Journal of Proteomics
·
2023
·
IF 3.3
Yuanyuan Zhang,Yutong Han,Wenjie Zhu,Jing Yuan,Xin Liu
Protein C-termini containing valuable biological information plays a vital role in various physiological processes , such as protein localization, protein recognition, and signal transduction in organisms. However, C-terminal peptide identification is still challenging due to their low abundance and similar physicochemical properties to other digested peptides. Herein, we developed a simple and mild strategy for the enrichment of C-terminal peptides that incorporates selectively 2-pyridinecarbaldehyde (2-PCA) derivatization of α-amine with negative enrichment by NHS resin. Two synthesized peptides were utilized to evaluate the efficiency of 2-PCA derivatization and optimize the coupling conditions of NHS resin. The feasibility of the method was further validated by enriching the C-terminus of the bovine serum albumin (BSA). Finally, this method was successfully applied to the C-terminus analysis of mouse brain tissue, identifying 404 protein C-termini with physicochemical properties unbiasedly. Additionally, the GO and KEGG analyses revealed that these identified proteins are crucial for proper brain function. In summary, our proposed method is effective and has the potential to facilitate comprehensive C-terminal analysis of proteins . Significance Effective enrichment methods are essential for the identification of the proteins C-terminus. In this study, a mild and simple method for negative C-terminal enrichment combined with site-specific derivatization was developed. The enrichment process was simplified and minimized sample loss simultaneously, using 2-PCA derivatization which has high α-amino specificity. Up to 346C-terminal proteins were identified in mouse brain tissue unbiasedly and reliably. This approach has the potential to facilitate comprehensive analysis of protein C-termini in a variety of biological contexts.
研究领域:
生物化学
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蛋白质组学
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系统生物学
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DOI
PubMed
高影响因子
PROTEIN EXPRESSION AND PURIFICATION
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2022
·
IF 2.025
Yi Rong,Chaofeng Zhang,Wen-Chao Gao,Cheng Zhao
The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a vital role in viral replication. To study the function of M pro and screen inhibitors targeting M pro , it is necessary to prepare high-purity and high-activity M pro . In this study, four types of SARS-CoV-2 M pro s containing different termini were prepared, and their activities were determined successfully. The results showed that the activity of wild-type (WT) M pro was the highest, and the additional residues at the N-terminus but not at the C-terminus had a major effect on the enzyme activity. To explain this, the alignment of structures of different forms of M pro was determined, and the additional residues at the N-terminus were found to interfere with the formation of the substrate binding pocket. This study confirms the importance of the natural N-terminus to the activity of M pro and suggests that WT-GPH 6 (M pro with eight additional residues at the C-terminus) can be used as a substitute for authentic M pro to screen inhibitors. In short, this study provides a reference for the expression and purification of new coronaviruses confronted in the future.
研究领域:
病毒学
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生物化学
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分子生物学
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DOI
PubMed
高影响因子
CHROMATOGRAPHIA
·
2022
·Vol. 85
·期 8
·743-754
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IF 2.213
Lin Min,Li Xinxin,Zhang Hongfeng,Ji Wenquan,Shi Yuhan,Li Qinran,Zhang Chenxi,Deng Qiliang
Abstract The C-terminal epitope imprinted polymers on the silica were prepared by reversible addition-fragmentation chain transfer (RAFT) strategy with C-terminal nonapeptide of cytochrome c (Cyt c) as the template. 4-cyano-4-(phenylcarbonothioylthio) phetanoic acid was immobilized on the silica as a chain transfer agent to regulate the polymerization of the imprinted layer to enhance the recognition performance of the imprinted materials for the peptide and target protein. Additionally, zinc methacrylate was used as a functional monomer to form the imprinted sites through the synergistic effect of Zn 2+ chelating, hydrogen bonding and electrostatic attraction, which further improved the recognition between polymers and protein. The molecularly imprinted polymers prepared with RAFT strategy show good recognition for the epitope peptide and Cyt c with imprinting factors of 7.96 and 6.17, respectively, which is higher than those prepared without RAFT strategy. Furthermore, the imprinted polymers have a good binding capacity and imprinting factor for Cyt c in multi-proteins selective recognition and have good reusability. The performance of Cyt c recognition in bovine serum by the epitope imprinted polymers was calculated by HPLC and the results demonstrated the well selectivity and potential application for Cyt c recognition in biological sample. Graphical abstract
研究领域:
生物化学
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材料科学
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DOI
高影响因子
Molecular Informatics
·
2017
·Vol. 36
·期 9
·1600157
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IF 1.955
Chunyan Qi,Guimei Lin,Rong Zhang,Wenjuan Wu
Graphical 3D-QSAR, molecular docking and activity evaluation were used to study the bioactivities of ACE-inhibitory peptides with phenylalanine C-terminus. Both CoMFA ( Q 2 =0.773, R 2 =0.992) and CoMSIA ( Q 2 =0.664, R 2 =0.990) models were constructed. According to the established models, four novel potent ACE-inhibitory tripeptides GEF, VEF, VRF, and VKF were synthesized. The IC 50 values were respectively determined to be 13 μM, 23 μM, 5 μM, and 11 μM by in vitro evaluation. The results show good agreement with the predicted values. The established models play an important role in revealing the structure-activity relationship of ACE-inhibitory peptides and designing novel peptides with enhanced biological activity.
研究领域:
药理学
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生物化学
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计算化学
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DOI
PubMed
高影响因子
MOLECULAR CELL
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2022
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IF 19.328
Di Chen,Mohan Lyu,Xiaoxia Kou,Jing Li,Zhixuan Yang,Lulu Gao,Yue Li,Liu-min Fan,Hui Shi,Shangwei Zhong
Summary Light and temperature in plants are perceived by a common receptor, phytochrome B (phyB). How phyB distinguishes these signals remains elusive. Here, we report that phyB spontaneously undergoes phase separation to assemble liquid-like droplets. This capacity is driven by its C terminus through self-association, whereas the intrinsically disordered N-terminal extension (NTE) functions as a biophysical modulator of phase separation. Light exposure triggers a conformational change to subsequently alter phyB condensate assembly, while temperature sensation is directly mediated by the NTE to modulate the phase behavior of phyB droplets. Multiple signaling components are selectively incorporated into phyB droplets to form concentrated microreactors, allowing switch-like control of phyB signaling activity through phase transitions. Therefore, light and temperature cues are separately read out by phyB via allosteric changes and spontaneous phase separation, respectively. We provide a conceptual framework showing how the distinct but highly correlated physical signals are interpreted and sorted by one receptor.
研究领域:
植物生物学
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分子生物学
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细胞生物学
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DOI
PubMed
高影响因子
JOURNAL OF COLLOID AND INTERFACE SCIENCE
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2016
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IF 3.782
Ruipu Xin,Faez Iqbal Khan,Zexin Zhao,Zedong Zhang,Bo Yang,Yonghua Wang
The mechanism of lipase binding to the lipid-water interface is crucial for substrate specificity and kinetic properties. In this study, the chain-length specificity, regiospecificity and substrate specificity of Phospholipase A 1 (PLA 1 ) and its parent enzyme Thermomyces lanuginosus lipase (TLL) have been investigated using a classical emulsion system. The results show that both PLA 1 and TLL are 1,3-regioselective lipases. Additionally, the hydrolytic activity of PLA 1 is comparatively lower on short-chain triacylglyceride (TAG) and higher on phosphatidylcholine (PC) than the hydrolytic activity of TLL. Further, the results obtained with monolayer film techniques demonstrate that the C-terminal region regulates the binding of PLA 1 to PC. A hypothesis is presented according to which the α9 helix of C-terminal region in PLA 1 not only controls the opening of lid but also serves as a membrane anchor that assists in binding to PC. These findings bring new insight into rational design of novel lipases with intriguing functionalities.
研究领域:
酶学
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生物化学
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分子生物学
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DOI
PubMed
高影响因子
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
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2025
·
IF 4
Shu-Lin Li,Fu-Peng Li,Zi-Xuan Yang,Yu-Jie Zhao,Zhao-Qun Li,Nai-Yong Liu
The cerambycid beetles are important components in the terrestrial ecosystem as they play a dual role in both degrading dying trees and killing healthy plants. The factors including human activity, habitat contraction, climate changes and pesticide use have been shaping the adaptation of beetles to host plants and the environment. As suggested in research on the functions of beetles' olfactory proteins, odorant binding proteins (OBPs) have been found to be involved in insecticide resistance other than chemoreception. Here, we assessed the importance of antenna/leg-enriched PantOBPs from Pharsalia antennata in the adaptation of hosts and habitats. Transcriptome analyses led to the yields of 60 OBP-coding genes in P. antennata , with the largest set of 44 Minus-C OBPs. Using RNA sequencing and PCR approaches, we obtained tissue-enriched and sex-biased PantOBPs. Binding studies revealed that 10 PantOBPs had diverse binding properties against 92 plant-derived odorants and 32 contact insecticides. Three plant volatiles of β-ionone, ethyl-(2 E ,4 Z )-deca-2,4-dienoate and syringaldehyde as well as seven insecticides including chlorpyrifos, phoxim and rotenone were strong ligands for most PantOBPs (dissociation constant, K i < 11.70 μM). Docking simulations and point-mutation experiments demonstrated the importance of C-terminal residues in the interactions of PantOBP12, OBP38 and OBP39 with good ligands, but, in some cases, they exhibited different binding mechanisms. Our results indicate that PantOBPs in P. antennata serve a dual function in chemoreception and insecticide binding, providing insights into the strong adaptation of this beetle to host plants and the environment.
研究领域:
昆虫学
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分子生物学
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生态学
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害虫治理
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生物化学
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DOI
PubMed
高影响因子
ADVANCED FUNCTIONAL MATERIALS
·
2024
·
IF 18.5
Na Wen,Shuangshuang Li,Hongzhi Jiang,Jiachao Yang,Weibo Yang,Yunhao Song,Jinlin Long,Jiwu Zhao,Zhihui Lin,Xunbin Yu,Yen Wei,Shiyun Lu,Xueping Huang,Tianhua Zhou
Gastric ulcers accompanied by acute or chronic bleeding represent a significant risk of fatality. However, the development of effective strategies for achieving rapid hemostasis and wound healing in gastric ulcer bleeding represents a formidable challenge. To address this challenge, thrombin-derived C-terminal peptide (TCP-25) is employed as a targeted agent, and it is incorporated into two novel injectable and biocompatible carboxymethyl chitosan (CMCs) hydrogels via Schiff's base reaction. The TCP-25 peptide hydrogels display optimal adaptability within the distinctive gastrointestinal microenvironment, demonstrating a balance of acid resistance and degradation, along with controlled release and bioactivity, and good bio-adhesive properties. Both in vitro and in vivo reveal that the hydrogel achieves rapid hemostasis. In an ethanol-induced gastric ulcer model in rats, it demonstrates that the hydrogel effectively inhibits gastric ulcer bleeding by 92% within 24-h, exhibiting efficacy that surpasses that of omeprazole medicine, a commonly used clinical treatment. This enhanced performance is attributed to the synergistic effects of the CMCs hydrogel and TCP-25 peptide in effectively achieving hemostasis, inhibiting bacterial growth, and promoting gastric wound healing in acute or chronic bleeding gastric ulcers. Consequently, the present work offers promising clinical applications for rapid hemostasis and wound healing in gastric ulcers.
研究领域:
生物医学工程
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材料科学
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药学
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胃肠病学
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产品关联
DOI
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2024
·
IF 12.2
Falin He,Huijian Shi,Shaoyang Hu,Rutao Liu
Currently, the binding of iron-binding protein transferrin (TF) with NPs and their interaction mechanisms have not been completely elucidated yet. Here, we probed the conformation-dependent release of Fe ions from TF induced by nano-sized polystyrene plastics (PS-NPs) using dialysis, ICP-MS, multi-spectroscopic techniques, and computational simulation. The results showed that the release of free Fe ions from TF was activated after PS-NPs binding, which displayed a clear dose-effect correlation. PS-NPs binding can induce the unfolding and loosening of polypeptide chain and backbone of TF. Alongside this we found that the TF secondary structure was destroyed, thereby causing TF protein misfolding and denaturation. In parallel, PS-NPs interacted with the chromophores , resulting in the occurrence of fluorescence sensitization effects and the disruption of the surrounding micro-environment of aromatic amino acids . Also, the binding of PS-NPs induced the formation of new aggregates in the PS-NPs-TF system. Further simulations indicated that PS-NPs exhibited a preference for binding to the hinge region that connects the C-lobe and N-lobe, which is responsible for the Fe ions release and structural alterations of TF. This finding provides a new understanding about the regulation of the release of Fe ions of iron-loaded TF through NPs-induced conformational and structural changes.
研究领域:
生物化学
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分子生物学
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纳米技术
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蛋白质化学
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DOI
PubMed
高影响因子
Analytical Methods
·
2019
·Vol. 11
·期 46
·5919-5928
·
IF 2.378
Nasibeh Saeedzadeh Amiri,Mohammad-Reza Milani-Hosseini
A facile and environmental-friendly strategy was used to prepare ratiometric fluorescence sensor-modified mesoporous-structured epitope-imprinted polymer (QDs@SiO2@EMSiO2) for highly sensitive and selective determination of cytochrome c (Cyt c), using Cu-doped ZnS QDs and Mn-doped ZnS QDs as fluorescent dyes. In this sensor, C-terminal and N-terminal nonapeptides were employed as the template molecules, and C18MIMCl was utilized as a template for mesoporous silica. APTES and PTESMIC were utilized as functional monomers and TEOS was applied as the cross-linker. The as-prepared fluorescence sensor displayed great selectivity and sensitivity by merging ratiometric fluorescence methodology with mesoporous silica materials to create one system. The composite was employed for the recognition of Cyt c, which displayed good linearity in the range from 0.4 nM to 200.0 nM with a detection limit as low as 0.15 nM, which was much lower than those of non-mesoporous and single emission composites. The sensor also exhibited outstanding applicability in complex matrices, which enabled its employment for Cyt c tracing in human serum samples without any pretreatment.
研究领域:
分析化学
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材料科学
·
生物传感器
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生物技术
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DOI
高影响因子
IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL
·
2024
·
IF 1.5
Zheng Zhen,Fan Ying,Zhang Jingyun,Wang Jian,Li Zhenyu
Pharmacological studies have shown that Cedrol (CE) exhibits extensive biological activities, including anti-inflammatory and analgesic. Moreover, it can inhibit the NF-κB pathway and the expression of various associated proteins. This study aimed to investigate the role of CE in postmenopausal osteoporosis. The results showed that intragastric administration of CE (10 and 20 mg/kg) significantly improved the bone microstructure damage and increased bone mineral density, trabecular bone volume, and bone trabecular thickness in ovariectomized (OVX) rats ( p < 0.05). CE treatment additionally made a well-organized arrangement of bone trabeculae and improved its thickness and density. Compared with the OVX group, the levels of tartrate-resistant acid phosphatase from 5b and C-terminal telopeptide of type I collagen were significantly reduced by 42.75% and 49.27% in the OVX + CE rats ( p < 0.05). TRAP staining visually showed that the number of osteoclasts in the femur tissue of CE-treated rats was less than that of the OVX group. The expressions of nuclear factor of activated T-cells, cytoplasmic 1, acid phosphatase 5, and cathepsin K in OVX + CE rats were significantly decreased by 51.61%, 46.07%, and 50.34% compared to the OVX group ( p < 0.01). In addition, CE intervention effectively reduced the phosphorylation levels of P65 and IκBα and inhibited the NF-κB signaling pathway. Meanwhile, CE diminished the number of multinucleated osteoclasts induced by receptor activator for nuclear factor-κB ligand and hindered cell fusion as well as nuclear translocation of osteoclast precursor cells P65. In conclusion, CE inhibits osteoclastogenesis by suppressing the activation of the NF-κB signaling pathway, thereby alleviating postmenopausal osteoporosis.
研究领域:
药理学
·
生物学
·
医学
·
内分泌学
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产品关联
DOI
PubMed
高影响因子
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