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In silico analysis of aptamer-RNA conjugate interactions with human transferrin receptor 拟合物-RNA 共轭物与人类转铁蛋白受体相互作用的硅学分析
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-10 DOI: 10.1016/j.bpc.2024.107308
Daniel Vasconcelos , André Pina , Nagy Habib , Sérgio Sousa

The human transmembrane protein Transferrin Receptor-1 is regarded as a promising target for the systemic delivery of therapeutic agents, particularly of nucleic acid therapeutics, such as short double stranded RNAs. This ubiquitous receptor is involved in cellular iron uptake, keeping intracellular homeostasis. It is overexpressed in multiple cancer cell types and is internalized via clathrin-mediated endocytosis. In previous studies, a human transferrin receptor-1 RNA aptamer, identified as TR14 ST1–3, was shown to be capable of effectively internalizing into cells in culture and to deliver small, double stranded RNAs in vitro and in vivo, via systemic administration.

To understand, at the molecular level, the aptamer binding to the receptor and the impact of conjugation with the therapeutic RNA, a multi-level in silico protocol was employed, including protein-aptamer docking, molecular dynamics simulations and free energy calculations. The competition for the binding pocket, between the aptamer and the natural ligand human Transferrin, was also evaluated.

The results show that the aptamer binds to the same region as Transferrin, with residues from the helical domain showing a critical role. Moreover, the conjugation to the therapeutic RNA, was shown not to affect aptamer binding. Overall, this study provides an atomic-level understanding of aptamer association to human Transferrin Receptor-1 and of its conjugation with a short model-therapeutic RNA, providing also important clues for futures studies aiming to deliver other oligonucleotide-based therapeutics via Transferrin Receptor.

人类跨膜蛋白转铁蛋白受体-1 被认为是一种很有前景的全身性给药靶标,尤其是核酸治疗药物,如短双链 RNA。这种无处不在的受体参与细胞铁的吸收,维持细胞内的平衡。它在多种癌症细胞中过度表达,并通过凝集素介导的内吞作用内化。为了在分子水平上了解转铁蛋白受体-1 RNA适配体与受体的结合以及与治疗性 RNA 连接的影响,我们采用了多层次的硅学方案,包括蛋白质-适配体对接、分子动力学模拟和自由能计算。结果表明,适配体与转铁蛋白结合在相同的区域,其中螺旋结构域的残基起着关键作用。此外,与治疗用 RNA 连接也不会影响适配体的结合。总之,这项研究从原子层面了解了适配体与人类转铁蛋白受体-1的结合及其与短模型治疗RNA的共轭,也为旨在通过转铁蛋白受体递送其他寡核苷酸治疗药物的未来研究提供了重要线索。
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引用次数: 0
Introns with branchpoint-distant 3′ splice sites: Splicing mechanism and regulatory roles 具有远离分支点的 3′剪接位点的内含子:剪接机制和调控作用
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-08 DOI: 10.1016/j.bpc.2024.107307
Anupa T Anil , Rakesh Pandian , Shravan Kumar Mishra

The two transesterification reactions of pre-mRNA splicing require highly complex yet well-controlled rearrangements of small nuclear RNAs and proteins (snRNP) in the spliceosome. The efficiency and accuracy of these reactions are critical for gene expression, as almost all human genes pass through pre-mRNA splicing. Key parameters that determine the splicing outcome are the length of the intron, the strengths of its splicing signals and gaps between them, and the presence of splicing controlling elements. In particular, the gap between the branchpoint (BP) and the 3′ splice site (ss) of introns is a major determinant of the splicing efficiency. This distance falls within a small range across the introns of an organism. The constraints exist possibly because BP and 3'ss are recognized by BP-binding proteins, U2 snRNP and U2 accessory factors (U2AF) in a coordinated manner. Furthermore, varying distances between the two signals may also affect the second transesterification reaction since the intervening RNA needs to be accurately positioned within the complex RNP machinery. Splicing such pre-mRNAs requires cis-acting elements in the RNA and many trans-acting splicing regulators. Regulated pre-mRNA splicing with BP-distant 3'ss adds another layer of control to gene expression and promotes alternative splicing.

前核糖核酸剪接的两个酯化反应需要剪接体中的小核 RNA 和蛋白质(snRNP)进行高度复杂但控制良好的重新排列。这些反应的效率和准确性对基因表达至关重要,因为几乎所有人类基因都要经过前 mRNA 剪接。决定剪接结果的关键参数是内含子的长度、剪接信号的强度和信号之间的间隙,以及是否存在剪接控制元件。其中,内含子的分支点(BP)与 3′剪接位点(ss)之间的间隙是决定剪接效率的主要因素。这一距离在生物内含子中的范围很小。之所以存在这种限制,可能是因为 BP 和 3'ss 被 BP 结合蛋白、U2 snRNP 和 U2 辅助因子(U2AF)以协调的方式识别。此外,两个信号之间的不同距离也会影响第二次酯化反应,因为中间的 RNA 需要在复杂的 RNP 机制中准确定位。剪接这类前 mRNA 需要 RNA 中的顺式作用元件和许多反式作用的剪接调节因子。具有 BP 远端 3'ss 的受控前 mRNA 剪接为基因表达增加了另一层控制,并促进了替代剪接。
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引用次数: 0
Rhamnolipids and fengycins interact differently with biomimetic lipid membrane models of Botrytis cinerea and Sclerotinia sclerotiorum: Lipidomics profiles and biophysical studies 鼠李糖脂和鼠李素与灰霉病菌和硬皮病菌的生物仿生脂膜模型的相互作用不同:脂质组学分析和生物物理研究。
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-07 DOI: 10.1016/j.bpc.2024.107305
Camille Botcazon , Francisco Ramos-Martín , Nely Rodríguez-Moraga , Thomas Bergia , Sébastien Acket , Catherine Sarazin , Sonia Rippa

Rhamnolipids (RLs) and Fengycins (FGs) are biosurfactants with very promising antifungal properties proposed to reduce the use of synthetic pesticides in crops. They are amphiphilic molecules, both known to target the plasma membrane. They act differently on Botrytis cinerea and Sclerotinia sclerotiorum, two close Sclerotiniaceae phytopathogenic fungi. RLs are more efficient at permeabilizing S. sclerotiorum, and FGs are more efficient at permeabilizing B. cinerea mycelial cells. To study the link between the lipid membrane composition and the activity of RLs and FGs, we analyzed the lipid profiles of B. cinerea and S. sclerotiorum. We determined that unsaturated or saturated C18 and saturated C16 fatty acids are predominant in both fungi. We also showed that phosphatidylethanolamine (PE), phosphatidic acid (PA), and phosphatidylcholine (PC) are the main phospholipids (in this order) in both fungi, with more PA and less PC in S. sclerotiorum. The results were used to build biomimetic lipid membrane models of B. cinerea and S. sclerotiorum for all-atom molecular dynamic simulations and solid-state NMR experiments to more deeply study the interactions between RLs or FGs with different compositions of lipid bilayers. Distinctive effects are exerted by both compounds. RLs completely insert in all the studied model membranes with a fluidification effect. FGs tend to form aggregates out of the bilayer and insert individually more easily into the models representative of B. cinerea than those of S. sclerotiorum, with a higher fluidification effect. These results provide new insights into the lipid composition of closely related fungi and its impact on the mode of action of very promising membranotropic antifungal molecules for agricultural applications.

鼠李糖脂(RLs)和芬吉霉素(FGs)是一种生物表面活性剂,具有很好的抗真菌性能,可减少农作物中合成杀虫剂的使用。它们都是两亲性分子,都以质膜为靶标。它们对灰霉病菌(Botrytis cinerea)和硬皮病菌(Sclerotinia sclerotiorum)这两种近缘硬皮病菌科植物致病真菌的作用各不相同。RLs 能更有效地渗透 S. sclerotiorum,而 FGs 能更有效地渗透 B. cinerea 菌丝细胞。为了研究脂膜成分与 RLs 和 FGs 活性之间的联系,我们分析了 B. cinerea 和 S. sclerotiorum 的脂质概况。我们确定这两种真菌中主要存在不饱和或饱和的 C18 脂肪酸和饱和的 C16 脂肪酸。我们还发现,磷脂酰乙醇胺(PE)、磷脂酸(PA)和磷脂酰胆碱(PC)是两种真菌中的主要磷脂(按此顺序排列),其中硬皮菌中的 PA 较多,PC 较少。研究结果被用于建立 B. cinerea 和 S. sclerotiorum 的生物仿真脂膜模型,以进行全原子分子动力学模拟和固态核磁共振实验,从而更深入地研究 RLs 或 FGs 与不同组成的脂双层之间的相互作用。两种化合物都产生了不同的作用。RLs 可完全插入所有研究的模型膜,并具有流化效应。FGs 往往会在双分子层外形成聚集体,并且比 S. sclerotiorum 更容易单独插入具有代表性的 B. cinerea 模型中,具有更高的流化效应。这些结果为了解近缘真菌的脂质组成及其对农业应用中非常有前景的膜抗真菌分子的作用模式的影响提供了新的视角。
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引用次数: 0
Probing and gauging of D-Penicillamine xenobiotics in hepatic Wilson disease patients 肝性威尔逊病患者体内 D-青霉胺异生物体的探查和测量。
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-05 DOI: 10.1016/j.bpc.2024.107306
Ashish Gupta , Moinak Sen Sarma , Anuj Kumar , Khushbhu Meena , Bikash Baishya , Amrita Mathias , Amresh Kumar Mishra , Neeraj Kumar Rao , Nitu Singh , Parul Singh

D-penicillamine (PA) is the primary chelator of choice to treat Wilson disease (WD). There are limitations in obtaining comprehensive data on PA metabolites in biological specimens by conventional approaches. Hence, the aim of the present was to identify the major hepatic PA metabolites and draw clear conclusions of the drug's xenobiotic in WD. Urine samples were collected from children with hepatic WD (n = 63, aged 14.8 ± 4 years) 5 h after PA administration (16.3 ± 3.8 mg/kg/day) and age-matched healthy volunteers comprised as controls (n = 30). High-resolution 800 MHz nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry was applied to reveal unambiguous appraisals of different excretory by-products of PA metabolism. Four new products comprising penicillamine disulphide (PD), penicillamine cysteine disulphide (PCD), S-methyl penicillamine (SMP), and N-acetyl penicillamine (NAP) of PA xenobiotic metabolites were identified using high-resolution NMR spectroscopy. Quantitative levels of PCD and SMP were approximately three-fold higher than those of PD and NAP, respectively. High-resolution NMR identifies the major PA metabolites with certainty. Reduction, sulfation, and methylation are the predominant pathways of PA metabolism. There is a potential application for assessing therapeutic monitoring of chelation in hepatic WD.

D-青霉胺(PA)是治疗威尔逊病(WD)的主要螯合剂。传统方法难以获得生物样本中 PA 代谢物的全面数据。因此,本研究旨在确定 PA 的主要肝脏代谢物,并就该药物在 WD 中的异生物性得出明确结论。研究人员收集了肝性 WD 患儿(63 人,年龄为 14.8 ± 4 岁)在服用 PA(16.3 ± 3.8 毫克/千克/天)5 小时后的尿液样本,以及年龄匹配的健康志愿者对照组(30 人)的尿液样本。应用高分辨率 800 MHz 核磁共振波谱(NMR)和质谱法对 PA 代谢的不同排泄副产物进行了明确评估。利用高分辨率核磁共振光谱鉴定了 PA 异生物代谢物的四种新产物,包括青霉胺二硫化物(PD)、青霉胺半胱氨酸二硫化物(PCD)、S-甲基青霉胺(SMP)和 N-乙酰青霉胺(NAP)。PCD和SMP的定量水平分别比PD和NAP高出约三倍。高分辨率核磁共振能确定 PA 的主要代谢物。还原、硫化和甲基化是 PA 代谢的主要途径。该方法可用于评估肝WD的螯合治疗监测。
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引用次数: 0
NTPs compete in the active site of RNA polymerases I and II NTP 在 RNA 聚合酶 I 和 II 的活性位点上相互竞争
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-03 DOI: 10.1016/j.bpc.2024.107302
Kaila B. Fuller , Ryan M. Requijo , David A. Schneider , Aaron L. Lucius

Eukaryotes express at least three RNA polymerases (Pols) carry out transcription, while bacteria and archaea use only one. Using transient state kinetics, we have extensively examined and compared the kinetics of both single and multi-nucleotide additions catalyzed by the three Pols. In single nucleotide addition experiments we have observed unexpected extension products beyond one incorporation, which can be attributed to misincorporation, the presence of nearly undetectable amounts of contaminating NTPs, or a mixture of the two. Here we report the development and validation of an analysis strategy to account for the presence of unexpected extension products, when they occur. Using this approach, we uncovered evidence showing that non-cognate nucleotide, thermodynamically, competes with cognate nucleotide for the active site within the elongation complex of Pol I, ΔA12 Pol I, and Pol II. This observation is unexpected because base pairing interactions provide favorable energetics for selectivity and competitive binding indicates that the affinities of cognate and non-cognate nucleotides are within an order of magnitude. Thus, we show that application of our approach will allow for the extraction of additional information that reports on the energetics of nucleotide entry and selectivity.

真核生物至少表达三种 RNA 聚合酶(Pols)进行转录,而细菌和古细菌只使用一种。利用瞬态动力学,我们对三种 Pols 催化的单核苷酸和多核苷酸添加的动力学进行了广泛的研究和比较。在单核苷酸加成实验中,我们观察到了超出一次加成的意外延伸产物,这可能是由于误加成、存在几乎检测不到的污染 NTP 或两者的混合所致。在此,我们报告了一种分析策略的开发和验证情况,该策略可在出现意外延伸产物时对其进行解释。利用这种方法,我们发现有证据表明,在 Pol I、ΔA12 Pol I 和 Pol II 的延伸复合体中,非识别核苷酸在热力学上与识别核苷酸竞争活性位点。这一观察结果出乎意料,因为碱基配对相互作用为选择性提供了有利的能量,而竞争性结合表明同源核苷酸和非同源核苷酸的亲和力在一个数量级之内。因此,我们的研究表明,应用我们的方法可以提取更多信息,报告核苷酸进入和选择性的能量学。
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引用次数: 0
Tailoring solid-state DNP methods to the study of α-synuclein LLPS 调整固态 DNP 方法以研究 α-synuclein LLPS。
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-30 DOI: 10.1016/j.bpc.2024.107303
Ribal Jabbour , Sreejith Raran-Kurussi , Vipin Agarwal , Asif Equbal

Dynamic Nuclear Polarization (DNP) is a technique that leverages the quantum sensing capability of electron spins to enhance the sensitivity of nuclear magnetic resonance (NMR) signals, especially for insensitive samples. Glassing agents play a crucial role in the DNP process by facilitating the transfer of polarization from the unpaired electron spins to the nuclear spins along with cryoprotection of biomolecules. DNPjuice comprising of glycerol-d8/D2O/H2O has been extensively used for this purpose over the past two decades. Polyethylene glycol (PEG), also used as a cryoprotectant, is often used as a crowding agent in experimental setups to mimic cellular conditions, particularly the invitro preparation of liquid-liquid phase separated (LLPS) condensates. In this study, we investigate the efficacy of PEG as an alternative to glycerol in the DNP juice, critical for signal enhancement. The modified DNP matrix leads to high DNP enhancement which enables direct study of LLPS condensates by solid-state DNP methods without adding any external constituents. An indirect advantage of employing PEG is that the PEG signals appear at 72.5 ppm and are relatively well-separated from the aliphatic region of the protein spectra. Large cross-effect DNP enhancement is attained for 13C-glycine by employing the PEG-water mixture as a glassing agent and ASYMPOL-POK as the state-of-art polarizing agent, without any deuteration. The DNP enhancement and the buildup rates are similar to results obtained with DNP juice, conforming to that PEG serves as a good candidate for both inducing crowding and glassing agent in the study of LLPS.

动态核极化(DNP)是一种利用电子自旋的量子感应能力来提高核磁共振(NMR)信号灵敏度的技术,尤其适用于不敏感的样品。玻璃化剂在 DNP 过程中起着至关重要的作用,它可以促进极化从未配对的电子自旋转移到核自旋,同时对生物大分子进行低温保护。在过去的二十年中,由甘油-d8/D2O/H2O 组成的 DNP 胶液已被广泛用于这一目的。聚乙二醇(PEG)也被用作低温保护剂,在模拟细胞条件的实验装置中,尤其是在体外制备液-液相分离(LLPS)冷凝物时,它经常被用作拥挤剂。在本研究中,我们研究了 PEG 在 DNP 果汁中替代甘油的功效,这对增强信号至关重要。改良后的 DNP 基质具有很高的 DNP 增强效果,因此可以通过固态 DNP 方法直接研究 LLPS 冷凝物,而无需添加任何外部成分。使用 PEG 的一个间接优势是 PEG 信号出现在 ∼72.5 ppm 处,与蛋白质光谱的脂肪族区域相对分离。使用 PEG 与水的混合物作为玻璃化剂,ASYMPOL-POK 作为最先进的极化剂,在不进行任何氘化的情况下,13C-甘氨酸的 DNP 得到了很大的交叉效应增强。DNP 增强效果和累积率与使用 DNP 果汁得到的结果相似,这表明在 LLPS 研究中,PEG 既是诱导拥挤的理想候选物质,也是玻璃化剂。
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引用次数: 0
Bridging in silico and in vitro perspectives to unravel molecular mechanisms underlying the inhibition of β-glucuronidase by coumarins from Hibiscus trionum 打通硅学和体外研究的视角,揭示芙蓉三香豆素抑制β-葡糖醛酸酶的分子机制
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-26 DOI: 10.1016/j.bpc.2024.107304
Emadeldin M. Kamel , Faris F. Aba Alkhayl , Haifa A. Alqhtani , May Bin-Jumah , Hassan A. Rudayni , Al Mokhtar Lamsabhi

Unraveling the intricacies of β-glucuronidase inhibition is pivotal for developing effective strategies in applications specific to gastrointestinal health and drug metabolism. Our study investigated the efficacy of some Hibiscus trionum phytochemicals as β-glucuronidase inhibitors. The results showed that cleomiscosin A and mansonone H emerged as the most potent inhibitors, with IC50 values of 3.97 ± 0.35 μM and 10.32 ± 1.85 μM, respectively. Mechanistic analysis of β-glucuronidase inhibition indicated that cleomiscosin A and the reference drug EGCG displayed a mixed inhibition mode against β-glucuronidase, while mansonone H exhibited noncompetitive inhibition against β-glucuronidase. Docking studies revealed that cleomiscosin A and mansonone H exhibited the lowest binding affinities, occupying the same site as EGCG, and engaged significant key residues in their binding mechanisms. Using a 30 ns molecular dynamics (MD) simulation, we explored the interaction dynamics of isolated compounds with β-glucuronidase. Analysis of various MD parameters showed that cleomiscosin A and mansonone H exhibited consistent trajectories and significant energy stabilization with β-glucuronidase. These computational insights complemented experimental findings, underscoring the potential of cleomiscosin A and mansonone H as β-glucuronidase inhibitors.

揭示β-葡糖醛酸酶抑制作用的复杂性对于开发胃肠道健康和药物代谢特定应用领域的有效策略至关重要。我们的研究调查了一些芙蓉三叶草植物化学物质作为β-葡糖醛酸酶抑制剂的功效。结果表明,cleomiscosin A 和 mansonone H 是最有效的抑制剂,其 IC50 值分别为 3.97 ± 0.35 μM 和 10.32 ± 1.85 μM。对β-葡萄糖醛酸酶抑制作用的机理分析表明,裂袂木香苷 A 和参考药物 EGCG 对β-葡萄糖醛酸酶具有混合抑制作用,而曼松酮 H 对β-葡萄糖醛酸酶具有非竞争性抑制作用。Docking 研究表明,cleomiscosin A 和 mansonone H 与 EGCG 的结合亲和力最低,占据了相同的位点,并且在其结合机制中参与了重要的关键残基。利用 30 ns 分子动力学(MD)模拟,我们探索了分离化合物与 β-葡萄糖醛酸酶的相互作用动力学。对各种 MD 参数的分析表明,cleomiscosin A 和 mansonone H 与 β-葡萄糖醛酸酶表现出一致的轨迹和显著的能量稳定。这些计算见解与实验结果相辅相成,凸显了裂米苷 A 和曼松酮 H 作为 β-葡萄糖醛酸酶抑制剂的潜力。
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引用次数: 0
Erratum to “Isolated auto-citrullinated regions of PADI4 associate to the intact protein without altering their disordered conformation” [Biophysical Chemistry …(2024) …] 对 "PADI4 的分离自瓜氨酸区与完整蛋白质结合而不改变其无序构象 "的勘误 [Biophysical Chemistry ...(2024) ...]..
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-23 DOI: 10.1016/j.bpc.2024.107295
José L. Neira , Bruno Rizzuti , Olga Abian , Adrian Velazquez-Campoy
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引用次数: 0
Computational and in vitro binding studies of theophylline against phosphodiesterases functioning in sperm in presence and absence of pentoxifylline 茶碱与精子中存在和不存在的磷酸二酯酶的计算和体外结合研究
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-14 DOI: 10.1016/j.bpc.2024.107294
Gupta Raj , Kulhar Nitin , Suman Abhishek, Sreenath Dey, Eerappa Rajakumara

Fertility is a result of a synergy among the sperm's various functions including capacitation, motility, chemotaxis, acrosome reaction, and, finally, the fertilization of the oocyte. Subpar motility is the most common cause of infertility in males. Cyclic adenosine monophosphate (cAMP) signalling underlies motility and is depleted by the phosphodiesterases (PDEs) in sperm, such as PDE10A, PDE1, and PDE4. Therefore, the PDE inhibitor (PDEI) category of fertility drugs aim to enhance motility in assisted reproduction technologies (ARTs) through inhibition of PDEs, though they might have adverse effects on other physiological variables. For example, the popular drug pentoxifylline (PTX), widely used in ARTs, improves motility but causes premature acrosome reaction and exerts toxicity on the fertilized oocyte. Another xanthine-derived drug, theophylline (TP), has been repurposed for treating infertility, but its mechanism of PDE inhibition remains unexplored. Here, using biophysical and computational approaches, we identified that TP binds to the same binding pocket as PTX with higher affinity than PTX. We also found that PTX and TP co-bind to the same binding pocket, but at different sites.

生育能力是精子各种功能协同作用的结果,这些功能包括获能、运动、趋化、顶体反应,以及最终使卵细胞受精。精子活力不足是导致男性不育的最常见原因。环磷酸腺苷(cAMP)信号是精子活力的基础,而精子中的磷酸二酯酶(PDEs),如 PDE10A、PDE1 和 PDE4,会耗尽环磷酸腺苷(cAMP)信号。因此,PDE 抑制剂(PDEI)类生育药物旨在通过抑制 PDEs 来提高辅助生殖技术(ART)中的精子活力,尽管它们可能会对其他生理变量产生不利影响。例如,在辅助生殖技术中广泛使用的常用药喷托维林(PTX)可提高运动能力,但会导致过早的顶体反应,并对受精卵细胞产生毒性。另一种黄嘌呤衍生药物茶碱(TP)已被重新用于治疗不孕症,但其抑制PDE的机制仍未被探索。在此,我们使用生物物理和计算方法确定了 TP 与 PTX 结合到相同的结合口袋,其亲和力高于 PTX。我们还发现 PTX 和 TP 共同结合到同一个结合袋中,但结合的位点不同。
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引用次数: 0
Calcium ions do not influence the Aβ(25–35) triggered morphological changes of lipid membranes 钙离子不会影响 Aβ(25-35)引发的脂膜形态变化。
IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-11 DOI: 10.1016/j.bpc.2024.107292
Sergei Kurakin , Oleksandr Ivankov , Ermuhammad Dushanov , Tatiana Murugova , Elena Ermakova , Sergey Efimov , Timur Mukhametzyanov , Svetlana Smerdova , Vladimir Klochkov , Alexander Kuklin , Norbert Kučerka

We have studied the effect of calcium ions (Ca2+) at various concentrations on the structure of lipid vesicles in the presence of amyloid-beta peptide Aβ(25–35). In particular, we have investigated the influence of calcium ions on the formation of recently documented bicelle-like structures (BLSs) emerged as a result of Aβ(25–35) triggered membrane disintegration. First, we have shown by using small-angle X-ray and neutron scattering that peptide molecules rigidify the lipid bilayer of gel phase DPPC unilamellar vesicles (ULVs), while addition of the calcium ions to the system hinders this effect of Aβ(25–35). Secondly, the Aβ(25–35) demonstrates a critical peptide concentration at which the BLSs reorganize from ULVs due to heating and cooling the samples through the lipid main phase transition temperature (Tm). However, addition of calcium ions does not affect noticeably the Aβ-induced formation of BLSs and their structural parameters, though the changes in peptide's secondary structure, e.g. the increased α-helix fraction, has been registered by circular dichroism spectroscopy. Finally, according to 31P nuclear magnetic resonance (NMR) measurements, calcium ions do not affect the lipid-peptide arrangement in BLSs and their ability to align in the magnetic field of NMR spectrometer. The influences of various concentrations of calcium ions on the lipid-peptide interactions may prove biologically important because their local concentrations vary widely in in-vivo conditions. In the present work, calcium ions were investigated as a possible tool aimed at regulating the lipid-peptide interactions that demonstrated the disruptive effect of Aβ(25–35) on lipid membranes.

我们研究了不同浓度的钙离子(Ca2+)对存在淀粉样β肽Aβ(25-35)的脂质囊泡结构的影响。特别是,我们研究了钙离子对最近记录的因淀粉样β肽Aβ(25-35)引发的膜解体而形成的双核样结构(BLSs)的影响。首先,我们利用小角 X 射线和中子散射证明,肽分子能使凝胶相 DPPC 单拉美米尔囊泡的脂质双分子层僵化,而钙离子的加入则会阻碍 Aβ(25-35)的这种作用。其次,Aβ(25-35)显示了一个临界肽浓度,在该浓度下,由于加热和冷却样品使其达到脂质主相转变温度(Tm),BLS 从 ULV 重组。然而,加入钙离子并不会明显影响 Aβ 诱导的 BLS 的形成及其结构参数,尽管圆二色谱法记录了肽二级结构的变化,如 α 螺旋部分的增加。最后,根据 31P 核磁共振(NMR)测量,钙离子不会影响 BLS 中脂肽的排列及其在 NMR 光谱仪磁场中的排列能力。不同浓度的钙离子对脂肽相互作用的影响可能具有重要的生物学意义,因为钙离子在体内的局部浓度变化很大。本研究将钙离子作为调节脂质-肽相互作用的一种可能工具进行研究,结果表明 Aβ(25-35)对脂质膜具有破坏作用。
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Biophysical chemistry
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