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Tropical paleobiology discovers biodiversity in a warmer past 热带古生物学发现温暖时代的生物多样性
Pub Date : 2024-04-01 DOI: 10.1073/pnas.2404036121
Moriaki Yasuhara, C. Deutsch, Jingwen Zhang
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引用次数: 0
Correction to Supporting Information for Wiedmann et al., The material footprint of nations 对 Wiedmann 等人 "国家的物质足迹 "佐证资料的更正
Pub Date : 2023-12-08 DOI: 10.1073/pnas.2319720120
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引用次数: 0
Reply to Giglio and Roy: Aggregate infant mortality estimates robust to choice of burned area product 答复 Giglio 和 Roy:婴儿总死亡率估计值与烧毁面积乘积的选择关系密切
Pub Date : 2023-12-07 DOI: 10.1073/pnas.2318188120
H. Pullabhotla, Mustafa Zahid, S. Heft-Neal, Vaibhav Rathi, Marshall Burke
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引用次数: 0
FireCCILT11 artifacts may confound the link between biomass burning and infant mortality FireCCILT11 的假象可能会混淆生物质燃烧与婴儿死亡率之间的联系
Pub Date : 2023-12-07 DOI: 10.1073/pnas.2317759120
Louis Giglio, David P. Roy
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引用次数: 0
Structural origins of Escherichia coli RNA polymerase open promoter complex stability 大肠杆菌RNA聚合酶开放启动子复合物稳定性的结构起源
Pub Date : 2021-09-09 DOI: 10.1101/2021.09.08.459427
R. Saecker, James Chen, C. Chiu, B. Malone, J. Sotiris, Mark Ebrahim, L. Y. Yen, E. Eng, S. Darst
Significance The modulation of the rate of formation and of the lifetime of transcription initiation complexes is a critical point in gene expression control. In Escherichia coli, single-nucleotide changes can change the half-life of an RNA polymerase (RNAP)–promoter DNA complex by more than an order of magnitude. The origins of these effects are poorly understood. Using cryoelectron microscopy, we find that small alterations in the sequence or size of the transcription bubble trigger global changes in RNAP–DNA interactions and in DNA base stacking. Our results reveal that nonadditive structural changes allow a few crucial DNA positions to tune the transcription initiation complex lifetime from seconds to hours, influencing the rate and efficiency of the initial steps of RNA synthesis. The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms “open” complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λPR (t1/2 ∼10 h), T7A1 (t1/2 ∼4 min), and a point mutant in λPR (λPR-5C) (t1/2 ∼2 h). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA–RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand “scrunches” inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.
意义调控转录起始复合物的形成速率和寿命是基因表达调控的关键。在大肠杆菌中,单核苷酸的变化可以将RNA聚合酶(RNAP)启动子DNA复合体的半衰期改变一个数量级以上。人们对这些效应的起源知之甚少。利用低温电镜,我们发现转录泡的序列或大小的微小变化会引发rna - DNA相互作用和DNA碱基堆叠的全局变化。我们的研究结果表明,非加性结构变化允许一些关键的DNA位置将转录起始复合物的寿命从几秒调整到几小时,从而影响RNA合成初始步骤的速率和效率。在所有生物体中,基因表达的第一步都需要打开DNA双链,暴露其中一条链用于模板化RNA合成。在大肠杆菌中,启动子DNA序列从根本上决定了RNA聚合酶(RNAP)形成“开放”复合物(RPo)的速度,RPo是持续数秒还是数小时,以及RNAP从起始到延伸的转变速度。这些速率控制着体内启动子的强度,但它们的结构起源在很大程度上仍然未知。在这里,我们使用低温电子显微镜来确定在37°C下三个不同寿命的启动子中重新形成的RPo的结构:λPR (t1/2 ~ 10小时),T7A1 (t1/2 ~ 4分钟)和λPR的点突变体(λPR- 5c) (t1/2 ~ 2小时)。在λPR上填充了两种不同的RPo构象,可能代表了在溶液研究中观察到的RPo的生产和非生产形式。我们发现,转录泡中DNA序列和长度的变化在起始位点上游(+1)整体上改变了DNA - rnap相互作用网络、碱基堆叠和转录泡单链DNA的链顺序;这些差异在气泡之外传播到上游和下游的DNA。在转录泡扩大一个碱基(T7A1)后,非模板链在活性位点裂缝内“卷曲”;模板链在气泡上游边缘的裂缝外凸起。这些结构说明了有限的序列变化如何触发转录泡中的全局改变,从而调节RPo寿命并影响转录周期的后续步骤。
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引用次数: 18
Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins 用于膜蛋白基础辅助低温电镜研究的通用纳米体结合Fab模块的开发
Pub Date : 2021-08-20 DOI: 10.1101/2021.08.20.457137
J. Bloch, S. Mukherjee, J. Kowal, E. Filippova, M. Niederer, E. Pardon, J. Steyaert, A. Kossiakoff, K. Locher
Significance Structural studies of membrane proteins by cryogenic electron microscopy (cryo-EM) often require antibody fragments (Fabs) to facilitate particle alignments and achieve high resolution. While conformational nanobodies have been developed to lock specific states of many membrane proteins, they only add 15 kDa of mass to the complex. We developed a synthetic Fab (NabFab) that rigidly binds the conserved scaffold of nanobodies, providing a universally applicable fiducial for cryo-EM studies of protein–nanobody complexes. We demonstrate the concept by determining two high-resolution structures of membrane proteins bound to specific nanobodies and NabFab. As the structural epitope for NabFab can be incorporated into the scaffold of virtually any nanobody, this raises the prospect of facile structure determination of many nanobody–protein complexes. With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody–target protein interaction. Here, we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon complementary-determining region grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryogenic electron microscopy (cryo-EM) structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of ∼50 kDa. Using an additional anti-Fab nanobody further facilitated reliable initial three-dimensional structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, is humanized, and can be conveniently expressed in Escherichia coli in large amounts, it may be useful not only for structural biology but also for biomedical applications.
通过低温电子显微镜(cryo-EM)进行膜蛋白结构研究通常需要抗体片段(fab)来促进颗粒排列并实现高分辨率。虽然构象纳米体已被开发用于锁定许多膜蛋白的特定状态,但它们仅为复合物增加了15 kDa的质量。我们开发了一种合成Fab (NabFab),它可以与纳米体的保守支架紧密结合,为蛋白质-纳米体复合物的低温电镜研究提供了普遍适用的基础。我们通过确定与特定纳米体和NabFab结合的膜蛋白的两个高分辨率结构来证明这一概念。由于NabFab的结构表位可以结合到几乎任何纳米体的支架中,这为许多纳米体-蛋白质复合物的简单结构测定提供了前景。随着构象特异性纳米体被广泛用于结构、生化和细胞生物学的应用,需要抗原结合片段(fab)来特异性和紧密地结合这些纳米体,而不干扰纳米体与靶蛋白的相互作用。在这里,我们描述了一种合成Fab(称为NabFab)的发展,它结合了羊驼衍生的纳米体的支架,具有皮摩尔亲和力。我们证明,在互补决定区嫁接到这个亲本纳米体支架上后,识别来自美洲驼或骆驼的多种靶蛋白的纳米体可以与NabFab交叉反应而不会失去亲和力。使用NabFab作为基准和尺寸增强剂(50 kDa),我们确定了纳米体结合的VcNorM和ScaDMT的高分辨率低温电镜(cro - em)结构,这两种小膜蛋白都是~ 50 kDa。使用额外的抗fab纳米体进一步促进了从小型低温电镜测试数据集确定可靠的初始三维结构。鉴于NabFab是人工合成的,是人源化的,并且可以方便地在大肠杆菌中大量表达,它不仅可以用于结构生物学,还可以用于生物医学应用。
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引用次数: 24
MEKK3–TGFβ crosstalk regulates inward arterial remodeling MEKK3-TGFβ串扰调控动脉内重构
Pub Date : 2021-08-19 DOI: 10.1101/2021.08.19.456893
H. Deng, Yanying Xu, Xiaoyue Hu, Zhuang W. Zhen, Yuzhou Chang, Yewei Wang, A. Ntokou, M. Schwartz, Bing Su, M. Simons
Significance Inward remodeling of arteries to reduce lumen diameter is a major factor in disease progression and morbidity in multiple vascular diseases, including hypertension and atherosclerosis. However, molecular mechanisms controlling inward arterial remodeling remain largely undefined. In this study, we identify endothelial MEKK3 as an unexpected regulator of inward remodeling via inhibition of TGFβ-Smad2/3 signaling. Genetic deletion of MEKK3 in adult endothelium results in induction of TGFβ-Smad2/3 signaling, endothelial-to-mesenchymal transition, and inward remodeling in both pulmonary and arterial circuits. The latter process results in pulmonary and systemic hypertension and accelerates atherosclerosis. These results provide a basis for understanding the inward artery remodeling that leads to reduced blood flow to affected tissues and exacerbates hypertension in vascular disease. Arterial remodeling is an important adaptive mechanism that maintains normal fluid shear stress in a variety of physiologic and pathologic conditions. Inward remodeling, a process that leads to reduction in arterial diameter, plays a critical role in progression of such common diseases as hypertension and atherosclerosis. Yet, despite its pathogenic importance, molecular mechanisms controlling inward remodeling remain undefined. Mitogen-activated protein kinases (MAPKs) perform a number of functions ranging from control of proliferation to migration and cell-fate transitions. While the MAPK ERK1/2 signaling pathway has been extensively examined in the endothelium, less is known about the role of the MEKK3/ERK5 pathway in vascular remodeling. To better define the role played by this signaling cascade, we studied the effect of endothelial-specific deletion of its key upstream MAP3K, MEKK3, in adult mice. The gene’s deletion resulted in a gradual inward remodeling of both pulmonary and systematic arteries, leading to spontaneous hypertension in both vascular circuits and accelerated progression of atherosclerosis in hyperlipidemic mice. Molecular analysis revealed activation of TGFβ-signaling both in vitro and in vivo. Endothelial-specific TGFβR1 knockout prevented inward arterial remodeling in MEKK3 endothelial knockout mice. These data point to the unexpected participation of endothelial MEKK3 in regulation of TGFβR1-Smad2/3 signaling and inward arterial remodeling in artery diseases.
动脉向内重构以减小管腔直径是高血压、动脉粥样硬化等多种血管疾病进展和发病的重要因素。然而,控制向内动脉重塑的分子机制在很大程度上仍未明确。在这项研究中,我们通过抑制tgf - β- smad2 /3信号,发现内皮细胞MEKK3是一个意想不到的内向重塑调节剂。成人内皮中MEKK3基因缺失可诱导tgf - β- smad2 /3信号转导、内皮向间质转化以及肺动脉回路和动脉回路的内向重构。后一过程导致肺动脉和全身高血压,并加速动脉粥样硬化。这些结果为理解动脉内重构导致受影响组织血流量减少和血管疾病高血压加重提供了基础。动脉重构是在各种生理和病理条件下维持正常流体剪切应力的重要适应性机制。向内重构是一个导致动脉直径减小的过程,在高血压和动脉粥样硬化等常见疾病的进展中起着关键作用。然而,尽管其致病重要性,控制向内重塑的分子机制仍然不明确。丝裂原活化蛋白激酶(MAPKs)具有多种功能,从控制增殖到迁移和细胞命运转变。虽然MAPK ERK1/2信号通路在内皮中被广泛研究,但对于MEKK3/ERK5信号通路在血管重构中的作用知之甚少。为了更好地定义这一信号级联的作用,我们研究了其上游关键MAP3K MEKK3在成年小鼠中内皮特异性缺失的影响。该基因的缺失导致肺动脉和全身动脉逐渐向内重构,导致血管回路自发性高血压,并加速高脂血症小鼠动脉粥样硬化的进展。分子分析显示tgf - β-信号在体内和体外均被激活。内皮特异性TGFβR1敲除可阻止MEKK3内皮敲除小鼠动脉内重构。这些数据表明,在动脉疾病中,内皮细胞MEKK3出人意料地参与了tgf - β r1 - smad2 /3信号的调控和向内动脉重塑。
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引用次数: 10
Vectorial channeling as a mechanism for translational control by functional prions and condensates 载体通道作为功能朊病毒和凝聚体的翻译控制机制
Pub Date : 2021-08-19 DOI: 10.1101/2021.08.19.457025
Xinyu Gu, Nicholas P. Schafer, P. Wolynes
Significance Messenger RNA (mRNA)/protein assemblies such as functional prions and condensates are involved in locally regulating translation in eukaryotic cells. The mode of regulation depends on the structure of these assemblies. We show that the vectorial processive nature of translation can couple to transport via diffusion so as to repress or activate translation depending on the structure of the RNA protein assembly. We find that multiple factors including diffusivity changes and free energy biases in the assemblies can regulate the translation rate of mRNA by changing the balance between substrate recycling and competition between mRNAs. We mainly focus on the example of CPEB, a functional prion that has been implicated in the mechanism of synaptic plasticity of neurons and in memory. Translation of messenger RNA (mRNA) is regulated through a diverse set of RNA-binding proteins. A significant fraction of RNA-binding proteins contains prion-like domains which form functional prions. This raises the question of how prions can play a role in translational control. Local control of translation in dendritic spines by prions has been invoked in the mechanism of synaptic plasticity and memory. We show how channeling through diffusion and processive translation cooperate in highly ordered mRNA/prion aggregates as well as in less ordered mRNA/protein condensates depending on their substructure. We show that the direction of translational control, whether it is repressive or activating, depends on the polarity of the mRNA distribution in mRNA/prion assemblies which determines whether vectorial channeling can enhance recycling of ribosomes. Our model also addresses the effect of changes of substrate concentration in assemblies that have been suggested previously to explain translational control by assemblies through the introduction of a potential of mean force biasing diffusion of ribosomes inside the assemblies. The results from the model are compared with the experimental data on translational control by two functional RNA-binding prions, CPEB involved in memory and Rim4 involved in gametogenesis.
在真核细胞中,信使RNA (mRNA)/蛋白组合物(如功能性朊病毒和凝聚物)参与局部调节翻译。监管模式取决于这些议会的结构。我们表明,翻译的载体过程性质可以通过扩散偶联运输,从而根据RNA蛋白组装的结构抑制或激活翻译。我们发现,包括扩散率变化和组件中的自由能偏差在内的多种因素可以通过改变底物循环和mRNA之间竞争的平衡来调节mRNA的翻译速率。我们主要关注CPEB的例子,CPEB是一种与神经元突触可塑性和记忆机制有关的功能性朊病毒。信使RNA (mRNA)的翻译是通过一系列不同的RNA结合蛋白来调节的。很大一部分rna结合蛋白含有朊病毒样结构域,形成功能性朊病毒。这就提出了朊病毒如何在转译控制中发挥作用的问题。朊病毒对树突棘翻译的局部控制被认为是突触可塑性和记忆的机制。我们展示了通过扩散和过程翻译的通道如何在高度有序的mRNA/朊病毒聚集体中以及在依赖于它们的亚结构的较不有序的mRNA/蛋白质凝聚体中合作。我们表明,翻译控制的方向,无论是抑制还是激活,取决于mRNA/朊病毒组装中mRNA分布的极性,这决定了载体通道是否可以增强核糖体的再循环。我们的模型还解决了组合物中底物浓度变化的影响,该影响先前被建议通过引入组合内核糖体的平均力偏倚扩散势来解释组合物的翻译控制。将模型结果与两种功能性rna结合朊病毒(参与记忆的CPEB和参与配子发生的Rim4)的翻译控制实验数据进行了比较。
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引用次数: 5
Metagenomic discovery of CRISPR-associated transposons crispr相关转座子的宏基因组发现
Pub Date : 2021-08-16 DOI: 10.1101/2021.08.16.456562
James R. Rybarski, Kuang Hu, A. Hill, C. Wilke, Ilya J. Finkelstein
Significance CRISPR-Cas systems confer bacteria and archaea with adaptive immunity against mobile genetic elements. These systems also participate in other cellular processes. For example, CRISPR-associated Tn7 transposons (CASTs) have co-opted nuclease-inactive CRISPR effector proteins to guide their transposition. We bioinformatically survey metagenomic databases to uncover CASTs, including systems with new architectures and ones that use distinct CRISPR subtypes. We also describe a putative non-Tn7 CAST that co-opts Cas12. Our findings propose mechanisms for vertical and horizontal CAST targeting and shed light on how CASTs have coevolved with CRISPR-Cas systems. CRISPR-associated Tn7 transposons (CASTs) co-opt cas genes for RNA-guided transposition. CASTs are exceedingly rare in genomic databases; recent surveys have reported Tn7-like transposons that co-opt Type I-F, I-B, and V-K CRISPR effectors. Here, we expand the diversity of reported CAST systems via a bioinformatic search of metagenomic databases. We discover architectures for all known CASTs, including arrangements of the Cascade effectors, target homing modalities, and minimal V-K systems. We also describe families of CASTs that have co-opted the Type I-C and Type IV CRISPR-Cas systems. Our search for non-Tn7 CASTs identifies putative candidates that include a nuclease dead Cas12. These systems shed light on how CRISPR systems have coevolved with transposases and expand the programmable gene-editing toolkit.
CRISPR-Cas系统赋予细菌和古细菌对移动遗传元件的适应性免疫。这些系统还参与其他细胞过程。例如,CRISPR相关的Tn7转座子(cast)已经选择了非核酸酶活性的CRISPR效应蛋白来指导它们的转座。我们对宏基因组数据库进行了生物信息学调查,以发现铸型,包括具有新架构的系统和使用不同CRISPR亚型的系统。我们还描述了一种推测的非tn7 CAST,它可以选择Cas12。我们的发现提出了垂直和水平CAST靶向的机制,并阐明了CAST如何与CRISPR-Cas系统共同进化。crispr相关的Tn7转座子(cast)在rna引导转座中共同选择cas基因。铸型在基因组数据库中极为罕见;最近的调查报道了tn7样转座子可选择I-F型、I-B型和V-K型CRISPR效应子。在这里,我们通过对宏基因组数据库的生物信息学搜索扩大了报道的CAST系统的多样性。我们发现了所有已知投射的架构,包括级联效应器的安排,目标制导模式和最小的V-K系统。我们还描述了采用I-C型和IV型CRISPR-Cas系统的铸型家族。我们对非tn7铸型的研究确定了包括核酸酶死亡Cas12的推定候选铸型。这些系统揭示了CRISPR系统如何与转座共同进化,并扩展了可编程基因编辑工具包。
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引用次数: 29
A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces 水辅助质子通过蛋白质和其他密闭空间的定量范例
Pub Date : 2021-07-20 DOI: 10.1101/2021.07.19.452976
Chenghan Li, G. Voth
Significance As first proposed more than 200 y ago by Grotthuss, proton transport is enabled by a chemical bond-breaking and bond-making proton-hopping mechanism through water networks or “wires,” often contained within confined systems such as protein channels or nanotubes. Herein, concepts from graph theory are utilized in order to define a continuously differentiable collective variable for water wire connectivity and facile proton transport. As such, the water connectivity can be explicitly quantified via free-energy sampling to both qualitatively and quantitatively describe the thermodynamics and kinetics of water-facilitated proton transport via Grotthuss hopping—something that has been lacking since the first conceptual identification of this key chemical process in nature. Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge—and thus to define a quantitative paradigm for facile proton transport in confined spaces—a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl−/H+ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and—by the simple measure of the mere existence of a water structure—the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.
正如Grotthuss在200多年前首次提出的那样,质子传输是通过化学断键和成键质子跳跃机制通过水网络或“线”实现的,这些水网络或“线”通常包含在蛋白质通道或纳米管等受限系统中。本文利用图论的概念来定义水线连通性和质子易输运的连续可微集体变量。因此,水的连通性可以通过自由能采样来明确量化,从而定性和定量地描述水促进质子通过Grotthuss跳跃的热力学和动力学,这是自自然界中这一关键化学过程的第一次概念识别以来一直缺乏的东西。水辅助质子在密闭空间中的传输影响着生物分子和纳米材料系统中的许多现象。在这种情况下,在受限通道中波动的水分子为水合过剩质子通过Grotthuss穿梭迁移提供了环境和介质。然而,一个明确的集体变量(CV),准确地耦合水合作用和质子线连通性与质子易位仍然是难以捉摸的。为了解决这一重要挑战,并因此定义了一个在有限空间中质子传输的定量范式,本研究从图论中推导了一个CV,该CV被验证可以准确地描述与碳纳米管和Cl - /H+反转运蛋白(Cl -ec1)中质子易位相关的水丝形成和断裂。引入多余的质子后,发现水线的构象和热力学发生了重大变化。根据新的CV,当水线被定义为断连时,在质子易位自由能谱中发现了巨大的障碍,即使相关的受限空间仍然相当水合,并且通过水结构存在的简单测量,质子传输将通过过度简化的测量被预测为容易的。然而,在这个范例中,水的简单存在不足以推断质子的移位,因为多余的质子本身能够驱动水合作用,此外,水分子本身必须充分连接以促进任何成功的质子运输。
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引用次数: 12
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Proceedings of the National Academy of Sciences
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