@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
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。
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
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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).
- Ruff, K. M. et al Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell189, 323–342 (2025).
- 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)
- 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)
- 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
@BioSpace9:利用基于扩散的系综采样进行蛋白质开关的从头设计
这篇bioRxiv预印本介绍了Diff-Switch框架,该框架利用基于扩散的系综采样生成构象状态,用于从头设计蛋白质开关,从而提高找到开关兼容序列的成功率。
@Nature: Nature研究论文:AI重新设计的起点和结果增强了蛋白质进化
该Nature研究论文介绍了一种AI方法,该方法重新设计起点和结果以增强蛋白质进化。
自然界蛋白质折叠的不合理冗余
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
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
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。