AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs.
AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs.
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DOI：
10.1371/journal.pbio.3001962
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发表时间：
2023-03
期刊：
影响因子：
9.8
通讯作者：
中科院分区：
文献类型：
--
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巨自噬/自噬是真核细胞中细胞内稳态和防御病原体的细胞内降解过程。自噬的调节依赖于自噬货物受体和衔接子与ATG 8/LC 3蛋白家族成员的分级结合。与ATG 8/LC 3的相互作用通常由保守的短线性序列促进，称为ATG 8/LC 3相互作用基序/区域（AIM/LIR），存在于自噬衔接子和受体以及靶向宿主自噬机制的病原体毒力因子中。由于典型的AIM/LIR序列可以在许多蛋白质中找到，因此鉴定功能性AIM/LIR基序已被证明具有挑战性。在这里，我们表明，蛋白质建模使用Alphafold-Multimer（AF 2-多聚体）识别典型和非典型的AIM/LIR基序具有很高的准确性。AF 2多聚体可以通过使用在主要AIM/LIR残基中具有突变的蛋白质序列来修饰以检测另外的功能性AIM/LIR基序。通过结合蛋白质建模数据从AF 2-多聚体与蛋白质序列的系统发育分析和蛋白质-蛋白质相互作用测定，我们证明AF 2-多聚体预测的生理相关的AIM基序在ATG 8相互作用蛋白2（ATI-2），以及以前未表征的非典型的AIM基序在马铃薯（马铃薯）的ATG 3。AF 2多聚体还鉴定了病原体编码的毒力因子中的AIM/LIR基序，这些毒力因子靶向其植物和人类宿主中的ATG 8成员，揭示了跨王国ATG 8-LIR/AIM关联也可以通过AF 2多聚体预测。我们的结论是，AF 2引导的自噬适配器/受体的发现将大大加快我们对所有生物王国中自噬的分子基础的理解。巨自噬/自噬是真核细胞中细胞内稳态和防御病原体的细胞内降解过程。自噬的调节依赖于自噬货物受体和衔接子与ATG 8/LC 3蛋白家族成员的分级结合。与ATG 8/LC 3的相互作用通常由保守的短线性序列促进，称为ATG 8/LC 3相互作用基序/区域（AIM/LIR），存在于自噬衔接子和受体以及靶向宿主自噬机制的病原体毒力因子中。由于典型的AIM/LIR序列可以在许多蛋白质中找到，因此识别功能性AIM/LIR基序已被证明具有挑战性。在这里，我们表明，蛋白质建模使用Alphafold-Multimer（AF 2-多聚体）确定规范和非典型的AIM/LIR基序具有很高的准确性。AF 2多聚体可以通过使用在主要AIM/LIR残基中具有突变的蛋白质序列来修饰以检测另外的功能性AIM/LIR基序。通过结合蛋白质建模数据从AF 2-多聚体与蛋白质序列的系统发育分析和蛋白质-蛋白质相互作用测定，我们证明AF 2-多聚体预测的生理相关的AIM基序在ATG 8相互作用蛋白2（ATI-2），以及以前未表征的非典型的AIM基序在马铃薯（马铃薯）的ATG 3。AF 2多聚体还鉴定了病原体编码的毒力因子中的AIM/LIR基序，这些毒力因子靶向其植物和人类宿主中的ATG 8成员，揭示了跨王国ATG 8- LIR/AIM关联也可以通过AF 2多聚体预测。我们的结论是，AF 2引导的自噬适配器/受体的发现将大大加快我们对所有生物王国中自噬的分子基础的理解。
Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein–protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms. Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2- multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized non-canonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8- LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.
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影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
DOI：
10.1074/jbc.m116.744995
发表时间：
2016-09-16
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Maqbool A;Hughes RK;Dagdas YF;Tregidgo N;Zess E;Belhaj K;Round A;Bozkurt TO;Kamoun S;Banfield MJ
通讯作者：
Banfield MJ
影响因子：
7.2
作者：
Koh, S;André, A;Somerville, S
通讯作者：
Somerville, S
影响因子：
3.7
作者：
Chouquet A;Païdassi H;Ling WL;Frachet P;Houen G;Arlaud GJ;Gaboriaud C
通讯作者：
Gaboriaud C
影响因子：
64.5
作者：
Kaufmann, Anna;Beier, Viola;Wollert, Thomas
通讯作者：
Wollert, Thomas