Biochimica et biophysica acta. Proteins and proteomics最新文献_第7页

TMB Stab-pred: Predicting the stability of transmembrane β-barrel proteins using their sequence and structural signatures TMB Stab-pred：利用β-桶跨膜蛋白的序列和结构特征预测其稳定性。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-04-04 DOI: 10.1016/j.bbapap.2025.141070

P. Ramakrishna Reddy, A. Kulandaisamy, M. Michael Gromiha

Understanding the folding and stability of transmembrane β-barrel proteins (TMBs) provides insights into their structural integrity, functional mechanisms, and implications for disease states. In this work, we have characterized the important features that influence the folding and stability of TMBs. Our results showed that lipid accessible surface area and transition energy are important for understanding the stability of TMBs. Further, this information was utilized to develop a linear regression-based method for predicting the stability of TMBs. Our method achieved a correlation and mean absolute error (MAE) of 0.96 and 0.94 kcal/mol on the jack-knife test. Moreover, we compared the stability of TMBs with globular all-β proteins and observed that long-range interactions and energetic properties are crucial for maintaining the stability of both β-barrel membrane and all-β globular proteins. On the other hand, side-chain – side-chain hydrogen bonds and lipid accessible surface area are specific to membrane proteins. These features are critical for membrane proteins because they influence a protein to embed within the membrane environment. Further, we have developed a web server, TMB Stab-pred for predicting the stability of TMBs, and it is accessible at https://web.iitm.ac.in/bioinfo2/TMBB/index.html.

了解跨膜β桶蛋白（TMBs）的折叠和稳定性，有助于深入了解其结构完整性、功能机制和疾病状态。在这项工作中，我们描述了影响TMBs折叠和稳定性的重要特征。我们的研究结果表明，脂质可达表面积和过渡能对了解TMBs的稳定性很重要。此外，利用这些信息开发了一种基于线性回归的方法来预测TMBs的稳定性。该方法的相关系数和平均绝对误差（MAE）分别为0.96和0.94 kcal/mol。此外，我们还比较了TMBs与球状all-β蛋白的稳定性，发现β桶膜和球状all-β蛋白的远程相互作用和能量特性对维持其稳定性至关重要。另一方面，侧链-侧链氢键和脂质可达表面积是膜蛋白所特有的。这些特征对膜蛋白至关重要，因为它们影响蛋白质嵌入膜环境。此外，我们还开发了一个web服务器，TMB Stab-pred，用于预测TMB的稳定性，可以访问https://web.iitm.ac.in/bioinfo2/TMBB/index.html。

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引用次数: 0

Synovial fluid glycoproteome profiling in knee osteoarthritis: Molecular insights into type 2 diabetes-associated biomarkers and therapeutic targets 膝关节骨关节炎的滑液糖蛋白组分析：2型糖尿病相关生物标志物和治疗靶点的分子见解

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-03-27 DOI: 10.1016/j.bbapap.2025.141067

Monidipa Konar , Bhavneet Kaur , Uttam Chand Saini , Sanjay K. Bhadada , Sadhna Sharma

Type 2 diabetes mellitus (T2DM) and Osteoarthritis (OA) share common risk factors like age, obesity and hypertension. Currently, 52 % of diabetic patients suffer from arthritis. Diabetes facilitates OA by altering lipid metabolism, levels of adipokines & cytokines, accumulation of advanced glycation end products, etc., which affects cartilage & bone health. However, the molecular mechanisms of the association of OA with T2DM remain unexplored. Since diabetes greatly affects the glycosylation status of proteins, the present study focused on identifying glycoproteins that could serve as diagnostic and prognostic markers for identifying osteoarthritis in diabetic individuals by LC-MS/MS. Comparative proteomic analysis revealed 20 significantly altered glycoproteins; among them, thyroxine-binding globulin (THBG), alpha-1-antitrypsin (A1AT), fibrinogen gamma chain (FGG) and angiotensinogen (AGT) were further validated. THBG, A1AT and AGT showed promising potential to identify the comorbid condition in serum and synovial fluid, however, ROC analysis identified THBG as the best candidate glycoprotein marker. Upregulation of THBG in OADM disrupts the bone remodeling cycle, degrades insulin, and promotes the expression of GLUT-1 and MMP-9. Overall, THBG could also serve as a therapeutic target for reducing the progression of osteoarthritis and alleviating pain and bone stiffness associated with the disease.

2型糖尿病（T2DM）和骨关节炎（OA）有共同的危险因素，如年龄、肥胖和高血压。目前，52. %的糖尿病患者患有关节炎。糖尿病通过改变脂质代谢、脂肪因子和细胞因子的水平、晚期糖基化终产物的积累等来促进骨关节炎，从而影响软骨和骨骼的健康。然而，骨性关节炎与2型糖尿病相关的分子机制尚不清楚。由于糖尿病极大地影响了蛋白质的糖基化状态，因此本研究的重点是通过LC-MS/MS鉴定可作为糖尿病患者骨关节炎诊断和预后标志物的糖蛋白。对比分析发现20个糖蛋白显著改变；其中，甲状腺素结合球蛋白（THBG）、α -1-抗胰蛋白酶（A1AT）、纤维蛋白原γ链（FGG）和血管紧张素原（AGT）进一步验证。THBG、A1AT和ANGT在血清和滑液中显示出识别合并症的潜力，然而，ROC分析发现THBG是最佳候选糖蛋白标志物。OADM中THBG的上调破坏骨重塑周期，降解胰岛素，促进GLUT-1和MMP-9的表达。总的来说，THBG也可以作为治疗靶点，减少骨关节炎的进展，减轻与疾病相关的疼痛和骨僵硬。

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引用次数: 0

Efficient production of a novel recombinant fusion protein of EIEC effector IpaD and EGFP: Biophysical characterization and functional studies 一种新的EIEC效应物IpaD和EGFP重组融合蛋白的高效生产：生物物理特性和功能研究。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-03-12 DOI: 10.1016/j.bbapap.2025.141066

Sudeshna Halder, Namita Jaiswal, Salari Charan Balajee, Nibedita Mahata

The conserved invasion plasmid antigen D (IpaD) protein demonstrates broad protective capabilities against bacillary dysentery caused by Enteroinvasive Escherichia coli (EIEC) and Shigella. However, the instability of the IpaD protein at room temperature limits its therapeutic potential. The stabilization and efficient production of functional recombinant proteins remain critical challenges in therapeutic and vaccine development. This study presents a novel fluorescence fusion strategy for producing a stable IpaD-EGFP recombinant protein using a flexible linker (GGGGS)₃. The fusion technique enhances the expression level (∼53 %), solubility (∼77 %), and stability of the IpaD-EGFP fusion protein. Biophysical characterization studies suggest that the IpaD-EGFP fusion protein is stable at refrigerated temperatures for extended periods and up to 1 month at 25 °C. The IpaD-EGFP protein triggers apoptosis in Raw 267.4 cells through activation of caspases 3/7. The protein also induces antibody response in BALB/c mice indicating its immunogenicity. Together, these findings indicate that IpaD-EGFP generated in this study is a potential approach for the design and production of stable IpaD-based protein therapeutics, breaking the expensive “cold chain” of continuous refrigeration. Fusion approach significantly enhanced the solubility, yield, and stability of IpaD, while enabling efficient purification.

保守的侵袭质粒抗原D （IpaD）蛋白对肠侵袭性大肠杆菌（EIEC）和志贺氏菌（Shigella）引起的细菌性痢疾具有广泛的保护作用。然而，IpaD蛋白在室温下的不稳定性限制了它的治疗潜力。功能性重组蛋白的稳定和高效生产仍然是治疗和疫苗开发中的关键挑战。该研究提出了一种新的荧光融合策略，用于使用柔性连接体（GGGGS）₃产生稳定的IpaD-EGFP重组蛋白。融合技术提高了IpaD-EGFP融合蛋白的表达水平（~53 %）、溶解度（~77 %）和稳定性。生物物理特性研究表明，IpaD-EGFP融合蛋白在25 °C的冷藏温度下长时间稳定，可达1 个月。IpaD-EGFP蛋白通过激活caspases 3/7触发Raw 267.4细胞凋亡。该蛋白还在BALB/c小鼠中诱导抗体反应，表明其免疫原性。总之，这些发现表明，本研究中产生的IpaD-EGFP是设计和生产稳定的基于ipad的蛋白质疗法的潜在方法，打破了昂贵的连续冷藏“冷链”。融合方法显著提高了IpaD的溶解度、产率和稳定性，同时实现了高效的纯化。

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引用次数: 0

Tracking heme biology with resonance Raman spectroscopy 用共振拉曼光谱跟踪血红素生物学。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-02-23 DOI: 10.1016/j.bbapap.2025.141065

Amanda Bartkowiak, Ewa Szczesny-Malysiak, Jakub Dybas

Heme proteins are a large group of biomolecules with heme incorporated as a prosthetic group. Apart from cytochromes present in almost all cell types, many other specific heme proteins are expressed in different kinds of cells, e.g. hemoglobin in the erythrocytes, myoglobin (skeletal and vascular smooth muscle cells), cytoglobin (fibroblasts) and neuroglobin (neurons and retina). Among their wide and diverse biological functions, the most important is their unique ability to bind, store, and transport gaseous molecules, such as oxygen, carbon monoxide, and nitric oxide. Resonance Raman (RR) spectroscopy is an exceptional analytical tool that allows for qualitative and quantitative characterization of heme proteins in biological systems. Due to its high sensitivity, even subtle structural alterations of the heme group can be monitored and tracked during cellular processes. Resonance Raman excitation within the Soret absorption band (390–440 nm) provides rich information on the environment of heme's active site, allowing differentiation of the iron ion oxidation and spin states, and tracking the movement of the porphyrin ring plane in response to the changes in oxygenation status. Herein, we summarize and discuss recent developments in RR applications aimed to link the structure-function relationship of heme proteins within biological systems, connected, e.g., with the formation of hemoglobin (Hb) adducts (nitrosylhemoglobin, cyanhemoglobin, sulfhemoglobin), irreversible Hb alterations deteriorating oxygen binding and differentiation of heme proteins oxidation state within live cells in situ.

血红素蛋白是一大类以血红素为假体的生物分子。除了存在于几乎所有细胞类型中的细胞色素外，许多其他特定的血红素蛋白在不同类型的细胞中表达，例如红细胞中的血红蛋白、肌红蛋白（骨骼和血管平滑肌细胞）、细胞红蛋白（成纤维细胞）和神经红蛋白（神经元和视网膜）。在它们广泛而多样的生物功能中，最重要的是它们结合、储存和运输气态分子（如氧气、一氧化碳和一氧化氮）的独特能力。共振拉曼光谱是一种特殊的分析工具，可以对生物系统中的血红素蛋白进行定性和定量表征。由于其高灵敏度，即使是细微的结构改变血红素组可以监测和跟踪在细胞过程中。Soret吸收带（390-440 nm）内的共振拉曼激发提供了血红素活性位点环境的丰富信息，允许铁离子氧化和自旋状态的区分，并跟踪卟啉环平面响应氧合状态变化的运动。在此，我们总结并讨论了RR应用的最新进展，旨在将血红素蛋白在生物系统中的结构-功能关系联系起来，例如与血红蛋白（Hb）加合物（亚硝基血红蛋白、氰化血红蛋白、亚硫酸盐血红蛋白）的形成、不可逆的Hb改变、氧结合恶化以及活细胞内血红素蛋白氧化状态的分化有关。

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引用次数: 0

DSP-1, the major fibronectin type-II protein of donkey seminal plasma is a small heat-shock protein and exhibits chaperone-like activity against thermal and oxidative stress DSP-1是驴精浆中主要的ii型纤维连接蛋白，是一种小的热休克蛋白，对热应激和氧化应激具有类似伴侣蛋白的活性。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-02-15 DOI: 10.1016/j.bbapap.2025.141064

Sk Alim , Sudheer K. Cheppali , Sonali S. Pawar, Musti J. Swamy

Fibronectin type-II (FnII) proteins are major constituents in the seminal plasma of many mammals and play a crucial role in sperm capacitation. Additionally, the seminal FnII proteins from bull and horse exhibit chaperone-like activity (CLA), by acting as small heat shock proteins (shsps). The present work demonstrates that the major FnII protein of donkey seminal plasma, DSP-1 exhibits CLA with broad specificity and protects various client proteins such as alcohol dehydrogenase, lactate dehydrogenase and enolase against thermal and oxidative stress. Binding of phosphorylcholine (PrC) – the head group moiety of choline phospholipids, which are the physiological ligands of DSP-1 – decreased the CLA whereas binding of 1,2-dioleoyl-sn-glycero-3-phospholcholine (DOPC) increased the CLA. Biophysical studies suggested that these contrasting effects on the CLA by phosphorylcholine and diacyl phosphatidylcholine could be attributed to changes in the surface hydrophobicity of DSP-1 upon binding to these ligands. Interestingly, binding of PrC reduced DSP-1 tetramers to monomers with lower surface hydrophobicity, whereas binding to DOPC liposomes increased its surface hydrophobicity. These results, which demonstrate that DSP-1 exhibits CLA and functions as a molecular chaperone, expand the family of mammalian seminal FnII proteins that function as shsps.

纤维连接蛋白ii型（FnII）蛋白是许多哺乳动物精浆中的主要成分，在精子获能中起着至关重要的作用。此外，牛和马的精液FnII蛋白通过作为小热休克蛋白（shsps）表现出伴侣蛋白样活性（CLA）。本研究表明，驴精浆中主要的FnII蛋白DSP-1具有广泛特异性的CLA，并保护多种客户蛋白，如酒精脱氢酶、乳酸脱氢酶和烯醇化酶抵抗热应激和氧化应激。磷酸胆碱（PrC）是胆碱磷脂的头基团，是DSP-1的生理配体，它的结合降低了CLA，而1,2-二油基- asn -甘油-3-磷脂（DOPC）的结合增加了CLA。生物物理学研究表明，磷酸胆碱和二酰基磷脂酰胆碱对CLA的不同影响可能归因于这些配体结合后DSP-1表面疏水性的变化。有趣的是，PrC的结合将DSP-1四聚体还原为具有较低表面疏水性的单体，而与DOPC脂质体的结合则增加了其表面疏水性。这些结果表明，DSP-1表现出CLA和作为分子伴侣的功能，扩大了哺乳动物精液FnII蛋白家族，可以作为shsps发挥作用。

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引用次数: 0

Participation of a cysteine tetrad in the recycling mechanism of methionine sulfoxide reductase A from radiation-tolerant Deinococcus bacteria 半胱氨酸四分体参与耐辐射球菌甲硫氨酸亚砜还原酶a的循环机制。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-02-08 DOI: 10.1016/j.bbapap.2025.141063

Pascal Rey , Nicolas Rouhier , Chloé Carassus , Arjan de Groot , Laurence Blanchard

Methionine oxidation leads to the formation of methionine sulfoxide (MetO), which is reduced back to Met by methionine sulfoxide reductases (Msrs). The catalytic mechanism used by A-type Msr (MsrA) for MetO reduction requires a catalytic cysteine (Cys), which is converted to a sulfenic acid. In general, two resolving Cys are required for the regeneration of the catalytic Cys forming two consecutive disulfide bridges, the last one being efficiently reduced by thioredoxin (Trx). Here, we performed the biochemical characterization of MsrA from Deinococcus deserti. It possesses four Cys, two present in the active site motif (18 and 21) and two distal ones (53 and 163). We produced MsrA variants mutated for these cysteines and analyzed their capacity to reduce MetO in the presence of the NADPH-Trx reductase/Trx system, their ability to form heterodimers with Trxs, and their redox status after incubation with MetO. We show that all four Cys are involved in the regeneration process of enzyme activity by Trx. After MetO reduction by Cys18, a first disulfide bridge is formed with Cys21. A second disulfide involving Cys21 with either Cys53 or Cys163 is reduced by Trx, and a third Cys53-Cys163 disulfide can be formed and also reduced by Trx. These findings highlighting for the first time the involvement of a Cys tetrad in the catalytic and regeneration mechanisms for a MsrA are placed in a structural context by performing 3D modelling and discussed in relation to the known recycling mechanisms involving a Cys triad.

蛋氨酸氧化会形成蛋氨酸亚砜（MetO），蛋氨酸亚砜还原酶（Msrs）会将其还原成蛋氨酸。A 型 Msr（MsrA）还原 MetO 的催化机制需要一个催化半胱氨酸（Cys），并将其转化为亚硫酸。一般来说，催化半胱氨酸的再生需要两个解析半胱氨酸，形成两个连续的二硫桥，最后一个被硫代氧化还蛋白（Trx）有效还原。在这里，我们对沙漠化德氏球菌的 MsrA 进行了生化鉴定。它拥有四个 Cys，其中两个位于活性位点图案中（18 和 21），另外两个位于远端（53 和 163）。我们制作了这些半胱氨酸突变的 MsrA 变体，并分析了它们在 NADPH-Trx 还原酶/Trx 系统存在下还原 MetO 的能力、与 Trxs 形成异二聚体的能力以及与 MetO 培养后的氧化还原状态。我们发现，所有四个 Cys 都参与了 Trx 的酶活性再生过程。Cys18 还原 MetO 后，与 Cys21 形成第一个二硫桥。涉及 Cys21 与 Cys53 或 Cys163 的第二个二硫化物会被 Trx 还原，第三个 Cys53-Cys163 二硫化物也会形成并被 Trx 还原。这些发现首次强调了 Cys 四元组在 MsrA 催化和再生机制中的参与，并通过三维建模将其置于结构背景中，同时结合已知的涉及 Cys 三元组的循环机制进行了讨论。

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引用次数: 0

Elucidation of cytotoxicity of α-Synuclein fibrils on immune cells α-突触核蛋白原纤维对免疫细胞的细胞毒性研究。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-02-01 DOI: 10.1016/j.bbapap.2024.141061

Mikhail Matveyenka , Abid Ali , Charles L. Mitchell , Mikhail Sholukh , Dmitry Kurouski

Progressive aggregation of α-synuclein (α-Syn), a small cytosolic protein involved in cell vesicle trafficking, in the midbrain, hypothalamus, and thalamus is linked to Parkinson's disease (PD). Amyloid oligomers and fibrils formed as a result of such aggregation are highly toxic to neurons. However, it remains unclear whether amyloid-induced toxicity of neurons is the primary mechanism of the progressive neurodegeneration observed upon PD. In the current study, we investigated cytotoxicity exerted by α-Syn fibrils formed in the lipid-free environment, as well as in the presence of two phospholipids, on macrophages, dendritic cells, and microglia. We found that α-Syn fibrils are far more toxic to dendritic cells and microglia compared to neurons. We also observe low toxicity levels of such amyloids to macrophages. Real-time polymerase chain reaction (RT-PCR) results suggest that toxicity of amyloids aggregates is linked to the levels of autophagy in cells. These results suggest that a strong impairment of the immune system in the brain may be the first stop of neurodegenerative processes that are taking place upon the onset of PD.

α-突触核蛋白（α-Syn）是一种参与细胞囊泡运输的小细胞质蛋白，在中脑、下丘脑和丘脑中逐渐聚集与帕金森病（PD）有关。淀粉样蛋白低聚物和原纤维是这种聚集的结果，对神经元具有高度毒性。然而，淀粉样蛋白诱导的神经元毒性是否是PD患者进行性神经变性的主要机制尚不清楚。在目前的研究中，我们研究了在无脂环境中以及两种磷脂存在下形成的α-Syn原纤维对巨噬细胞、树突状细胞和小胶质细胞的细胞毒性。我们发现α-Syn原纤维对树突细胞和小胶质细胞的毒性比神经元大得多。我们还观察到这种淀粉样蛋白对巨噬细胞的毒性很低。实时聚合酶链反应（RT-PCR）结果表明，淀粉样蛋白聚集体的毒性与细胞自噬水平有关。这些结果表明，大脑免疫系统的严重损伤可能是PD发病时发生的神经退行性过程的第一站。

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引用次数: 0

Replacement of the essential catalytic aspartate with serine leads to an active form of copper-containing nitrite reductase from the denitrifier Sinorhizobium meliloti 2011 用丝氨酸取代必需的催化天门冬氨酸导致反硝化菌Sinorhizobium meliloti 2011中含铜亚硝酸盐还原酶的活性形式。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2025-02-01 DOI: 10.1016/j.bbapap.2024.141062

Lorieth A. Guevara Cuasapud , Pablo J. González , Félix M. Ferroni , Andrea B. Duré , Sergio D. Dalosto , Maria G. Rivas , Carlos D. Brondino

We report the molecular, biochemical and spectroscopic characterization and computational calculations of a variant of the copper-containing nitrite reductase from the rhizobial microorganism S. meliloti (SmNirK), in which the catalytic aspartate residue (Asp_CAT) has been replaced with serine (Ser_CAT, D134S) by site-directed mutagenesis. Like the wild-type enzyme, D134S is a homotrimer with the typical catalytic pocket of two-domain NirK containing two copper centers, one of type 1 (T1) and another of type 2 (T2). The T1 electron transfer center is similar to that of the wild-type enzyme but the electronic and covalent properties of T2 active site are altered by the mutation. As for the wild-type enzyme, the enzymatic activity of D134S is pH-dependent, i.e. it is higher at lower pH values, but the k_cat is an order of magnitude lower. EPR studies showed a decrease in g_‖ and an increase in A_‖ of D134S relative to wild-type enzyme. This indicates changes in the electronic and covalent properties of T2 upon mutation, which affects the reduction potential of T2 and the T1-T2 reduction potential gap. Taken together, this evidence points to the importance of the ligands of the second coordination sphere of T2 in controlling critical parameters in catalysis. The possibility that Asp_CAT/Ser_CAT is the switch that triggers T1 → T2 electron transfer upon T2 nitrite binding and the importance of His_CAT for the pH-dependent catalytic activity of NirK are discussed.

我们报道了根生微生物S. meliloti （SmNirK）含铜亚硝酸盐还原酶的分子、生化和光谱表征和计算计算，其中催化的天冬氨酸残基（AspCAT）被丝氨酸（SerCAT, D134S）取代。与野生型酶一样，D134S是一种具有典型的双域NirK催化袋的同型三聚体，含有两个铜中心，一个是1型（T1），另一个是2型（T2）。T1的电子转移中心与野生型酶相似，但T2活性位点的电子和共价性质因突变而改变。对于野生型酶，D134S的酶活性是pH依赖性的，即在较低的pH值下它的酶活性较高，而kcat则低一个数量级。EPR研究表明，与野生型酶相比，D134S的g‖降低，a‖升高。这表明突变后T2的电子和共价性质发生了变化，影响了T2的还原电位和T1-T2的还原电位间隙。综上所述，这一证据表明T2的第二配位球的配体在控制催化过程中的关键参数中的重要性。讨论了AspCAT/SerCAT是触发T1 → T2亚硝酸盐结合时T2电子转移的开关的可能性以及HisCAT对ph依赖性NirK催化活性的重要性。

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引用次数: 0

Unlocking the wound-healing potential: An integrative in silico proteomics and in vivo analysis of Tacorin, a bioactive protein fraction from Ananas comosus (L.) Merr. Stem 打开伤口愈合的潜力：一个集成的硅蛋白质组学和体内分析Tacorin，一个生物活性蛋白组分，从Ananas comosus （L.）稳定。茎

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2024-11-26 DOI: 10.1016/j.bbapap.2024.141060

Puji Rahayu , Doni Dermawan , Florensia Nailufar , Erna Sulistyaningrum , Raymond R. Tjandrawinata

Tacorin, a bioactive protein fraction derived from pineapple stem (Ananas comosus), has emerged as a promising therapeutic agent for wound healing. This study employs an integrated approach, combining in silico proteomics and in vivo investigations, to unravel the molecular mechanisms underlying Tacorin's wound healing properties. In the domain of in silico proteomics, the composition of Tacorin is elucidated through LC/MS-MS protein sequencing, revealing ananain (23.77 kDa) and Jacalin-like lectin (14.99 kDa) as its predominant constituents. Molecular protein-protein docking simulations unveil favorable interactions between Tacorin's components and key regulators of wound healing, including TGF-β, TNF-α, and MMP-2. The calculated free binding energies indicate strong binding affinities between Tacorin proteins and their target receptors. Specifically, ananain demonstrates a binding affinity of −12.2 kcal/mol with TGF-β, suggesting its potential as a potent activator of TGF-β-mediated signaling, while Jacalin-like lectin exhibits the most favorable binding affinity of −8.7 kcal/mol with TNF-α. Subsequent 100 ns molecular dynamics (MD) simulations provide insights into the dynamic behavior and stability of Tacorin-receptor complexes, shedding light on the molecular determinants of Tacorin's therapeutic effects. Complementing the in silico analyses, in vivo studies evaluate Tacorin's efficacy in wound healing using skin and uterine incision models. Tacorin treatment accelerates wound closure and promotes tissue repair in both models, as evidenced by macroscopic observations and histological assessments. Overall, this study provides compelling evidence of Tacorin's therapeutic potential in wound healing and underscores the importance of elucidating its molecular mechanisms for further development and clinical translation.

塔可林是一种从菠萝茎（Ananas comosus）中提取的生物活性蛋白，已成为一种有前景的伤口愈合治疗剂。本研究采用综合方法，结合硅蛋白质组学和体内研究，揭示他可林伤口愈合特性的分子机制。在硅蛋白组学领域，通过LC/MS-MS蛋白测序对Tacorin的组成进行了分析，发现其主要成分为ananain （23.77 kDa）和jacalin样凝集素（14.99 kDa）。分子蛋白对接模拟揭示了Tacorin成分与伤口愈合关键调节因子（包括TGF-β、TNF-α和MMP-2）之间有利的相互作用。计算的自由结合能表明Tacorin蛋白与其靶受体之间具有很强的结合亲和力。具体而言，ananain与TGF-β的结合亲和力为- 12.2 kcal/mol，表明其可能是TGF-β介导的信号传导的有效激活剂，而jacalin样凝集素与TNF-α的结合亲和力为- 8.7 kcal/mol。随后的100ns分子动力学（MD）模拟提供了对他可林受体复合物的动态行为和稳定性的深入了解，揭示了他可林治疗效果的分子决定因素。作为计算机分析的补充，体内研究通过皮肤和子宫切口模型评估了他可林在伤口愈合中的功效。宏观观察和组织学评估证明，他可林治疗在两种模型中都能加速伤口愈合并促进组织修复。总的来说，这项研究提供了令人信服的证据，证明了他可林在伤口愈合中的治疗潜力，并强调了阐明其分子机制对进一步开发和临床转化的重要性。

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引用次数: 0

A distinct co-expressed sulfurtransferase extends the physiological role of mercaptopropionate dioxygenase in Pseudomonas aeruginosa PAO1 铜绿假单胞菌 PAO1 中一种独特的共表达硫基转移酶扩展了巯丙酸二氧酶的生理作用。

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. Proteins and proteomics

Pub Date : 2024-10-28 DOI: 10.1016/j.bbapap.2024.141059

Chukwuemeka S. Adindu , Katie Tombrello , Luke A. Martz , Tonya N. Zeczycki , Holly R. Ellis

Oxidation and assimilation of persulfides in bacteria is often catalyzed by a persulfide dioxygenase and sulfurtransferase in consecutive reactions. Enzymes responsible for the oxidation of persulfides have not been clearly defined in Pseudomonas aeruginosa PAO1. The characterized mercaptopropionate dioxygenase (MDO) in P. aeruginosa PAO1 has been proposed to catalyze the oxidation of 3-mercaptopropionate. However, the physiological role of MDO is uncertain given the expression of a sulfurtransferase (ST) enzyme on the same operon as the thiol dioxygenase. The st gene had a co-occurrence frequency with mdo of 0.94 demonstrating the co-expression and physiological link of the two genes. There are four tandem rhodanese domains in the ST enzyme with two of the domains containing potential catalytic Cys residues (Cys191 and Cys435) capable of forming a persulfide. Only Cys435 was accessible in thiol quantification assays, and results from H/D-X MS analyses further established the accessibility of the domain containing Cys435. Both thiosulfate and mercaptopyruvate served as sulfur donors to the ST enzyme, with Cys435 forming the persulfide intermediate. Kinetic investigations of MDO suggested the enzyme had a broader substrate specificity than previously identified, oxidizing both mercaptopropionate and mercaptopyruvate thiol and persulfide substrates. The results obtained from these investigations provide insight into the overall mechanism and physiological role of the mdo operon in sulfide oxidation and assimilation.

细菌中过硫化物的氧化和同化通常是由过硫化物二氧化酶和硫转移酶在连续反应中催化的。铜绿假单胞菌 PAO1 中负责氧化过硫化物的酶尚未明确定义。有人提出，铜绿假单胞菌 PAO1 中特征性的巯基丙酸二氧酶（MDO）可催化 3-巯基丙酸的氧化。然而，由于硫醇二氧酶在同一操作子上表达硫转移酶（ST），MDO 的生理作用尚不确定。ST 基因与 mdo 基因的共现频率为 0.94，表明这两个基因的共同表达和生理联系。ST 酶中有四个串联的菱形结构域，其中两个结构域含有能形成过硫化物的潜在催化 Cys 残基（Cys191 和 Cys435）。在硫醇定量分析中，只有 Cys435 是可触及的，H/D-X MS 分析结果进一步确定了含有 Cys435 的结构域的可触及性。硫代硫酸盐和巯基丙酮酸都是 ST 酶的硫供体，Cys435 形成过硫化物中间体。对 MDO 的动力学研究表明，该酶的底物特异性比以前发现的更广，可氧化巯基丙酸盐和巯基丙酮酸盐硫醇和过硫化物底物。这些研究结果有助于深入了解 mdo 操作子在硫化物氧化和同化过程中的总体机制和生理作用。

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引用次数: 0