@Nature:《自然》研究论文:用于序列-功能研究的无序蛋白质理性设计

X AI KOLs Timeline 论文

摘要

《自然》研究论文提出了一种用于固有无序蛋白质的理性设计方法,以研究序列-功能关系,介绍了开源工具GOOSE,并提供了分析脚本和数据。

《自然》研究论文:用于序列-功能研究的无序蛋白质理性设计 https://t.co/BRWg6DS0Er
查看原文
查看缓存全文

缓存时间: 2026/08/03 19:49

Nature 研究论文:无序蛋白的理性设计用于序列–功能研究

https://t.co/BRWg6DS0Er


无序蛋白的理性设计用于序列–功能研究

来源:https://www.nature.com/articles/s41586-026-10849-1?utm_source=x&utm_medium=social&utm_campaign=nature&linkId=63004835&error=cookies_not_supported&code=6960ef02-92f3-4072-a214-e565079b6853

数据可用性

本文用于图表和分析的数据与分析脚本可在 GitHub 获取(https://github.com/sukeniklab/GOOSE_2026 和 https://github.com/holehouse-lab/supportingdata/tree/master/2026/GOOSE_2026)。原始测序数据已存入 Zenodo82(https://www.nature.com/articles/s41586-026-10849-1#ref-CR82)(https://zenodo.org/records/18774462)。

代码可用性

GOOSE 完全开源,可在 GitHub 获取(https://github.com/idptools/goose/)。GOOSE 的使用文档可在线获取(https://goose.readthedocs.io/en/latest/)。GOOSE 的部分功能可通过两个 Colab Notebook 使用。用于序列生成和变异设计,请使用以下 notebook:https://colab.research.google.com/drive/1U9B-TfoNEZbbjhPUG5lrMPS0JL0nDB3o?usp=sharing。用于创建具有特定同型/异型 IDR–IDR 相互作用的序列,请使用以下 notebook:https://colab.research.google.com/drive/1aJajo1IK66ApFSMwCCBumCZixlfshw7A?usp=sharing。

参考文献

  1. Holehouse, A. S. & Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered protein regions.*Nat. Rev. Mol. Cell Biol.*25, 187–211 (2024). Article (https://doi.org/10.1038%2Fs41580-023-00673-0)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=37957331)Google Scholar (http://scholar.google.com/scholar_lookup?&title=The%20molecular%20basis%20for%20cellular%20function%20of%20intrinsically%20disordered%20protein%20regions&journal=Nat.%20Rev.%20Mol.%20Cell%20Biol.&doi=10.1038%2Fs41580-023-00673-0&volume=25&pages=187-211&publication_year=2024&author=Holehouse%2CAS&author=Kragelund%2CBB)
  2. Albanese, K. I., Barbe, S., Tagami, S., Woolfson, D. N. & Schiex, T. Computational protein design.Nat. Rev. Methods Primers5, 13 (2025). Article (https://doi.org/10.1038%2Fs43586-025-00383-1)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Computational%20protein%20design&journal=Nat.%20Rev.%20Methods%20Primers&doi=10.1038%2Fs43586-025-00383-1&volume=5&publication_year=2025&author=Albanese%2CKI&author=Barbe%2CS&author=Tagami%2CS&author=Woolfson%2CDN&author=Schiex%2CT)
  3. Tesei, G., Pesce, F. & Lindorff-Larsen, K. Computational design of intrinsically disordered proteins.*Curr. Opin. Struct. Biol.*96, 103210 (2026). Article (https://doi.org/10.1016%2Fj.sbi.2025.103210)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=41579411)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Computational%20design%20of%20intrinsically%20disordered%20proteins&journal=Curr.%20Opin.%20Struct.%20Biol.&doi=10.1016%2Fj.sbi.2025.103210&volume=96&publication_year=2026&author=Tesei%2CG&author=Pesce%2CF&author=Lindorff-Larsen%2CK)
  4. Moses, D. et al. Structural biases in disordered proteins are prevalent in the cell.*Nat. Struct. Mol. Biol.*31, 283–292 (2024). Article (https://doi.org/10.1038%2Fs41594-023-01148-8)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=38177684)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10873198)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Structural%20biases%20in%20disordered%20proteins%20are%20prevalent%20in%20the%20cell&journal=Nat.%20Struct.%20Mol.%20Biol.&doi=10.1038%2Fs41594-023-01148-8&volume=31&pages=283-292&publication_year=2024&author=Moses%2CD)
  5. Das, R. K., Ruff, K. M. & Pappu, R. V. Relating sequence encoded information to form and function of intrinsically disordered proteins.*Curr. Opin. Struct. Biol.*32, 102–112 (2015). Article (https://doi.org/10.1016%2Fj.sbi.2015.03.008)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=25863585)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512920)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Relating%20sequence%20encoded%20information%20to%20form%20and%20function%20of%20intrinsically%20disordered%20proteins&journal=Curr.%20Opin.%20Struct.%20Biol.&doi=10.1016%2Fj.sbi.2015.03.008&volume=32&pages=102-112&publication_year=2015&author=Das%2CRK&author=Ruff%2CKM&author=Pappu%2CRV)
  6. Das, R. K. & Pappu, R. V. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.Proc. Natl Acad. Sci. USA110, 13392–13397 (2013). Article (https://doi.org/10.1073%2Fpnas.1304749110)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2013PNAS..11013392D)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=23901099)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3746876)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Conformations%20of%20intrinsically%20disordered%20proteins%20are%20influenced%20by%20linear%20sequence%20distributions%20of%20oppositely%20charged%20residues&journal=Proc.%20Natl%20Acad.%20Sci.%20USA&doi=10.1073%2Fpnas.1304749110&volume=110&pages=13392-13397&publication_year=2013&author=Das%2CRK&author=Pappu%2CRV)
  7. Staller, M. V. et al. A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain.*Cell Syst.*6, 444–455 (2018). Article (https://doi.org/10.1016%2Fj.cels.2018.01.015)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=29525204)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920710)Google Scholar (http://scholar.google.com/scholar_lookup?&title=A%20high-throughput%20mutational%20scan%20of%20an%20intrinsically%20disordered%20acidic%20transcriptional%20activation%20domain&journal=Cell%20Syst.&doi=10.1016%2Fj.cels.2018.01.015&volume=6&pages=444-455&publication_year=2018&author=Staller%2CMV)
  8. Pesce, F. et al. Design of intrinsically disordered protein variants with diverse structural properties.*Sci. Adv.*10, eadm9926 (2024). Article (https://doi.org/10.1126%2Fsciadv.adm9926)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=39196930)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11352843)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Design%20of%20intrinsically%20disordered%20protein%20variants%20with%20diverse%20structural%20properties&journal=Sci.%20Adv.&doi=10.1126%2Fsciadv.adm9926&volume=10&publication_year=2024&author=Pesce%2CF)
  9. Zarin, T., Tsai, C. N., Nguyen Ba, A. N. & Moses, A. M. Selection maintains signaling function of a highly diverged intrinsically disordered region.Proc. Natl Acad. Sci. USA114, E1450–E1459 (2017). Article (https://doi.org/10.1073%2Fpnas.1614787114)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2017PNAS..114E1450Z)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=28167781)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338452)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Selection%20maintains%20signaling%20function%20of%20a%20highly%20diverged%20intrinsically%20disordered%20region&journal=Proc.%20Natl%20Acad.%20Sci.%20USA&doi=10.1073%2Fpnas.1614787114&volume=114&pages=E1450-E1459&publication_year=2017&author=Zarin%2CT&author=Tsai%2CCN&author=Nguyen%20Ba%2CAN&author=Moses%2CAM)
  10. Das, R. K., Huang, Y., Phillips, A. H., Kriwacki, R. W. & Pappu, R. V. Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling.Proc. Natl Acad. Sci. USA113, 5616–5621 (2016). Article (https://doi.org/10.1073%2Fpnas.1516277113)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2016PNAS..113.5616D)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=27140628)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878473)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Cryptic%20sequence%20features%20within%20the%20disordered%20protein%20p27Kip1%20regulate%20cell%20cycle%20signaling&journal=Proc.%20Natl%20Acad.%20Sci.%20USA&doi=10.1073%2Fpnas.1516277113&volume=113&pages=5616-5621&publication_year=2016&author=Das%2CRK&author=Huang%2CY&author=Phillips%2CAH&author=Kriwacki%2CRW&author=Pappu%2CRV)
  11. Holehouse, A. S., Das, R. K., Ahad, J. N., Richardson, M. O. G. & Pappu, R. V. CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins.*Biophys. J.*112, 16–21 (2017). Article (https://doi.org/10.1016%2Fj.bpj.2016.11.3200)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2017BpJ…112…16H)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=28076807)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5232785)Google Scholar (http://scholar.google.com/scholar_lookup?&title=CIDER%3A%20resources%20to%20analyze%20sequence-ensemble%20relationships%20of%20intrinsically%20disordered%20proteins&journal=Biophys.%20J.&doi=10.1016%2Fj.bpj.2016.11.3200&volume=112&pages=16-21&publication_year=2017&author=Holehouse%2CAS&author=Das%2CRK&author=Ahad%2CJN&author=Richardson%2CMOG&author=Pappu%2CRV)
  12. Novak, B., Lotthammer, J. M., Emenecker, R. J. & Holehouse, A. S. Accurate predictions of disordered protein ensembles with STARLING.Nature652, 240–250 (2026). Article (https://doi.org/10.1038%2Fs41586-026-10141-2)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=41708867)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC13043300)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Accurate%20predictions%20of%20disordered%20protein%20ensembles%20with%20STARLING&journal=Nature&doi=10.1038%2Fs41586-026-10141-2&volume=652&pages=240-250&publication_year=2026&author=Novak%2CB&author=Lotthammer%2CJM&author=Emenecker%2CRJ&author=Holehouse%2CAS)
  13. González-Foutel, N. S. et al. Conformational buffering underlies functional selection in intrinsically disordered protein regions.*Nat. Struct. Mol. Biol.*29, 781–790 (2022). Article (https://doi.org/10.1038%2Fs41594-022-00811-w)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=35948766)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10262780)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Conformational%20buffering%20underlies%20functional%20selection%20in%20intrinsically%20disordered%20protein%20regions&journal=Nat.%20Struct.%20Mol.%20Biol.&doi=10.1038%2Fs41594-022-00811-w&volume=29&pages=781-790&publication_year=2022&author=Gonz%C3%A1lez-Foutel%2CNS)
  14. Zeno, W. F. et al. Molecular mechanisms of membrane curvature sensing by a disordered protein.*J. Am. Chem. Soc.*141, 10361–10371 (2019). Article (https://doi.org/10.1021%2Fjacs.9b03927)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2019JAChS.14110361Z)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=31180661)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6610580)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Molecular%20mechanisms%20of%20membrane%20curvature%20sensing%20by%20a%20disordered%20protein&journal=J.%20Am.%20Chem.%20Soc.&doi=10.1021%2Fjacs.9b03927&volume=141&pages=10361-10371&publication_year=2019&author=Zeno%2CWF)
  15. Halladin, D. K. et al. Entropy-driven translocation of disordered proteins through the Gram-positive bacterial cell wall.*Nat. Microbiol.*6, 1055–1065 (2021). Article (https://doi.org/10.1038%2Fs41564-021-00942-8)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=34326523)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10265014)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Entropy-driven%20translocation%20of%20disordered%20proteins%20through%20the%20Gram-positive%20bacterial%20cell%20wall&journal=Nat.%20Microbiol.&doi=10.1038%2Fs41564-021-00942-8&volume=6&pages=1055-1065&publication_year=2021&author=Halladin%2CDK)
  16. Berlow, R. B., Dyson, H. J. & Wright, P. E. Hypersensitive termination of the hypoxic response by a disordered protein switch.Nature543, 447–451 (2017). Article (https://doi.org/10.1038%2Fnature21705)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2017Natur.543..447B)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=28273070)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5375031)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Hypersensitive%20termination%20of%20the%20hypoxic%20response%20by%20a%20disordered%20protein%20switch&journal=Nature&doi=10.1038%2Fnature21705&volume=543&pages=447-451&publication_year=2017&author=Berlow%2CRB&author=Dyson%2CHJ&author=Wright%2CPE)
  17. Schuler, B., König, I., Soranno, A. & Nettels, D. Impact of in-cell and in-vitro crowding on the conformations and dynamics of an intrinsically disordered protein.*Angew. Chem. Int. Ed.*https://doi.org/10.1002/anie.202016804(2021).
  18. Ruff, K. M. et al Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell189, 323–342 (2025).
  19. Moses, D. et al. Revealing the hidden sensitivity of intrinsically disordered proteins to their chemical environment.*J. Phys. Chem. Lett.*11, 10131–10136 (2020). Article (https://doi.org/10.1021%2Facs.jpclett.0c02822)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=33191750)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092420)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Revealing%20the%20hidden%20sensitivity%20of%20intrinsically%20disordered%20proteins%20to%20their%20chemical%20environment&journal=J.%20Phys.%20Chem.%20Lett.&doi=10.1021%2Facs.jpclett.0c02822&volume=11&pages=10131-10136&publication_year=2020&author=Moses%2CD)
  20. Marsh, J. A. & Forman-Kay, J. D. Sequence determinants of compaction in intrinsically disordered proteins.*Biophys. J.*98, 2383–2390 (2010). Article (https://doi.org/10.1016%2Fj.bpj.2010.02.006)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2010BpJ….98.2383M)PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=20483348)PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872267)Google Scholar (http://scholar.google.com/scholar_lookup?&title=Sequence%20determinants%20of%20compaction%20in%20intrinsically%20disordered%20proteins&journal=Biophys.%20J.&doi=10.1016%2Fj.bpj.2010.02.006&volume=98&pages=2383-2390&publication_year=2010&author=Marsh%2CJA&author=Forman-Kay%2CJD)
  21. Müller-Späth, S. et al. From the cover: charge interactions can dominate the dimensions of intrinsically disordered proteins.Proc. Natl Acad. Sci. USA107, 14609–14614 (2010). Article (https://doi.org/10.1073%2Fpnas.1001743107)ADS (http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2010PNAS..10714609M)PubMed (http://www.ncbi.nlm.nih.gov/entrez/que

相似文章

自然界蛋白质折叠的不合理冗余

Hacker News Top

来自Ligo的一篇博客文章,讨论了天然蛋白质折叠的冗余性,以及为生成式生物分子模型扩展结构数据所面临的挑战,文中提及了AlphaFold3和其他最新模型。

Design-CP:蛋白质纳米颗粒设计的上下文并行技术

arXiv cs.LG

Design-CP 为 RFdiffusion 3 引入了上下文并行推理策略,通过将二次激活分布到多个 GPU 上,实现了大型多聚体蛋白质纳米颗粒的全原子设计,从而在较小的 GPU 集群上使大规模组装蛋白质设计变得可行。

蛋白质先导化合物优化的入门指南

Hacker News Top

本文旨在作为药物设计中蛋白质先导化合物优化的初学者指南,具体解释了 Cradle-1 流程以及蛋白质结构和功能的基础概念。