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PreprintCited by 22Protein Structure and DynamicsEnzyme Structure and FunctionDrug Transport and Resistance Mechanisms

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Comprehensive collection and prediction of ABC transmembrane protein structures in the AI era of structural biology

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Tordai, Hedvig, Suhajda, Erzsébet, Sillitoe, Ian, Nair, Sreenath, Váradi, Mihály, Hegedűs, Tamás·2022·International Journal of Molecular Sciences
DOI 10.1101/2022.07.08.499254PMC PMC9408558

Preprint — published as 10.3390/ijms23168877 · Paper page

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Abstract

The number of unique transmembrane (TM) protein structures doubled in the last four years that can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.

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Research works printed but not linked: 65

  1. George, A.M. ABC Transporters - 40 Years On; Springer Cham, 2016; ISBN 978-3-319-23476-2. · DOI
  2. 10.1016/j.drudis.2007.12.010 · DOI
  3. 10.1152/physrev.00007.2018 · DOI · Paper page
  4. 10.1016/j.tibs.2018.10.005 · DOI
  5. 10.1091/mbc.E14-04-0935 · DOI
  6. 10.1002/1873-3468.13947 · DOI
  7. 10.1007/978-981-13-7647-4_5 · DOI
  8. 10.1038/nsmb.3216 · DOI · Paper page
  9. 10.1038/s41594-019-0280-4 · DOI
  10. 10.1002/1873-3468.13966 · DOI
  11. 10.3390/ijms20112783 · DOI
  12. 10.1021/acs.biochem.7b01031 · DOI
  13. 10.1146/annurev-bioeng-092115-025322 · DOI
  14. 10.1038/nrd.2016.230 · DOI · Paper page
  15. 10.1107/S2053230x13033141 · DOI
  16. 10.1016/j.sbi.2021.03.008 · DOI
  17. 10.1093/bioinformatics/btz539 · DOI
  18. 10.1002/prot.26171 · DOI · Paper page
  19. 10.1093/nar/gkab1061 · DOI · Paper page
  20. 10.1007/s00018-021-04112-1 · DOI · Paper page
  21. 10.1126/science.abm4805 · DOI · Paper page
  22. 10.1038/s41596-021-00628-9 · DOI
  23. 10.1002/1873-3468.13935 · DOI
  24. 10.1038/ng0297-137 · DOI
  25. 10.1016/S0005-2736(99)00161-3 · DOI
  26. 10.1124/mol.116.104190 · DOI
  27. 10.1042/BST20150047 · DOI
  28. 10.1016/j.str.2021.05.013 · DOI
  29. 10.1042/BST20180147 · DOI
  30. DALI and the Persistence of Protein Shape - PubMed Available online: https://pubmed.ncbi.nlm.nih.gov/31606894/ (accessed on 2 June 2022).
  31. 10.1093/nar/gkt1240 · DOI · Paper page
  32. 10.1093/nar/gkaa1038 · DOI · Paper page
  33. 10.1101/2021.10.04.463034 · DOI · Paper page
  34. 10.1371/journal.pcbi.1002195 · DOI · Paper page
  35. 10.1093/bioinformatics/btp163 · DOI · Paper page
  36. 10.1093/nar/gki524 · DOI · Paper page
  37. 10.1002/jcc.21787 · DOI
  38. 10.1038/s41586-020-2649-2 · DOI · Paper page
  39. 10.1093/nar/gkaa1100 · DOI · Paper page
  40. 10.21105/joss.04200 · DOI
  41. 10.1109/MCSE.2007.55 · DOI · Paper page
  42. 10.1038/s41422-019-0222-z · DOI
  43. 10.1038/s41422-021-00585-8 · DOI
  44. 10.1038/s41586-020-2072-8 · DOI
  45. 10.1126/sciadv.abj5363 · DOI
  46. 10.1073/pnas.2123268119 · DOI
  47. 10.1038/s42003-021-02318-4 · DOI
  48. 10.1038/s41467-021-24651-2 · DOI
  49. 10.1016/j.csbj.2018.10.008 · DOI
  50. 10.1074/jbc.274.18.12209 · DOI
  51. 10.1113/JP281933 · DOI
  52. 10.1007/s00018-020-03651-3 · DOI
  53. 10.1111/j.1742-4658.2008.06832.x · DOI
  54. 10.1038/s41467-020-16155-2 · DOI · Paper page
  55. 10.1073/pnas.1412246112 · DOI
  56. 10.1038/cr.2017.38 · DOI
  57. 10.1007/s00424-006-0116-z · DOI
  58. 10.1007/s13238-018-0530-y · DOI
  59. 10.1038/s41586-019-1498-3 · DOI
  60. 10.1016/S0006-3495(94)80887-2 · DOI
  61. 10.1126/science.280.5360.69 · DOI
  62. 10.1093/nar/gkab314 · DOI · Paper page
  63. 10.1093/bioinformatics/btaa217 · DOI
  64. 10.1002/humu.22138 · DOI
  65. 10.1093/database/bax023 · DOI

Metadata

Authors
Tordai, H., Suhajda, E., Sillitoe, I., Nair, S., Váradi, M., & Hegedűs, T.
Affiliations
  • Semmelweis University (HU)
  • Institute of Structural and Molecular Biology (GB)
  • European Bioinformatics Institute (GB)
Corresponding author
Hegedűs, Tamás
ORCID
Venue
International Journal of Molecular Sciences
Publisher
openRxiv
Published
2022-07-10
Volume
23
Issue
16
Pages
8877-8877
ISSN
1422-0067 (ISSN-L)
DOI
10.1101/2022.07.08.499254
PMC
PMC9408558
OpenAlex
W4292074325
Cited by
22
References
1
Citations by year
2025: 7 · 2024: 6 · 2023: 3 · 2022: 6
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • International Journal of Molecular Sciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • UCL Discovery (University College London) (submittedVersion)
Funders
  • Cystic Fibrosis Foundation (2020-2.1.1-ED-2021-00179, HEGEDU20I0, K127961, BB/S020071/1, K137610)
  • Nemzeti Kutatási Fejlesztési és Innovációs Hivatal (2020-2.1.1-ED-2021-00179, 2020-2.1.1-ED, K127961)
  • Biotechnology and Biological Sciences Research Council (2020-2.1.1-ED-2021-00179, BB/S020071/1, K127961, HEGEDU20I0, 2.1.1, K137610)
  • National Research, Development and Innovation Office (K137610, K127961, and 2020-2.1.1-ED-2021-00179)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
Keywords
ABC transporters, transmembrane proteins, protein structure prediction, AlphaFold2, conformational states, web application
MeSH terms
Artificial Intelligence, Biology, Furylfuramide, Humans, Models, Molecular, Protein Conformation, ATP-Binding Cassette Transporters, Cryoelectron Microscopy

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