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Augmented Reality in Scientific Publications - Taking the Visualization of 3D Structures to the Next Level.
ACS Chemical Biology ( IF 3.5 ) Pub Date : 2019-12-12 , DOI: 10.1021/acschembio.9b00951
Patrik Wolle , Matthias P Müller , Daniel Rauh

The QR codes that link to the data to display Figures 1a–d, 2b, and 3a,b in the augment app in augmented reality had to be changed since the links were not working anymore on certain mobile devices. In this corrigendum, updated QR codes have been supplied that ensure a future-proof application. Figure 1. Examples of three-dimensional structural representations of protein molecules. (A) The active site of the epidermal growth factor receptor (EGFR) kinase domain bound covalently via Cys797 to a pyrazolopyrimidine inhibitor (PDB ID 5j9y; 2FOFC map contoured at 1σ). (B) Small molecule inhibitor bound to the lipophilic binding pocket of the kinase p38α. Surrounding secondary structure elements (αEF/αF loop and helices 1L14 and 2L14) and amino acids (Trp197, Lys249, Ser251, and Asp294) involved in binding are shown. The 2FOFC electron density is depicted as a mesh at 1σ (PDB ID 5n67). (C) The small GTPase Rab1b bound to guanosine-5′-[β,γ- imido]-triphosphate (GppNHp) and Mg2+ (green sphere) in the active site and covalently modified with adenosine-5′-monophosphate at Tyr77 (the important switch I (red), switch II (blue), and P-loop (magenta) are highlighted; PDB ID 3nkv). (D) Model of the transcription factor Nrf2 (cartoon) bound to the major groove of a short stretch of DNA (surface representation) highlighting important basic residues that are presumably involved in recognition of the nucleic acid and interaction with the negatively charged phosphate groups of the DNA (the model is based on PDB ID 1skn). Figure 2. Simple visualization of complex stereochemistry. The small molecule X-ray structure of morphine including five asymmetric carbon atoms (∗) shown as a two-dimensional figure (A) and the corresponding Ortep plot (CCDC identifier EFASAH15). (B) The view in 3D AR allows the reader to directly appreciate the complex stereochemistry of this molecule (carbon, gray; oxygen, red; nitrogen, blue; Cl, green). Figure 3. Large molecular assemblies can also be visualized in augmented reality. (A) Cartoon representation of the pentameric toxin TcdA1 (PDB ID 4o9y) in two different orientations (the monomers are shown in orange, purple, gray, turquoise, and green and consist of ∼2500 amino acids each). Note the long channel within the pentamer of the protein that is used to funnel the toxin into infected cells. (B) The RNA-polymerase III open preinitiation complex (PDB ID 6eu0). The structure was obtained by cryoelectron microscopy and shows the polymerase bound to the partially unwound DNA and Mg2+ in the active site. The authors are sorry for any inconvenience caused. This article has not yet been cited by other publications. Figure 1. Examples of three-dimensional structural representations of protein molecules. (A) The active site of the epidermal growth factor receptor (EGFR) kinase domain bound covalently via Cys797 to a pyrazolopyrimidine inhibitor (PDB ID 5j9y; 2FOFC map contoured at 1σ). (B) Small molecule inhibitor bound to the lipophilic binding pocket of the kinase p38α. Surrounding secondary structure elements (αEF/αF loop and helices 1L14 and 2L14) and amino acids (Trp197, Lys249, Ser251, and Asp294) involved in binding are shown. The 2FOFC electron density is depicted as a mesh at 1σ (PDB ID 5n67). (C) The small GTPase Rab1b bound to guanosine-5′-[β,γ- imido]-triphosphate (GppNHp) and Mg2+ (green sphere) in the active site and covalently modified with adenosine-5′-monophosphate at Tyr77 (the important switch I (red), switch II (blue), and P-loop (magenta) are highlighted; PDB ID 3nkv). (D) Model of the transcription factor Nrf2 (cartoon) bound to the major groove of a short stretch of DNA (surface representation) highlighting important basic residues that are presumably involved in recognition of the nucleic acid and interaction with the negatively charged phosphate groups of the DNA (the model is based on PDB ID 1skn). Figure 2. Simple visualization of complex stereochemistry. The small molecule X-ray structure of morphine including five asymmetric carbon atoms (∗) shown as a two-dimensional figure (A) and the corresponding Ortep plot (CCDC identifier EFASAH15). (B) The view in 3D AR allows the reader to directly appreciate the complex stereochemistry of this molecule (carbon, gray; oxygen, red; nitrogen, blue; Cl, green). Figure 3. Large molecular assemblies can also be visualized in augmented reality. (A) Cartoon representation of the pentameric toxin TcdA1 (PDB ID 4o9y) in two different orientations (the monomers are shown in orange, purple, gray, turquoise, and green and consist of ∼2500 amino acids each). Note the long channel within the pentamer of the protein that is used to funnel the toxin into infected cells. (B) The RNA-polymerase III open preinitiation complex (PDB ID 6eu0). The structure was obtained by cryoelectron microscopy and shows the polymerase bound to the partially unwound DNA and Mg2+ in the active site.

中文翻译:

科学出版物中的增强现实-使3D结构的可视化更上一层楼。

链接到数据以在增强现实中的增强应用中显示图1a–d,2b和3a,b的QR码必须更改,因为这些链接在某些移动设备上不再起作用。在本勘误中,已提供了更新的QR码,以确保将来的应用。图1.蛋白质分子的三维结构表示示例。(A)通过Cys797与吡唑并嘧啶抑制剂共价结合的表皮生长因子受体(EGFR)激酶结构域的活性位点(PDB ID 5j9y; 2 F OF C轮廓为1σ的地图)。(B)小分子抑制剂与激酶p38α的亲脂性结合口袋结合。显示了参与结合的周围二级结构元件(αEF/αF环和螺旋1L14和2L14)和氨基酸(Trp197,Lys249,Ser251和Asp294)。2 F OF C电子密度以1σ(PDB ID 5n67)处的网格表示。(C)与鸟苷5'-[β,γ-亚氨基]-三磷酸(GppNHp)和Mg 2+结合的小GTPase Rab1b(绿色球体)在活性位点并在Tyr77(重要的开关I(红色),开关II(蓝色)和P环(品红色)突出显示; PDB ID 3nkv)上用5'-磷酸腺苷共价修饰。(D)转录因子Nrf2(卡通)结合到DNA短片段(表面表示)的主要凹槽上的模型,突出显示了重要的基本残基,可能参与了核酸的识别以及与带负电荷的磷酸基团的相互作用DNA(该模型基于PDB ID 1skn)。图2.复杂立体化学的简单可视化。吗啡的小分子X射线结构,包括五个不对称碳原子(*),以二维图形(A)表示,以及相应的Ortep图(CCDC标识符EFASAH15)。,绿色)。图3.大分子装配体也可以在增强现实中可视化。(A)五聚体毒素TcdA1(PDB ID 4o9y)在两个不同方向上的卡通表示(单体显示为橙色,紫色,灰色,绿松石和绿色,每个都有约2500个氨基酸)。注意该蛋白的五聚体中的长通道,该通道用于将毒素漏入感染的细胞中。(B)RNA聚合酶III开放的预启动复合物(PDB ID 6eu0)。该结构通过冷冻电子显微镜获得,显示聚合酶与部分解链的DNA和Mg 2+结合在活动站点中。不便之处,敬请原谅。本文尚未被其他出版物引用。图1.蛋白质分子的三维结构表示示例。(A)表皮生长因子受体(EGFR)激酶结构域的活性位点通过Cys797与吡唑并嘧啶抑制剂共价结合(PDB ID 5j9y; 2 F OF C图的轮廓为1σ)。(B)小分子抑制剂与激酶p38α的亲脂性结合口袋结合。显示了参与结合的周围二级结构元件(αEF/αF环和螺旋1L14和2L14)和氨基酸(Trp197,Lys249,Ser251和Asp294)。2 F OF C电子密度以1σ(PDB ID 5n67)的网格表示。(C)与鸟苷5'-[β,γ-亚氨基]-三磷酸(GppNHp)和Mg 2+结合的小GTPase Rab1b(绿色球体)在活性位点并在Tyr77(重要的开关I(红色),开关II(蓝色)和P环(品红色)突出显示; PDB ID 3nkv)上用5'-磷酸腺苷共价修饰。(D)转录因子Nrf2(卡通)结合到DNA短片段(表面表示)的主要凹槽上的模型,突出显示了重要的基本残基,可能参与了核酸的识别以及与带负电荷的磷酸基团的相互作用DNA(该模型基于PDB ID 1skn)。图2.复杂立体化学的简单可视化。吗啡的小分子X射线结构,包括五个不对称碳原子(*),以二维图形(A)表示,以及相应的Ortep图(CCDC标识符EFASAH15)。,绿色)。图3.大分子装配体也可以在增强现实中可视化。(A)五聚体毒素TcdA1(PDB ID 4o9y)在两个不同方向上的卡通表示(单体显示为橙色,紫色,灰色,绿松石和绿色,每个都有约2500个氨基酸)。注意该蛋白的五聚体中的长通道,该通道用于将毒素漏入感染的细胞中。(B)RNA聚合酶III开放的预启动复合物(PDB ID 6eu0)。通过冷冻电子显微镜获得该结构,并显示了在活性位点上与部分解链的DNA和Mg 2+结合的聚合酶。
更新日期:2019-12-13
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