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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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Peng S, Fu Y. FYN: emerging biological roles and potential therapeutic targets in cancer. J Transl Med 2023; 21:84. [PMID: 36740671 PMCID: PMC9901160 DOI: 10.1186/s12967-023-03930-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/25/2023] [Indexed: 02/07/2023] Open
Abstract
Src family protein kinases (SFKs) play a key role in cell adhesion, invasion, proliferation, survival, apoptosis, and angiogenesis during tumor development. In humans, SFKs consists of eight family members with similar structure and function. There is a high level of overexpression or hyperactivity of SFKs in tumor, and they play an important role in multiple signaling pathways involved in tumorigenesis. FYN is a member of the SFKs that regulate normal cellular processes. Additionally, FYN is highly expressed in many cancers and promotes cancer growth and metastasis through diverse biological functions such as cell growth, apoptosis, and motility migration, as well as the development of drug resistance in many tumors. Moreover, FYN is involved in the regulation of multiple cancer-related signaling pathways, including interactions with ERK, COX-2, STAT5, MET and AKT. FYN is therefore an attractive therapeutic target for various tumor types, and suppressing FYN can improve the prognosis and prolong the life of patients. The purpose of this review is to provide an overview of FYN's structure, expression, upstream regulators, downstream substrate molecules, and biological functions in tumors.
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Affiliation(s)
- SanFei Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yang Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
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Chen T, Fu X, Zhang Q, Mao D, Song Y, Feng C, Zhu X. A DNA logic gate with dual-anchored proximity aptamers for the accurate identification of circulating tumor cells. Chem Commun (Camb) 2021; 56:6961-6964. [PMID: 32436536 DOI: 10.1039/d0cc00564a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have designed a DNA logic gate that can integrate the recognition of multiple biomarkers with signal amplification to perform the accurate and sensitive analysis of circulating tumor cells (CTCs). It also has the potential to analyze rare cells that exist in small amounts but are of great significance (such as stem cells) in the fields of clinical diagnosis and biomedicine.
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Affiliation(s)
- Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
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Su L, Chen T, Xue T, Sheng A, Cheng L, Zhang J. Fabrication of pH-Adjusted Boronic Acid-Aptamer Conjugate for Electrochemical Analysis of Conjugated N-Glycolylneuraminic Acid. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7650-7657. [PMID: 31951374 DOI: 10.1021/acsami.9b23029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, the boronic acid-aptamer conjugate (BAAC) is elaborately designed and explored as a recognition unit. The admirable properties of the pH-dependent boronic acid ester are integrated with the specific capturing capability of the modified aptamer; thus, BAAC can efficiently and selectively bind with the target by adjusting the pH values. An electrochemical biosensor based on pH-adjusted BAAC has been further developed for the analysis of CNeu5Gc, an important biomarker of different kinds of cancer. The boronic acid moiety in BAAC can react with CNeu5Gc to form a BAAC-CNeu5Gc complex under acidic conditions, followed by the release of CNeu5Gc from the complex and subsequent capture by the aptamer moiety with the adjustment of the pH value to alkalinity. With simplicity, high specificity, and efficiency, the biosensor exhibits a wide linear range from 2.816 to 3603.960 ng/mL with a low detection limit of 1.224 ng/mL and can be applied to analyze CNeu5Gc in animal food samples. Besides, this work can also provide a kind of modified aptamer, i.e., the chemical capturing group-modified aptamer, to give a new viewpoint for the exploration of other functionalized aptamers.
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Affiliation(s)
- Lihong Su
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Tingjun Chen
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Tianxiang Xue
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Anzhi Sheng
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
- Shanghai Key Laboratory of Bio-Energy Crops , Shanghai University , Shanghai 200444 , P. R. China
| | - Liangfen Cheng
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Juan Zhang
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
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Zhang M, Zhou D, Ouyang Z, Yu M, Jiang Y. Sphingosine kinase 1 promotes cerebral ischemia-reperfusion injury through inducing ER stress and activating the NF-κB signaling pathway. J Cell Physiol 2020; 235:6605-6614. [PMID: 31985036 DOI: 10.1002/jcp.29546] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/15/2020] [Indexed: 01/02/2023]
Abstract
Endoplasm reticulum stress and inflammation response have been found to be linked to cerebral ischemia-reperfusion (IR) injury. Sphingosine kinase 1 (SPHK1) has been reported to be a novel endoplasm reticulum regulator. The aim of our study is to figure out the role of SPHK1 in cerebral IR injury and verify whether it has an ability to regulate inflammation and endoplasm reticulum stress. Hydrogen peroxide was used to induce cerebral IR injury. Enzyme-linked immunosorbent assay, quantitative polymerase chain reaction, western blots, and immunofluorescence were used to measure the alterations of cell viability, inflammation response, and endoplasm reticulum stress. The results demonstrated that after exposure to hydrogen peroxide, cell viability was reduced whereas SPHK1 expression was significantly elevated. Knockdown of SPHK1 attenuated hydrogen peroxide-mediated cell death and reversed cell viability. Our data also demonstrated that SPHK1 deletion reduced endoplasm reticulum stress and alleviated inflammation response in hydrogen peroxide-treated cells. In addition, we also found that SHPK1 modulated endoplasm reticulum stress and inflammation response to through the NF-κB signaling pathway. Inhibition of NF-κB signaling pathway has similar results when compared with the cells with SPHK1 deletion. Altogether, our results demonstrated that SPHK1 upregulation, induced by hydrogen peroxide, is responsible for cerebral IR injury through inducing endoplasm reticulum stress and inflammation response in a manner working through the NF-κB signaling pathway. This finding provides new insight into the molecular mechanism to explain the neuron death induced by cerebral IR injury.
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Affiliation(s)
- Mingming Zhang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dingzhou Zhou
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhu Ouyang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mengqiang Yu
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Zhang Y, Zhang H, Shi W, Wang W. Mief1 augments thyroid cell dysfunction and apoptosis through inhibiting AMPK-PTEN signaling pathway. J Recept Signal Transduct Res 2020; 40:15-23. [PMID: 31960779 DOI: 10.1080/10799893.2020.1716799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Objective: Inflammation-mediated thyroid cell dysfunction and apoptosis increases the like-hood of hypothyroidism.Aim: Our aim in the present study is to explore the role of mitochondrial elongation factor 1 (Mief1) in thyroid cell dysfunction induced by TNFα.Materials and methods: Different doses of TNFα were used to incubate with thyroid cells in vitro. The survival rate, apoptotic index and proliferation capacity of thyroid cells were measured. Cellular energy metabolism and endoplasmic reticulum function related to protein synthesis were detected.Results: In response to TNFα treatment, the levels of Mief1 were increased, coinciding with a drop in the viability of thyroid cells in vitro. Loss of Mief1 attenuates TNFα-induced cell death through reducing the ratio of cell apoptosis. Further, we found that Mief1 deletion reversed cell energy metabolism and this effect was attributable to mitochondrial protection. Mief1 knockdown sustained mitochondrial membrane potential and reduced mitochondrial ROS overproduction. In addition, Mief1 knockdown also reduced endoplasmic reticulum stress, as evidenced by decreased levels of Chop and Caspase-12. Finally, our data verified that TNFα treatment inhibited the activity of AMPK-PTEN pathway whereas Mief1 deletion reversed the activity of AMPK and thus promoted the upregulation of PTEN. However, inhibition of AMPK-PTEN pathways could abolish the beneficial effects exerted by Mief1 deletion on thyroid cells damage and dysfunction.Conclusions: Altogether, our data indicate that immune abnormality-mediated thyroid cell dysfunction and death are alleviated by Mief1 deletion possible driven through reversing the activity of AMPK-PTEN pathways.
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Affiliation(s)
- Yonglan Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Otorhinolaryngology Research Institute of Tianjin, Tianjin Key Laboratory of Auditory Speech Balance Medicine, Tianjin, People's Republic of China
| | - Haichao Zhang
- Department of Thyroid and Breast Surgery, Tianjin Fourth Central Hospital, Tianjin, People's Republic of China
| | - Wenjie Shi
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Otorhinolaryngology Research Institute of Tianjin, Tianjin Key Laboratory of Auditory Speech Balance Medicine, Tianjin, People's Republic of China
| | - Wei Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Otorhinolaryngology Research Institute of Tianjin, Tianjin Key Laboratory of Auditory Speech Balance Medicine, Tianjin, People's Republic of China
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Dong Q, Jie Y, Ma J, Li C, Xin T, Yang D. Renal tubular cell death and inflammation response are regulated by the MAPK-ERK-CREB signaling pathway under hypoxia-reoxygenation injury. J Recept Signal Transduct Res 2019; 39:383-391. [PMID: 31782334 DOI: 10.1080/10799893.2019.1698050] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Context: Cell death and inflammation response have been found to the primary features of acute kidney injury.Objective: The aim of our study is to figure out the molecular mechanism by which hypoxia-reoxygenation injury affects the viability of tubular cell death.Materials and methods: HK2 cells were treated with hypoxia-reoxygenation injury in vitro. Pathway agonist was added into the medium of HK2 cell to activate MAPK-EEK-CREB axis.Results: Hypoxia-reoxygenation injury reduced HK2 cell viability and increased cell apoptosis rate in vitro. Besides, inflammation response has been found to be induced by hypoxia-reoxygenation injury in HK2 cells in vitro. In addition, MAPK-ERK-CREB pathway was deactivated during hypoxia-reoxygenation injury. Interestingly, activation of MAPK-ERK-CREB pathway could attenuate hypoxia-reoxygenation injury-mediated HK2 cell apoptosis and inflammation. Mechanistically, MAPK-ERK-CREB pathway activation upregulated the transcription of anti-apoptotic genes and reduced the levels of pro-apoptotic factors under hypoxia-reoxygenation injury.Conclusions: Our results report a novel signaling pathway responsible for acute kidney injury-related tubular cell death. Activation of MAPK-ERK-CREB signaling could protect tubular cell against hypoxia-reoxygenation-related cell apoptosis and inflammation response.
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Affiliation(s)
- Qi Dong
- Department of Nephrology, Tianjin Hospital, Tianjin, P.R. China
| | - Yingxin Jie
- Department of Emergency, Tianjin Hospital, Tianjin, P.R. China
| | - Jian Ma
- Tianjin Women's and Children's Health Center, Tianjin Hospital, Tianjin, P.R. China
| | - Chen Li
- Department of Orthopaedics, Tianjin Hospital, Tianjin, P.R. China
| | - Ting Xin
- Department of Cardiology, Tianjin First Central Hospital, Tianjin, P.R. China
| | - Dingwei Yang
- Department of Nephrology, Tianjin Hospital, Tianjin, P.R.China
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Chai H, Cheng W, Xu L, Gui H, He J, Miao P. Fabrication of Polymeric Ferrocene Nanoparticles for Electrochemical Aptasensing of Protein with Target-Catalyzed Hairpin Assembly. Anal Chem 2019; 91:9940-9945. [DOI: 10.1021/acs.analchem.9b01673] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Jihua Laboratory, Foshan 528200, People’s Republic of China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Tianjin Guokeyigong Science and Technology Development Co., Ltd., Tianjin 300399, People’s Republic of China
| | - Lei Xu
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Huiqiang Gui
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jinlin He
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Jihua Laboratory, Foshan 528200, People’s Republic of China
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Yue X, Su L, Chen X, Liu J, Zheng L, Zhang J. A new method for the in situ assay of α-glucosidase activity and inhibitor screening through an enzyme substrate-mediated DNA hybridization chain reaction. NEW J CHEM 2019. [DOI: 10.1039/c9nj01868a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strategy is based on small molecule-mediated hybridization chain reaction.
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Affiliation(s)
- Xiquan Yue
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Lihong Su
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Xu Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Junfeng Liu
- Department of Orthopedics
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
- P. R. China
| | - Longpo Zheng
- Department of Orthopedics
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
- P. R. China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
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