOI
  49. 1993, Proteinase K (EC 3.4.21.14), Methods Mol Biol., 16, 305
  50. 2021, Bacterial Outer Membrane Proteins Are Targeted to the Bam Complex by Two Parallel Mechanisms, mBio, 12, e00597
  51. 10.1128/JB.185.22.6540-6547.2003 · DOI
  52. 10.1073/pnas.0912115107 · DOI
  53. Gasteiger E , Hoogland C , Gattiker A , Wilkins MR , Appel RD , Bairoch A . Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook. 2005:571–607. · DOI
  54. 2022, ColabFold: making protein folding accessible to all, Nature Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  55. Evans R , O’Neill M , Pritzel A , Antropova N , Senior A , Green T , et al. Protein complex prediction with AlphaFold-Multimer. BioRxiv. 2021:2021.10. 04.463034. · DOI · Paper page
  56. 10.1093/bioinformatics/btw554 · DOI
  57. 2015, CAVER: algorithms for analyzing dynamics of tunnels in macromolecules, IEEE/ACM transactions on computational biology and bioinformatics, 13, 505
  58. 10.1073/pnas.1115898108 · DOI
  59. 2021, Perturbing the energy landscape for improved packing during computational protein design, Proteins, 89, 436, 10.1002/prot.26030 · DOI · Paper page
  60. 10.1371/journal.pone.0020161 · DOI
  61. 2021, Inward-facing glycine residues create sharp turns in beta-barrel membrane proteins, Biochim Biophys Acta Biomembr, 1863, 183662, 10.1016/j.bbamem.2021.183662 · DOI
  62. 10.1073/pnas.0801965105 · DOI
  63. 10.1385/0-89603-332-5:203 · DOI
  64. 10.1038/msb4100050 · DOI · Paper page
  65. 10.1007/978-1-4939-2871-2_12 · DOI
  66. 10.1016/S0006-3495(97)78223-7 · DOI
  67. 10.1002/(SICI)1097-0231(19990315)13:5<315::AID-RCM483>3.0.CO;2-C · DOI
  68. 10.1109/mcse.2007.55 · DOI · Paper page

Metadata

Authors
Dhar, R., Bowman, A. M., Hatungimana, B., & Slusky, J. S.
Affiliations
University of Kansas (US)
Corresponding author
Slusky, Joanna SG
ORCID
Venue
Journal of Molecular Biology
Publisher
openRxiv
Published
2023-06-14
Volume
435
Issue
22
Pages
168292-168292
ISSN
0022-2836 (ISSN-L)
DOI
10.1101/2023.06.14.544993
PMC
PMC11215794
OpenAlex
W4387046787
Cited by
3
References
1
Citations by year
2026: 2 · 2024: 1
FWCI
0.27
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Journal of Molecular Biology (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
Funders
  • National Science Foundation (P20GM113117, 2226804, P20GM103418)
  • Directorate for Biological Sciences
  • National Institute of General Medical Sciences (DP2GM128201, P20GM113117, P20GM103418, R01GM148583)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
porin, protein evolution, fusion protein, beta-hairpin, protein stability, protein topology

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CoChat. (2026). Citation check: Evolutionary engineering a larger porin using a loop-to-hairpin mechanism. https://app.cochat.ai/papers/10.1101/2023.06.14.544993
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Dhar, R., Bowman, A. M., Hatungimana, B., & Slusky, J. S. (2023). Evolutionary engineering a larger porin using a loop-to-hairpin mechanism. Journal of Molecular Biology. https://doi.org/10.1101/2023.06.14.544993