Oncogenic Mutations in the DNA-Binding Domain of FOXO1 that Disrupt Folding: Quantitative Insights from Experiments and Molecular Simulations.
Oncogenic Mutations in the DNA-Binding Domain of FOXO1 that Disrupt Folding: Quantitative Insights from Experiments and Molecular Simulations.
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DOI：
10.1021/acs.biochem.2c00224
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发表时间：
2022-08-16
期刊：
影响因子：
2.9
通讯作者：
Baxter RHG
中科院分区：
文献类型：
--
作者：
Novack D;Qian L;Acker G;Voelz VA;Baxter RHG
FOXO 1是翼螺旋基序叉头盒（FOX）转录因子家族的成员，是成熟B细胞中表达最丰富的FOXO成员。弥漫性大B细胞淋巴瘤（DLBCL）肿瘤和细胞系的测序鉴定了与功能丧失相关的叉头结构域的特异性突变。差示扫描量热法和热位移测定被用来表征这些突变中的八个如何影响FOX结构域的稳定性。发现突变L183P和L183R特别不稳定。电泳迁移率变动分析表明，这些相同的突变也破坏了FOXO 1与其典型DNA序列的结合，表明功能丧失是由于折叠结构的不稳定。使用炼金术自由能微扰（FEP）对突变对FOXO 1折叠的影响进行了计算建模，并从大规模并行分子模拟中构建了整个折叠反应的马尔可夫模型，该模型预测了涉及螺旋α3晚期折叠的折叠途径。虽然FEP能够定性预测L183突变的不稳定性，但我们发现，一个简单的疏水转移模型，结合分子模拟中未折叠状态溶剂可及表面积的估计，能够更准确地预测突变引起的折叠自由能变化。这些结果表明，从模拟提供的原子细节是重要的准确预测突变对折叠稳定性的影响。其他FOX家族成员中相应的疾病相关突变支持FOX结构域折叠机制的进一步实验和计算研究。
FOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B-cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting the loss of function is due to destabilization of the folded structure. Computational modeling of the effects of mutations on FOXO1 folding was performed using alchemical free energy perturbation (FEP), and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix α3. Although FEP is able to qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent accessible surface areas from molecular simulation, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that atomic detail provided from simulation is important for accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.
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DOI：
10.1073/pnas.1101752108
发表时间：
2011-04-05
影响因子：
11.1
作者：
Banachewicz, Wiktor;Religa, Tomasz L.;Fersht, Alan R.
通讯作者：
Fersht, Alan R.
影响因子：
14.9
作者：
Buchan, Daniel W. A.;Jones, David T.
通讯作者：
Jones, David T.
影响因子：
14.9
作者：
Dai S;Qu L;Li J;Chen Y
通讯作者：
Chen Y
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
4.3
作者：
Eastman P;Swails J;Chodera JD;McGibbon RT;Zhao Y;Beauchamp KA;Wang LP;Simmonett AC;Harrigan MP;Stern CD;Wiewiora RP;Brooks BR;Pande VS
通讯作者：
Pande VS