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Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network 热厌氧菌假乙醇中嗜热仲醇脱氢酶三元配合物的晶体快照揭示了配体交换动力学和质子接力网络
Pub Date : 2022-03-31 DOI: 10.1002/prot.26339
T. Dinh, K. Rahn, R. Phillips
Three‐dimensional structures of I86A and C295A mutant secondary alcohol dehydrogenase (SADH) from Thermoanaerobacter pseudoethanolicus were determined by x‐ray crystallography. The tetrameric structure of C295A‐SADH soaked with NADP+ and dimethyl sulfoxide (DMSO) was determined to 1.85 Å with an Rfree of 0.225. DMSO is bound to the tetrahedral zinc in each subunit, with ligands from SG of Cys‐37, NE2 of His‐59, and OD2 of Asp‐150. The nicotinamide ring of NADP is hydrogen‐bonded to the N of Ala‐295 and the O of Val‐265 and Gly‐293. The O of DMSO is connected to a network of hydrogen bonds with OG of Ser‐39, the 3′‐OH of NADP, and ND1 of His‐42. The structure of I86A‐SADH soaked with 2‐pentanol and NADP+ contains (R)‐2‐pentanol bound in each subunit, ligated to the tetrahedral zinc, and connected to the proton relay network. The structure of I86A‐SADH soaked with 3‐methylcyclohexanol and NADP+ has alcohol bound in three subunits. Two of the sites have the alcohol ligated to the zinc in an axial position, with OE2 of Glu‐60 in the other axial position of a trigonal bipyramidal complex. One site has 3‐methylcyclohexanol bound noncovalently, with the zinc in an inverted tetrahedral geometry with Glu‐60. The fourth site also has the zinc in a trigonal bipyramidal complex with axial Glu‐60 and water ligands. These structures demonstrate that ligand exchange of SADH involves pentacoordinate and inverted zinc complexes with Glu‐60. Furthermore, we see a network of hydrogen bonds connecting the substrate oxygen to the external solvent that is likely to play a role in the mechanism of SADH.
用x射线晶体学方法测定了假乙醇热厌氧菌I86A和C295A突变体二次醇脱氢酶(SADH)的三维结构。经NADP+和二甲亚砜(DMSO)浸泡后,C295A‐SADH的四聚体结构为1.85 Å, Rfree为0.225。DMSO在每个亚基上与四面体锌结合,其配体来自Cys‐37的SG、His‐59的NE2和Asp‐150的OD2。NADP的烟酰胺环与Ala‐295的N、Val‐265和Gly‐293的O形成氢键。DMSO的O与Ser - 39的OG、NADP的3 ' - OH和His - 42的ND1的氢键网络相连。经2 -戊醇和NADP+浸泡的I86A - SADH的结构在每个亚基上都含有(R) - 2 -戊醇结合,连接到四面体锌上,并连接到质子接力网络。I86A‐SADH经3‐甲基环己醇和NADP+浸泡后,其结构具有三个亚基的醇结合。其中两个位点的醇在轴向连接到锌上,Glu‐60的OE2在另一个三角双锥体配合物的轴向位置。其中一个位点与3 -甲基环己醇非共价结合,锌与Glu - 60呈倒四面体结构。第四个位点也有锌在一个与轴向Glu‐60和水配体的三角双锥体配合物中。这些结构表明SADH的配体交换涉及Glu‐60的五配位和反向锌配合物。此外,我们看到连接底物氧和外部溶剂的氢键网络可能在SADH机制中发挥作用。
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引用次数: 0
De novo design of membrane transport proteins 膜转运蛋白的从头设计
Pub Date : 2022-03-19 DOI: 10.1002/prot.26336
Chen Zhou, P. Lu
Membrane transport proteins, which include transporters and channels, are delicate protein machineries that mediate the exchange of a variety of substances across biomembranes. Accumulated structural and functional knowledge allows for the de novo design of transport proteins with new structures that do not exist in nature. Analysis based on these novel proteins provides new insights into the principles that govern protein assembly, conformational change, and substrate recognition. Here, we review the advances in the de novo design of transporters and channels over recent years and highlight the challenges and opportunities in this field.
膜转运蛋白包括转运体和通道,是精细的蛋白质机器,介导多种物质在生物膜上的交换。积累的结构和功能知识允许重新设计具有自然界中不存在的新结构的转运蛋白。基于这些新蛋白质的分析为蛋白质组装、构象变化和底物识别的原理提供了新的见解。在这里,我们回顾了近年来转运体和通道从头设计的进展,并强调了该领域的挑战和机遇。
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引用次数: 1
Characterization of glutamate‐cysteine ligase and glutathione synthetase from the δ‐proteobacterium Myxococcus xanthus 黄原粘球菌δ -变形菌中谷氨酸-半胱氨酸连接酶和谷胱甘肽合成酶的研究
Pub Date : 2022-03-11 DOI: 10.1002/prot.26333
Misaki Okada, Y. Kimura
Glutathione (GSH) is synthesized in two ATP‐dependent reactions by glutamate‐cysteine ligase (Gcl) and glutathione synthetase (Gs). Myxococcus xanthus, a gram‐negative bacterium belonging to δ‐proteobacteria, possesses mxGcl and mxGs, which have high sequence identity with the enzymes from plants and bacteria, respectively. MxGcl2 was activated by Mn2+, but not by Mg2+, and stabilized in the presence of 5 mM Mn2+ or Mg2+. Sequence comparison of mxGcl2 and Brassica juncea Gcl indicated that they have the same active site residues, except for Tyr330, which interacts with Cys and which in mxGcl2 is represented by Leu267. The substitution of Leu267 with Tyr resulted in the loss of mxGcl2 activity, but that with Met (found in cyanobacterial Gcls) increased the mxGcl2 affinity for Cys. GSH and its oxidized form GSSG equally inhibited the activity of mxGcl2; the inhibition was augmented by ATP at concentrations >3 mM. Buthionine sulfoximine inactivated mxGcl2 with Ki = 2.1 μM, which was lower than those for Gcls from other organisms. The mxGcl2 activity was also suppressed by pyrophosphate and polyphosphates. MxGs was a dimer, and its activity was induced by Mg2+ but strongly inhibited by Mn2+ even in the presence of 10 mM Mg2+. MxGs was inhibited by GSSG at Ki = 3.6 mM. Approximately 1 mM GSH was generated with 3 units of mxGcl2 and 6 units of mxGs from 5 mM Glu, Cys, and Gly, and 10 mM ATP. Our results suggest that GSH production in M. xanthus mostly depends on mxGcl2 activity.
谷胱甘肽(GSH)是由谷氨酸-半胱氨酸连接酶(Gcl)和谷胱甘肽合成酶(Gs)两种ATP依赖性反应合成的。黄粘球菌(Myxococcus xanthus)是一种革兰氏阴性细菌,属于δ -变形菌门,具有mxGcl和mxGs,它们分别与植物和细菌中的酶具有高度的序列一致性。MxGcl2被Mn2+激活,而不被Mg2+激活,在5 mM Mn2+或Mg2+存在下稳定。mxGcl2与芥菜Gcl的序列比较表明,除了与Cys相互作用的Tyr330和在mxGcl2中以Leu267为代表的Tyr330外,它们具有相同的活性位点残基。用Tyr取代Leu267导致mxGcl2活性的丧失,而用Met(在蓝藻Gcls中发现)取代则增加了mxGcl2对Cys的亲和力。GSH及其氧化形式GSSG对mxGcl2活性的抑制作用相同;浓度为bbb30 mM的ATP增强了抑制作用。丁硫氨酸亚砜对mxGcl2的灭活作用Ki = 2.1 μM,低于其他生物的灭活作用。mxGcl2活性也受到焦磷酸盐和多磷酸盐的抑制。MxGs是一种二聚体,其活性受Mg2+的诱导,但在Mg2+浓度为10 mM时,其活性仍被Mn2+强烈抑制。在Ki = 3.6 mM时,GSSG对MxGs有抑制作用。5 mM Glu、Cys和Gly产生3单位mxGcl2和6单位mxGs,以及10 mM ATP,产生约1 mM GSH。我们的研究结果表明,黄原草中GSH的产生主要取决于mxGcl2的活性。
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引用次数: 3
A structural model of the human plasminogen and Aspergillus fumigatus enolase complex 人纤溶酶原与烟曲霉烯醇化酶复合物的结构模型
Pub Date : 2022-03-05 DOI: 10.1002/prot.26331
Stephanie Nguyen, Blagojce Jovcevski, J. Truong, T. Pukala, J. Bruning
The metabolic enzyme, enolase, plays a crucial role in the cytoplasm where it maintains cellular energy production within the process of glycolysis. The main role of enolase in glycolysis is to convert 2‐phosphoglycerate to phosphoenolpyruvate; however, enolase can fulfill roles that deviate from this function. In pathogenic bacteria and fungi, enolase is also located on the cell surface where it functions as a virulence factor. Surface‐expressed enolase is a receptor for human plasma proteins, including plasminogen, and this interaction facilitates nutrient acquisition and tissue invasion. A novel approach to developing antifungal drugs is to inhibit the formation of this complex. To better understand the structure of enolase and the interactions that may govern complex formation, we have solved the first X‐ray crystal structure of enolase from Aspergillus fumigatus (2.0 Å) and have shown that it preferentially adopts a dimeric quaternary structure using native mass spectrometry. Two additional X‐ray crystal structures of A. fumigatus enolase bound to the endogenous substrate 2‐phosphoglycerate and product phosphoenolpyruvate were determined and kinetic characterization was carried out to better understand the details of its canonical function. From these data, we have produced a model of the A. fumigatus enolase and human plasminogen complex to provide structural insights into the mechanisms of virulence and aid future development of small molecules or peptidomimetics for antifungal drug design.
代谢酶烯醇化酶在细胞质中起着至关重要的作用,它在糖酵解过程中维持细胞能量的产生。烯醇化酶在糖酵解中的主要作用是将2 -磷酸甘油酸转化为磷酸烯醇丙酮酸;然而,烯醇化酶可以完成偏离此功能的角色。在致病菌和真菌中,烯醇化酶也位于细胞表面,在那里它起着毒力因子的作用。表面表达的烯醇化酶是人血浆蛋白(包括纤溶酶原)的受体,这种相互作用促进了营养获取和组织入侵。一种开发抗真菌药物的新方法是抑制这种复合物的形成。为了更好地了解烯醇化酶的结构和可能控制复合物形成的相互作用,我们已经解决了烟曲霉烯醇化酶(2.0 Å)的第一个X射线晶体结构,并表明它优先采用二聚体四元结构。测定了烟曲霉烯醇化酶与内源性底物2 -磷酸甘油酸酯和产物磷酸烯醇丙酮酸酯结合的另外两个X射线晶体结构,并进行了动力学表征,以更好地了解其典型功能的细节。根据这些数据,我们建立了烟曲霉烯醇化酶和人纤溶酶原复合物的模型,为毒力机制提供结构见解,并有助于未来小分子或拟肽物的开发,用于抗真菌药物设计。
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引用次数: 0
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins 利用卷积神经网络的多重卷积窗口扫描有效预测转运蛋白中的ATP结合位点
Pub Date : 2022-03-04 DOI: 10.1002/prot.26329
Trinh-trung-duong Nguyen, Syun Chen, Quang-Thai Ho, Yu-Yen Ou
Protein multiple sequence alignment information has long been important features to know about functions of proteins inferred from related sequences with known functions. It is therefore one of the underlying ideas of Alpha fold 2, a breakthrough study and model for the prediction of three‐dimensional structures of proteins from their primary sequence. Our study used protein multiple sequence alignment information in the form of position‐specific scoring matrices as input. We also refined the use of a convolutional neural network, a well‐known deep‐learning architecture with impressive achievement on image and image‐like data. Specifically, we revisited the study of prediction of adenosine triphosphate (ATP)‐binding sites with more efficient convolutional neural networks. We applied multiple convolutional window scanning filters of a convolutional neural network on position‐specific scoring matrices for as much as useful information as possible. Furthermore, only the most specific motifs are retained at each feature map output through the one‐max pooling layer before going to the next layer. We assumed that this way could help us retain the most conserved motifs which are discriminative information for prediction. Our experiment results show that a convolutional neural network with not too many convolutional layers can be enough to extract the conserved information of proteins, which leads to higher performance. Our best prediction models were obtained after examining them with different hyper‐parameters. Our experiment results showed that our models were superior to traditional use of convolutional neural networks on the same datasets as well as other machine‐learning classification algorithms.
长期以来,蛋白质多序列比对信息一直是从已知功能的相关序列中推断蛋白质功能的重要特征。因此,它是Alpha fold 2的基本思想之一,Alpha fold 2是一项突破性的研究和模型,用于从蛋白质的初级序列预测蛋白质的三维结构。我们的研究以位置特异性评分矩阵的形式使用蛋白质多序列比对信息作为输入。我们还改进了卷积神经网络的使用,卷积神经网络是一种众所周知的深度学习架构,在图像和类图像数据方面取得了令人印象深刻的成就。具体来说,我们重新研究了用更有效的卷积神经网络预测三磷酸腺苷(ATP)结合位点的研究。我们将卷积神经网络的多个卷积窗口扫描滤波器应用于位置特定评分矩阵,以获得尽可能多的有用信息。此外,在进入下一层之前,通过一个最大池化层输出的每个特征映射中只保留最特定的主题。我们认为这种方法可以帮助我们保留最保守的基序,这些基序是预测的判别信息。我们的实验结果表明,一个没有太多卷积层的卷积神经网络就足以提取蛋白质的保守信息,从而获得更高的性能。我们的最佳预测模型是在用不同的超参数检验后得到的。我们的实验结果表明,在相同的数据集上,我们的模型优于传统的卷积神经网络,也优于其他机器学习分类算法。
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引用次数: 2
Issue Information ‐ Forthcoming 发行信息‐即将发布
Pub Date : 2022-03-01 DOI: 10.1002/prot.26103
P. V. Balaji, Rahul Banerjee
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引用次数: 0
Issue Information ‐ Table of Content 发行信息‐内容表
Pub Date : 2022-03-01 DOI: 10.1002/prot.26102
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引用次数: 0
Comprehensive folding variations for protein folding 蛋白质折叠的综合折叠变化
Pub Date : 2022-02-16 DOI: 10.1002/prot.26381
Jiaan Yang, Wenxiang Cheng, Xiaoyan Zhao, Gang Wu, Shi Tong Sheng, Qiyue Hu, Hu Ge, Qianshan Qin, Xinshen Jin, Lianshan Zhang, Peng Zhang
The revelation of protein folding is a challenging subject in both discovery and description. Except for acquirement of accurate 3D structure in protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to represent these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of five amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of five amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein. Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.
蛋白质折叠的揭示在发现和描述上都是一个具有挑战性的课题。除了在蛋白质稳定状态下获得精确的三维结构外,如何发现蛋白质固有特性的结构灵活性也是一个很大的障碍。即使已知大量的柔性构象,困难在于如何表示这些构象。蛋白质结构指纹图谱是一种新的方法,可以揭示蛋白质的局部折叠变化,从而构建整个蛋白质的折叠构象。首先确定了5个氨基酸残基的主链为一个通用折叠,然后推导出一套完全覆盖折叠空间的蛋白质折叠形状代码(PFSC)。随后,建立了一个数据库,收集了五种氨基酸所有排列的局部折叠变异的所有可能的折叠形状。蛋白质折叠变异矩阵(Protein Folding Variation Matrix, PFVM)依次组装了蛋白质沿序列的所有可能的局部折叠变异,具有几个突出的特征。首先,它显示了一定的折叠模式沿序列的波动,揭示了蛋白质折叠与氨基酸序列顺序的关系。其次,在PFVM中,整个蛋白质的所有折叠变化都可以同时一目了然。第三,所有的构象都可以通过PFVM的局部折叠变化来确定,因此对于任何蛋白质来说,构象的总数不再是模糊的。最后,利用PFVM获得最可能的折叠构象及其三维结构,用于蛋白质结构预测。因此,蛋白质结构指纹图谱方法为研究蛋白质折叠问题提供了重要的手段。
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引用次数: 3
Issue Information ‐ Table of Content 发行信息‐内容表
Pub Date : 2022-02-04 DOI: 10.1002/prot.26098
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引用次数: 0
Issue Information ‐ Forthcoming 发行信息‐即将发布
Pub Date : 2022-02-04 DOI: 10.1002/prot.26099
{"title":"Issue Information ‐ Forthcoming","authors":"","doi":"10.1002/prot.26099","DOIUrl":"https://doi.org/10.1002/prot.26099","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82386888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Proteins: Structure
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