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Péter B, Szekacs I, Horvath R. Label-free biomolecular and cellular methods in small molecule epigallocatechin-gallate research. Heliyon 2024; 10:e25603. [PMID: 38371993 PMCID: PMC10873674 DOI: 10.1016/j.heliyon.2024.e25603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Small molecule natural compounds are gaining popularity in biomedicine due to their easy access to wide structural diversity and their proven health benefits in several case studies. Affinity measurements of small molecules below 100 Da molecular weight in a label-free and automatized manner using small amounts of samples have now become a possibility and reviewed in the present work. We also highlight novel label-free setups with excellent time resolution, which is important for kinetic measurements of biomolecules and living cells. We summarize how molecular-scale affinity data can be obtained from the in-depth analysis of cellular kinetic signals. Unlike traditional measurements, label-free biosensors have made such measurements possible, even without the isolation of specific cellular receptors of interest. Throughout this review, we consider epigallocatechin gallate (EGCG) as an exemplary compound. EGCG, a catechin found in green tea, is a well-established anti-inflammatory and anti-cancer agent. It has undergone extensive examination in numerous studies, which typically rely on fluorescent-based methods to explore its effects on both healthy and tumor cells. The summarized research topics range from molecular interactions with proteins and biological films to the kinetics of cellular adhesion and movement on novel biomimetic interfaces in the presence of EGCG. While the direct impact of small molecules on living cells and biomolecules is relatively well investigated in the literature using traditional biological measurements, this review also highlights the indirect influence of these molecules on the cells by modifying their nano-environment. Moreover, we underscore the significance of novel high-throughput label-free techniques in small molecular measurements, facilitating the investigation of both molecular-scale interactions and cellular processes in one single experiment. This advancement opens the door to exploring more complex multicomponent models that were previously beyond the reach of traditional assays.
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Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
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Dutta D, Rahman S, Bhattacharje G, Bag S, Sing BC, Chatterjee J, Basak A, Das AK. Label-Free Method Development for Hydroxyproline PTM Mapping in Human Plasma Proteome. Protein J 2021; 40:741-755. [PMID: 33840009 DOI: 10.1007/s10930-021-09984-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) impart structural heterogeneities that can alter plasma proteins' functions in various pathophysiological processes. However, the identification and mapping of PTMs in untargeted plasma proteomics is still a challenge due to the presence of diverse components in blood. Here, we report a label-free method for identifying and mapping hydroxylated proteins using tandem mass spectrometry (MS/MS) in the human plasma sample. Our untargeted proteomics approach led us to identify 676 de novo sequenced peptides in human plasma that correspond to 201 proteins, out of which 11 plasma proteins were found to be hydroxylated. Among these hydroxylated proteins, Immunoglobulin A1 (IgA1) heavy chain was found to be modified at residue 285 (Pro285 to Hyp285), which was further validated by MS/MS study. Molecular dynamics (MD) simulation analysis demonstrated that this proline hydroxylation in IgA1 caused both local and global structural changes. Overall, this study provides a comprehensive understanding of the protein profile containing Hyp PTMs in human plasma and shows the future perspective of identifying and discriminating Hyp PTM in the normal and the diseased proteomes.
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Affiliation(s)
- Debabrata Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Swarnendu Bag
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Bidhan Chandra Sing
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Amit Basak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India. .,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Wang S, Khan A, Huang R, Ye S, Di K, Xiong T, Li Z. Recent advances in single extracellular vesicle detection methods. Biosens Bioelectron 2020; 154:112056. [PMID: 32093894 DOI: 10.1016/j.bios.2020.112056] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 01/03/2023]
Abstract
Extracellular vesicles (EVs) are secreted by a variety of cells. They are known for their pertinent role in intercellular communication, and participation in different pathological processes, making them ideal candidate for utilization as a biomarker for diagnosis and treatment of diseases. In contemporary years, the concept of a well-established liquid biopsy technology, and detection and utilization of EVs as a biomarkers have received unprecedented attention. Many rapid and precise EVs detection methods have been proposed, however, majority of them detect EVs in a bulk. As the prevalent heterogeneity of single extracellular vesicle (SEV) plays an important role in the analysis of disease progression, therefore, to prevent information loss, increased attention has been paid to SEV detection with remarkable successes. Technologies like fluorescence labeling, micro imaging and microfluidic chip were successfully employed for EVs detection at SEV level. This review summarizes the recent advances in SEV detection methods, their potential targets, applications as well as concludes future prospects for developing new SEV detection strategies.
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Affiliation(s)
- Su Wang
- College of Life Science, Yangtze University, Jingzhou, 434025, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), Southeast University, Nanjing 210096, PR China
| | - Rongrong Huang
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, PR China
| | - Shiyi Ye
- College of Life Science, Yangtze University, Jingzhou, 434025, China
| | - Kaili Di
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, PR China
| | - Tao Xiong
- College of Life Science, Yangtze University, Jingzhou, 434025, China.
| | - Zhiyang Li
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, 210008, China; Department of Clinical Laboratory, Yizheng Hospital of Nanjing Drum Tower Hospital Group, Yizheng 211900, PR China.
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