Biophysical chemistry最新文献_第3页

Development of an EPR-based methodology to study protein-lipid interaction 开发基于epr的方法来研究蛋白质-脂质相互作用。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-02-01 Epub Date: 2025-11-08 DOI: 10.1016/j.bpc.2025.107550

Clara Piersson , Shikhar Prakash , Victoria Lublin , Melanie Rossotti , Baptiste Fischer , Madhur Srivastava , Yann Fichou

{"title":"Development of an EPR-based methodology to study protein-lipid interaction","authors":"Clara Piersson , Shikhar Prakash , Victoria Lublin , Melanie Rossotti , Baptiste Fischer , Madhur Srivastava , Yann Fichou","doi":"10.1016/j.bpc.2025.107550","DOIUrl":"10.1016/j.bpc.2025.107550","url":null,"abstract":"<div><div>The interaction of protein with other biomolecules is central to all cellular processes. In particular, protein-lipid interactions play an essential role in regulating soluble and membrane protein function, structure, and dynamics. However, probing these interactions remains challenging due to the complexity and heterogeneity of membranes. Various methods have been developed to characterize protein-membrane interaction, each presenting advantages and limitations. This study presents a robust methodology based on continuous-wave Electron Paramagnetic Resonance (CW-EPR) spectroscopy to characterize protein–membrane interactions. We focused on the protein Tau, an intrinsically disordered protein associated with neurodegenerative diseases. We show that the interaction of labelled Tau with lipids gives rise to a very distinct lineshape, which can be used to quantify the fraction of bound protein. This allows to obtain the apparent binding mode and affinity through titration experiments. In addition, we show that a single measurement provides the absolute concentration of free and bound protein. We argue that this information, which is rarely obtained by other methods providing relative signals, is very useful for mechanistic studies. Furthermore, we developed a minimal-data approach and demonstrated that a single EPR measurement can be used to estimate an apparent binding constant. The approach is applied to the Tau-membrane interaction occurring in different conditions affecting the binding behavior. The presented methodology is expected to be applicable to other proteins.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"329 ","pages":"Article 107550"},"PeriodicalIF":2.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RufO, a cytochrome P450 (CYP) enzyme, recognition to putative substrates and a redox partner: Binding and structural insights 细胞色素P450 （CYP）酶RufO对假定底物和氧化还原伙伴的识别：结合和结构见解。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-02-01 Epub Date: 2025-10-26 DOI: 10.1016/j.bpc.2025.107546

Dubey Saniya , Parate Shivani , Suman Abhishek , Vadivelu Abithaa , Priyanka Bajaj , Eerappa Rajakumara

{"title":"RufO, a cytochrome P450 (CYP) enzyme, recognition to putative substrates and a redox partner: Binding and structural insights","authors":"Dubey Saniya , Parate Shivani , Suman Abhishek , Vadivelu Abithaa , Priyanka Bajaj , Eerappa Rajakumara","doi":"10.1016/j.bpc.2025.107546","DOIUrl":"10.1016/j.bpc.2025.107546","url":null,"abstract":"<div><div>RufO is a Cytochrome P450 enzyme involved in synthesising Rufomycin, a circular peptide with antibacterial activity. Herein, we present structural and biophysical analyses to resolve the ambiguity of RufO's substrate specificity. The structure of unliganded RufO, alongside a series of computational and biophysical studies investigating its substrate specificity in the presence of ferredoxin, which is known to serve as an effector of the redox activities of several P450 enzymes. Contrary to reports on RufO's catalytic activity, monomeric L-tyrosine was not recognized by RufO in our isothermal titration calorimetry (ITC) experiments. Instead, RufO recognizes a range of putative substrates, particularly those containing methyl and nitro groups, suggesting a broader substrate scope. Additionally, we see that RufO binds to its redox partner CamB with micromolar affinity, and its interaction significantly enhances the putative substrate binding by ∼10-fold. Our crystal structure of RufO reveals similarities and differences in putative substrates and ferredoxin binding regions compared to other CYP450 enzymes. Our findings establish RufO might be a substrate-promiscuous enzyme with potential applications in the biocatalytic nitration of industrially relevant compounds.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"329 ","pages":"Article 107546"},"PeriodicalIF":2.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145408282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Study of neurotransmitter dopamine interaction with DNA by electrochemical and spectroscopic methods 神经递质多巴胺与DNA相互作用的电化学和光谱研究。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-02-01 Epub Date: 2025-11-17 DOI: 10.1016/j.bpc.2025.107552

Poghos O. Vardevanyan , Gaspar H. Kocharyan , Marine A. Parsadanyan , Anna V. Vardanyan , Mariam A. Shahinyan , Ara P. Antonyan

{"title":"Study of neurotransmitter dopamine interaction with DNA by electrochemical and spectroscopic methods","authors":"Poghos O. Vardevanyan , Gaspar H. Kocharyan , Marine A. Parsadanyan , Anna V. Vardanyan , Mariam A. Shahinyan , Ara P. Antonyan","doi":"10.1016/j.bpc.2025.107552","DOIUrl":"10.1016/j.bpc.2025.107552","url":null,"abstract":"<div><div>Dopamine interaction with DNA has been studied using square-wave voltammetry (SWV), fluorescence, and absorption spectroscopy. The effect of dopamine on the binding of classical intercalating agents, such as acridine orange (AO), ethidium bromide (EtBr) as well as classical groove binding ligand Hoechst 33258 (H33258) was evaluated. The obtained results clarify the molecular mechanisms of dopamine interaction with DNA and reveal its potential competition for intercalation and minor groove binding sites which show that dopamine interacts with DNA by multimodal modes. On the basis of fluorescence measurements, the values of the binding constant (K) and the number of base pairs (n) per binding site were determined. It was revealed that the values of these binding parameters (K and n) depend on the ionic strength of the solution. Based on the changes of the binding parameters of AO, EtBr and H33258 with DNA in the absence and presence of dopamine, it was shown that the presence of the neurotransmitter reduces the affinity of these ligands toward DNA. The obtained data indicate that dopamine binds to DNA via intercalation and minor groove binding mechanisms, which leads to a decrease in the binding constants of these ligands with DNA. In the case of dopamine interaction with DNA in the presence of intercalators, the effect is especially pronounced for the strong (intercalation) binding mode of EtBr, as its binding constant with DNA in the presence of dopamine is significantly lower than that of AO.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"329 ","pages":"Article 107552"},"PeriodicalIF":2.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145572872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural basis of molecular recognition of pyridoxal 5′-phosphate in a bacterial periplasmic binding protein 细菌周围质结合蛋白中吡哆醛5′-磷酸分子识别的结构基础。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-02-01 Epub Date: 2025-10-26 DOI: 10.1016/j.bpc.2025.107547

Miriana Quaranta, Stefano Pascarella

{"title":"Structural basis of molecular recognition of pyridoxal 5′-phosphate in a bacterial periplasmic binding protein","authors":"Miriana Quaranta, Stefano Pascarella","doi":"10.1016/j.bpc.2025.107547","DOIUrl":"10.1016/j.bpc.2025.107547","url":null,"abstract":"<div><div>Vitamin B<sub>6</sub> and its vitamers are essential in bacteria. Many are auxotrophic for B<sub>6</sub> vitamers and require salvage pathways and membrane uptake systems. Despite the importance of the uptake systems, very few transporters have been structurally characterized. The structure of the periplasmic binding protein (P5PA) of an ABC uptake transporter from the pathogen <em>Actinobacillus pleuropneumoniae</em> has been recently solved in complex with pyridoxal 5′-phosphate (PLP). Another close homolog from the same organism, AfuA, had been structurally characterized as a complex with glucose-6-phosphate (G6P). To study the molecular recognition of PLP by P5PA, a comparative approach has been applied. The heterologous complexes P5PA-G6P and AfuA-PLP have been generated by docking. Systematic molecular dynamics simulations have been applied to the native and heterologous complexes. Binding energies and molecular interactions have been compared for all the complexes. The results suggest the selective binding of the ligand is achieved by a combination of structural factors specific to each protein, including shape of the binding site, steric hindrance, hydrogen bonding, electrostatic and hydrophobic interactions. No single residue is uniquely responsible for ligand specificity although a few side chains play a significant role. Heterologous ligands are subject to destabilizing interactions that provoke the distortion of the ligand itself and the alteration of the protein dynamics. Residue Q267 appears to provide a significant stabilization contribution in the P5PA-PLP complex but not in AfuA-PLP. Likewise, D207 provides stabilization in the AfuA-G6P complex and not in AfuA-PLP. The indications obtained suggest strategies for the design of specific inhibitors.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"329 ","pages":"Article 107547"},"PeriodicalIF":2.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Sustainable synthesis and functional profiling of Ipomoea hederifolia-derived terpenoids-assisted silver nanoparticles: Mechanistic insights into anticancer, antioxidant, antibiofilm, and anti-quorum sensing activities Ipomoea hederifolia衍生萜类辅助银纳米颗粒的可持续合成和功能分析：抗癌、抗氧化、抗生物膜和抗群体感应活性的机制见解

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-09-04 DOI: 10.1016/j.bpc.2025.107524

Khushboo Makwana , Reem Binsuwaidan , Mohd Adnan , Nawaf Alshammari , Mitesh Patel

{"title":"Sustainable synthesis and functional profiling of Ipomoea hederifolia-derived terpenoids-assisted silver nanoparticles: Mechanistic insights into anticancer, antioxidant, antibiofilm, and anti-quorum sensing activities","authors":"Khushboo Makwana , Reem Binsuwaidan , Mohd Adnan , Nawaf Alshammari , Mitesh Patel","doi":"10.1016/j.bpc.2025.107524","DOIUrl":"10.1016/j.bpc.2025.107524","url":null,"abstract":"<div><div>Silver nanoparticles (AgNPs) synthesized through green chemistry approaches offer a sustainable alternative to conventional methods, with potential applications in various biological fields. In this study, we report the synthesis of AgNPs using terpenoids derived from <em>Ipomoea hederifolia</em> L. (Convolvulaceae). The AgNPs (AgNPs-T) were characterized using UV–Vis spectroscopy, which revealed a surface plasmon resonance (SPR) peak at 452 nm, confirming successful synthesis. Fourier-transform infrared spectroscopy (FTIR) analysis identified functional groups such as hydroxyl and carbonyl that facilitated the reduction of silver ions and acted as stabilizing agents. Transmission electron microscopy (TEM) showed that the AgNPs-T were spherical in shape, with sizes ranging from 4 to 20 nm, and were well-dispersed due to the presence of capping agents from the plant extract. The biological activities of AgNPs-T were evaluated, showcasing potent antibacterial activity against several human pathogenic bacteria. Additionally, AgNPs-T exhibited significant antibiofilm and anti-quorum sensing activities, disrupting biofilm formation and inhibiting bacterial communication. The nanoparticles also demonstrated strong antioxidant properties by scavenging DPPH radicals in a dose-dependent manner. Moreover, cytotoxicity studies using the MTT assay revealed that AgNPs-T exerted dose-dependent anticancer effects against breast cancer (MCF-7) cells. These findings suggest that <em>Ipomoea hederifolia</em>-derived AgNPs possess multifunctional biological activities, making them promising candidates for applications in antimicrobial, antioxidant, and anticancer therapies.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107524"},"PeriodicalIF":2.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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K2P channels and ultrasound neuromodulation: A mechanosensitive memory perspective K2P通道和超声神经调节：机械敏感记忆的视角

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-09-22 DOI: 10.1016/j.bpc.2025.107530

Yuval Ben-Abu

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Cationic carboxymethyl chitosan nanofibers embedded with silver nanoparticles for enhanced antibacterial applications 嵌入银纳米粒子的阳离子羧甲基壳聚糖纳米纤维增强抗菌应用。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-10-14 DOI: 10.1016/j.bpc.2025.107537

Neha Devi , Satish Kumar Pandey , Nishima Wangoo

{"title":"Cationic carboxymethyl chitosan nanofibers embedded with silver nanoparticles for enhanced antibacterial applications","authors":"Neha Devi , Satish Kumar Pandey , Nishima Wangoo","doi":"10.1016/j.bpc.2025.107537","DOIUrl":"10.1016/j.bpc.2025.107537","url":null,"abstract":"<div><div>There has been a growing concern regarding antibiotic resistance which has led to the design of new antibacterial nanocomposite with high efficiency and low cytotoxicity. This report demonstrates an approach for the design of a nanocomposite comprising of histidine tagged silver nanoparticles (His@AgNPs) embedded it in a carboxymethyl chitosan hydrogel (CHG). Carboxymethyl chitosan was used as a cationic polymer substrate to reinforce the antibacterial activity of the embedded silver nanoparticles. ICP-MS showed sufficient release of silver ions which results in enhanced antibacterial activity. In addition, the hydrogel with embedded silver nanoparticles exhibited excellent antibacterial performance against gram-negative <em>Escherichia coli</em> and gram-positive <em>Staphylococcus aureus</em> through a “kill-release” stratagem, which was mainly due to the synergistic effect of CHG and Ag<sup>+</sup> ions release. The results showed that the cross-linking may enhance antibacterial activities of nanocomposite (CHG-His@AgNPs) by approximately 4-folds in comparison to His@AgNPs. A strong signal observed in confocal microscopy confirmed the successful internalization of the nanocomposite in tested microorganisms. The change in the morphology of the bacterial cells upon the treatment with nanocomposite was observed through FE-SEM microscopy which confirmed the antibacterial activity of the nanocomposite. The synthesized nanocomposite can thereby serve as an excellent candidate for tackling antibiotic resistance.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107537"},"PeriodicalIF":2.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SDS protein interactions SDS蛋白相互作用。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-10-10 DOI: 10.1016/j.bpc.2025.107534

Tsutomu Arakawa , Daisuke Ejima , Tomoto Ura , Teruo Akuta , Masamichi Oh-Ishi

引用次数: 0

Conformational transition of a polycationic hinge domain contributes to DNA binding 多阳离子铰链结构域的构象转变有助于DNA结合

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-09-26 DOI: 10.1016/j.bpc.2025.107531

Michael T. Harnish, Bill Pham, Avery B. Arons, Yingjie Xu, Elias J. Fernandez, Tongye Shen

{"title":"Conformational transition of a polycationic hinge domain contributes to DNA binding","authors":"Michael T. Harnish, Bill Pham, Avery B. Arons, Yingjie Xu, Elias J. Fernandez, Tongye Shen","doi":"10.1016/j.bpc.2025.107531","DOIUrl":"10.1016/j.bpc.2025.107531","url":null,"abstract":"<div><div>Nuclear receptors (NRs) are multidomain, ligand-activated transcription factors that play critical physiological roles. While the structured DNA-binding domain (DBD) and ligand-binding domain (LBD) have been well characterized, the function of intrinsically disordered regions—such as the hinge between the LBD and DBD—remains unclear. To illuminate the role of the hinge, we conducted five-microsecond molecular dynamics simulations of thyroid hormone receptor (TRα) alone versus bound to DNA. We reveal that DNA binding induces a significant structural change in the hinge region (helical to unwound coil), with a potentially important role in the regulation of TRα activity. Previously, hinge helicity has been reported to drive oligomerization and the consequent inhibition of coactivator binding, and such DNA-induced transition may promote TR activation. Protein-DNA binding is found to be multivalent and contains the direct interaction of the hinge with the DNA minor groove in addition to the canonical recognition helix of the DBD with the major groove. Furthermore, the poly-Arg segment of the hinge has a direct and significant influence on DNA conformation. This interaction promotes a bent DNA phosphate backbone, which might further contribute to the protein-DNA recognition. On a global scale, DNA binding induces a “closed-to-open” conformational change thus reducing direct DBD-LBD interactions, which corroborates previous calorimetric binding studies. Overall, our results provide insight into the mechanism of DNA recognition and the resulting conformational dynamics of the TRα-DNA complex.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107531"},"PeriodicalIF":2.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145263229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Probing the cytotoxicity and the dynamic interaction of IIKK cationic peptides with human melanoma cells 探索IIKK阳离子肽与人类黑色素瘤细胞的细胞毒性和动态相互作用。

IF 2.2 3区生物学

Biophysical chemistry Pub Date : 2026-01-01 Epub Date: 2025-10-11 DOI: 10.1016/j.bpc.2025.107536

Luciana Marciano Sergio , Amanda Sansone Semerdjian , Manoel Arcisio-Miranda

{"title":"Probing the cytotoxicity and the dynamic interaction of IIKK cationic peptides with human melanoma cells","authors":"Luciana Marciano Sergio , Amanda Sansone Semerdjian , Manoel Arcisio-Miranda","doi":"10.1016/j.bpc.2025.107536","DOIUrl":"10.1016/j.bpc.2025.107536","url":null,"abstract":"<div><div>Cationic peptides have emerged as promising candidates in anticancer therapy due to their ability to directly target the plasma membrane of cancer cells, a mechanism that could potentially bypass traditional drug resistance pathways. In this study, we evaluated the cytotoxic activity and cell-membrane binding properties of three amphiphilic cationic peptides from the G(IIKK)ₙI-NH₂ family (<em>n</em> = 2–4) against human melanoma cells (SK-MEL-28). By performing MTT assays and tracking the propidium iodide (PI) uptake throughout peptide-cell interaction, we evaluated peptides' cytotoxicity. Assessment of the interaction dynamics was conducted by fluorescence spectroscopy assays with FPE, a surface potential sensitive probe. This evaluation indicated that an increase in net positive charge was relatable to a lower dissociation constant (K<sub>d</sub>). Notably, G(IIKK)₄I-NH₂ showed the highest cytotoxicity, significant morphological alterations, rapid membrane permeabilization, and the lowest K<sub>d</sub>, indicating a stronger membrane affinity when compared to the other peptides. G(IIKK)<sub>3</sub>I-NH₂, in the same manner as G(IIKK)₄I-NH₂, revealed a cooperative binding behavior, evidenced by a Hill coefficient > 1. An inverse correlation between peptide-cell membrane dissociation constants and cytotoxicity was established, supporting the notion that membrane interaction is a critical determinant of anticancer activity. In addition, we used a cell surface membrane potential probe to possibly anticipate the in vitro activity of cationic peptides. Altogether, these findings provide mechanistic insights into peptide-cell membrane interactions and may offer a basis for the rational design of novel anticancer peptides targeting melanoma.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"328 ","pages":"Article 107536"},"PeriodicalIF":2.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0