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Upadhyay V, Lucas A, Patrick C, Mallela KMG. Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions. Methods 2024; 225:52-61. [PMID: 38492901 DOI: 10.1016/j.ymeth.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024] Open
Abstract
Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Casey Patrick
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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2
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Zhang H, Liu L, Li M. Mini-review of DNA Methylation Detection Techniques and Their Potential Applications in Disease Diagnosis, Prognosis, and Treatment. ACS Sens 2024; 9:1089-1103. [PMID: 38365574 DOI: 10.1021/acssensors.3c02328] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
DNA methylation is the dominant epigenetic mechanism for regulating gene expression in mammals, playing crucial roles in development, differentiation, and tissue homeostasis. Aberrations in DNA methylation are closely associated with the potential onset of various diseases. Consequently, numerous DNA methylation detection techniques have been successively developed. These methods not only facilitate the exploration of disease mechanisms but also hold significant promise for the development of diagnostic and prognostic strategies. In this Perspective, we present a comprehensive overview of commonly employed DNA methylation detection techniques as well as biosensing based on their underlying analytical techniques. For its medical applications, we begin by examining the pathogenesis of different diseases and then proceed to discuss how relevant technologies are applied in the context of these specific medical conditions. Additionally, we briefly discuss the current limitations of these techniques and highlight future challenges in advancing methylation detection and analysis methodologies.
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Affiliation(s)
- Huaming Zhang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Liu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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3
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Baardsnes J, Paul-Roc B. SARS-CoV-2S-Protein-Ace2 Binding Analysis Using Surface Plasmon Resonance. Methods Mol Biol 2024; 2762:71-87. [PMID: 38315360 DOI: 10.1007/978-1-0716-3666-4_5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Surface plasmon resonance (SPR) allows for the label-free determination of the binding affinity and rate constants of bimolecular interactions. Here, we describe the method used for the analysis of the Ace2-SARS-CoV2 S-protein interaction using indirect capture of the S-protein onto the SPR surface, and flowing monomeric Ace2. This method will allow for the determination of the rate constants for affinity, with additional analysis that is achievable using S-protein capture levels in conjunction with the sensorgram response for relative activity benchmarking.
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Affiliation(s)
- Jason Baardsnes
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada.
| | - Béatrice Paul-Roc
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada
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Wang Z, Wang X, Xu W, Li Y, Lai R, Qiu X, Chen X, Chen Z, Mi B, Wu M, Wang J. Translational Challenges and Prospective Solutions in the Implementation of Biomimetic Delivery Systems. Pharmaceutics 2023; 15:2623. [PMID: 38004601 PMCID: PMC10674763 DOI: 10.3390/pharmaceutics15112623] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Biomimetic delivery systems (BDSs), inspired by the intricate designs of biological systems, have emerged as a groundbreaking paradigm in nanomedicine, offering unparalleled advantages in therapeutic delivery. These systems, encompassing platforms such as liposomes, protein-based nanoparticles, extracellular vesicles, and polysaccharides, are lauded for their targeted delivery, minimized side effects, and enhanced therapeutic outcomes. However, the translation of BDSs from research settings to clinical applications is fraught with challenges, including reproducibility concerns, physiological stability, and rigorous efficacy and safety evaluations. Furthermore, the innovative nature of BDSs demands the reevaluation and evolution of existing regulatory and ethical frameworks. This review provides an overview of BDSs and delves into the multifaceted translational challenges and present emerging solutions, underscored by real-world case studies. Emphasizing the potential of BDSs to redefine healthcare, we advocate for sustained interdisciplinary collaboration and research. As our understanding of biological systems deepens, the future of BDSs in clinical translation appears promising, with a focus on personalized medicine and refined patient-specific delivery systems.
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Affiliation(s)
- Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; (Z.W.); (R.L.)
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Wanting Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Ruizhi Lai
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; (Z.W.); (R.L.)
| | - Xiaohui Qiu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Bobin Mi
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Meiying Wu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
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Nakagawa F, Kikkawa M, Chen S, Miyashita Y, Hamaguchi-Suzuki N, Shibuya M, Yamashita S, Nagase L, Yasuda S, Shiroishi M, Senda T, Ito K, Murata T, Ogasawara S. Anti-nanodisc antibodies specifically capture nanodiscs and facilitate molecular interaction kinetics studies for membrane protein. Sci Rep 2023; 13:11627. [PMID: 37468499 DOI: 10.1038/s41598-023-38547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Nanodisc technology has dramatically advanced the analysis of molecular interactions for membrane proteins. A nanodisc is designed as a vehicle for membrane proteins that provide a native-like phospholipid environment and better thermostability in a detergent-free buffer. This enables the determination of the thermodynamic and kinetic parameters of small molecule binding by surface plasmon resonance. In this study, we generated a nanodisc specific anti-MSP (membrane scaffold protein) monoclonal antibody biND5 for molecular interaction analysis of nanodiscs. The antibody, biND5 bound to various types of nanodiscs with sub-nanomolar to nanomolar affinity. Epitope mapping analysis revealed specific recognition of 8 amino acid residues in the exposed helix-4 structure of MSP. Further, we performed kinetics binding analysis between adenosine A2a receptor reconstituted nanodiscs and small molecule antagonist ZM241385 using biND5 immobilized sensor chips. These results show that biND5 facilitates the molecular interaction kinetics analysis of membrane proteins substituted in nanodiscs.
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Affiliation(s)
- Fuhito Nakagawa
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Marin Kikkawa
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Sisi Chen
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Yasuomi Miyashita
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Norie Hamaguchi-Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Minami Shibuya
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Soichi Yamashita
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Lisa Nagase
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-Ku, Tokyo, 125-8585, Japan
| | - Toshiya Senda
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-Dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Keisuke Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Institute for Advanced Academic Research, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
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Zheng S, Zou M, Shao Y, Wu H, Wu H, Wang X. Two-dimensional measurements of receptor-ligand interactions. Front Mol Biosci 2023; 10:1154074. [PMID: 36876050 PMCID: PMC9981951 DOI: 10.3389/fmolb.2023.1154074] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Gaining insight into the two-dimensional receptor-ligand interactions, which play a significant role in various pivotal biological processes such as immune response and cancer metastasis, will deepen our understanding of numerous physiological and pathological mechanisms and contribute to biomedical applications and drug design. A central issue involved is how to measure the in situ receptor-ligand binding kinetics. Here, we review several representative mechanical-based and fluorescence-based methods, and briefly discuss the strengths and weaknesses for each method. In addition, we emphasize the great importance of the combination of experimental and computational methods in studying the receptor-ligand interactions, and further studies should focus on the synergistic development of experimental and computational methods.
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Affiliation(s)
- Songjie Zheng
- Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Min Zou
- Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Shao
- Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Huaping Wu
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Helong Wu
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaohuan Wang
- Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing, China
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7
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Qiao X, He J, Yang R, Li Y, Chen G, Xiao S, Huang B, Yuan Y, Sheng Q, Yue T. Recent Advances in Nanomaterial-Based Sensing for Food Safety Analysis. Processes (Basel) 2022; 10:2576. [DOI: 10.3390/pr10122576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
The increasing public attention on unceasing food safety incidents prompts the requirements of analytical techniques with high sensitivity, reliability, and reproducibility to timely prevent food safety incidents occurring. Food analysis is critically important for the health of both animals and human beings. Due to their unique physical and chemical properties, nanomaterials provide more opportunities for food quality and safety control. To date, nanomaterials have been widely used in the construction of sensors and biosensors to achieve more accurate, fast, and selective food safety detection. Here, various nanomaterial-based sensors for food analysis are outlined, including optical and electrochemical sensors. The discussion mainly involves the basic sensing principles, current strategies, and novel designs. Additionally, given the trend towards portable devices, various smartphone sensor-based point-of-care (POC) devices for home care testing are discussed.
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Teixeira Rodrigues do Vale R, Maximiler Campos de Paula H, Luiza Coelho Y, De Paula Rezende J, Cristina Teixeira Ribeiro Vidigal M, Henrique Mendes Da Silva L, Clarissa Dos Santos Pires A. β-lactoglobulin and resveratrol nanocomplex formation is driven by solvation water release. Food Res Int 2022. [DOI: 10.1016/j.foodres.2022.111567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/14/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022]
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Ahmad Khushaini MA, Azeman NH, Mat Salleh M, Tg Abdul Aziz TH, A Bakar AA, De La Rue RM, Md Zain AR. Exploiting a strong coupling regime of organic pentamer surface plasmon resonance based on the Otto configuration for creatinine detection. Opt Express 2022; 30:14478-14491. [PMID: 35473189 DOI: 10.1364/oe.448947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The sandwiched material-analyte layer in the surface plasmon resonance (SPR)-Otto configuration emulates an optical cavity and, coupled with large optical nonlinearity material, the rate of light escaping from the system is reduced, allowing the formation of a strong coupling regime. Here, we report an organic pentamer SPR sensor using the Otto configuration to induce a strong coupling regime for creatinine detection. Prior to that, the SPR sensor chip was modified with an organic pentamer, 1,4-bis[2-(5-thiophene-2-yl)-1-benzothiopene]-2,5-dioctyloxybenzene (BOBzBT2). To improve the experimental calibration curve, a normalisation approach based on the strong coupling-induced second dip was also developed. By using this procedure, the performance of the sensor improved to 0.11 mg/dL and 0.36 mg/dL for the detection and quantification limits, respectively.
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Wu X, Zhang Q, Guo Y, Zhang H, Guo X, You Q, Wang L. Methods for the Discovery and Identification of Small Molecules Targeting Oxidative Stress-Related Protein–Protein Interactions: An Update. Antioxidants (Basel) 2022; 11:antiox11040619. [PMID: 35453304 PMCID: PMC9025695 DOI: 10.3390/antiox11040619] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
The oxidative stress response pathway is one of the hotspots of current pharmaceutical research. Many proteins involved in these pathways work through protein–protein interactions (PPIs). Hence, targeting PPI to develop drugs for an oxidative stress response is a promising strategy. In recent years, small molecules targeting protein–protein interactions (PPIs), which provide efficient methods for drug discovery, are being investigated by an increasing number of studies. However, unlike the enzyme–ligand binding mode, PPIs usually exhibit large and dynamic binding interfaces, which raise additional challenges for the discovery and optimization of small molecules and for the biochemical techniques used to screen compounds and study structure–activity relationships (SARs). Currently, multiple types of PPIs have been clustered into different classes, which make it difficult to design stationary methods for small molecules. Deficient experimental methods are plaguing medicinal chemists and are becoming a major challenge in the discovery of PPI inhibitors. In this review, we present current methods that are specifically used in the discovery and identification of small molecules that target oxidative stress-related PPIs, including proximity-based, affinity-based, competition-based, structure-guided, and function-based methods. Our aim is to introduce feasible methods and their characteristics that are implemented in the discovery of small molecules for different types of PPIs. For each of these methods, we highlight successful examples of PPI inhibitors associated with oxidative stress to illustrate the strategies and provide insights for further design.
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Affiliation(s)
- Xuexuan Wu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuqi Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hengheng Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaoke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Correspondence: (X.G.); (Q.Y.); (L.W.); Tel.: +86-025-83271351 (Q.Y.); +86-15261483858 (L.W.)
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Correspondence: (X.G.); (Q.Y.); (L.W.); Tel.: +86-025-83271351 (Q.Y.); +86-15261483858 (L.W.)
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (X.W.); (Q.Z.); (Y.G.); (H.Z.)
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Correspondence: (X.G.); (Q.Y.); (L.W.); Tel.: +86-025-83271351 (Q.Y.); +86-15261483858 (L.W.)
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11
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Erbaş A, Inci F. The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation Rates by Surface Plasmon Resonance (SPR) and Benchmarking Performance Metrics. Methods Mol Biol 2022; 2385:237-253. [PMID: 34888723 DOI: 10.1007/978-1-0716-1767-0_11] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Surface plasmon resonance (SPR) is a real-time kinetic measurement principle that can probe the kinetic interactions between ligands and their binding sites, and lies at the backbone of pharmaceutical, biosensing, and biomolecular research. The extraction of dissociation rates from SPR-response signals often relies on several commonly adopted assumptions, one of which is the exponential decay of the dissociation part of the response signal. However, certain conditions, such as high density of binding sites or high concentration fluctuations near the surface as compared to the bulk, can lead to non-exponential decays via ligand rebinding or facilitated dissociation. Consequently, fitting the data with an exponential function can underestimate or overestimate the measured dissociation rates. Here, we describe a set of alternative fit functions that can take such effects into consideration along with plasmonic sensor design principles with key performance metrics, thereby suggesting methods for error-free high-precision extraction of the dissociation rates.
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Affiliation(s)
- Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science Nanotechnology, Bilkent University, Ankara, Turkey.
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center and Institute of Materials Science Nanotechnology, Bilkent University, Ankara, Turkey.
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12
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de Castro ASB, de Paula HMC, Coelho YL, Hudson EA, Pires ACS, da Silva LHM. Kinetic and thermodynamic of lactoferrin - Ethoxylated-nonionic surfactants supramolecular complex formation. Int J Biol Macromol 2021; 187:325-331. [PMID: 34280448 DOI: 10.1016/j.ijbiomac.2021.07.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 11/19/2022]
Abstract
Understanding nonionic surfactant-protein interactions is fundamental from both technological and scientific points of view. However, there is a complete absence of kinetic data for such interactions. We employed surface plasmon resonance (SPR) to determine the kinetic and thermodynamic parameters of bovine lactoferrin-Brij58 interactions at various temperatures under physiological conditions (pH 7.4). The adsorption process was accelerated with increasing temperature, while the desorption rate decreased, resulting in a more thermodynamically stable complex. The kinetic energetic parameters obtained for the formation of the activated complex, [bLF-Brij58]‡, indicated that the potential energy barrier for [bLF-Brij58]‡ formation arises primarily from the reduction in system entropy. [bLF-Brij58]○ formation was entropically driven, indicating that hydrophobic interactions play a fundamental role in bLF interactions with Brij58.
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Affiliation(s)
- Alan Stampini Benhame de Castro
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Hauster Maximiler Campos de Paula
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Yara Luiza Coelho
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil; Colloid Chemistry Group, Chemistry Institute, Federal University of Alfenas (UNIFAL-MG), Rua Gabriel Monteiro da Silva, 700, 37130-000 Alfenas, MG, Brazil
| | - Eliara Acipreste Hudson
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Ana Clarissa S Pires
- Applied Molecular Thermodynamic (THERMA), Food Technology Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Luis Henrique M da Silva
- Colloidal, macromolecular and Green Chemistry (QUIVECOM), Chemistry Department, Federal University of Viçosa, Av. PH Rolfs, s/n, Viçosa, MG 36570-900, Brazil.
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13
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Chen H, Simoska O, Lim K, Grattieri M, Yuan M, Dong F, Lee YS, Beaver K, Weliwatte S, Gaffney EM, Minteer SD. Fundamentals, Applications, and Future Directions of Bioelectrocatalysis. Chem Rev 2020; 120:12903-12993. [DOI: 10.1021/acs.chemrev.0c00472] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Olja Simoska
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Koun Lim
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Matteo Grattieri
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Mengwei Yuan
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Fangyuan Dong
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Yoo Seok Lee
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Kevin Beaver
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Samali Weliwatte
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Erin M. Gaffney
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, Utah 84112, United States
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14
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Singh S, Singh PK, Umar A, Lohia P, Albargi H, Castañeda L, Dwivedi DK. 2D Nanomaterial-Based Surface Plasmon Resonance Sensors for Biosensing Applications. Micromachines (Basel) 2020; 11:E779. [PMID: 32824184 PMCID: PMC7463818 DOI: 10.3390/mi11080779] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022]
Abstract
The absorption and binding energy of material plays an important role with a large surface area and conductivity for the development of any sensing device. The newly grown 2D nanomaterials like black phosphorus transition metal dichalcogenides (TMDCs) or graphene have excellent properties for sensing devices' fabrication. This paper summarizes the progress in the area of the 2D nanomaterial-based surface plasmon resonance (SPR) sensor during last decade. The paper also focuses on the structure of Kretschmann configuration, the sensing principle of SPR, its characteristic parameters, application in various fields, and some important recent works related to SPR sensors have also been discussed, based on the present and future scope of this field. The present paper provides a platform for researchers to work in the field of 2D nanomaterial-based SPR sensors.
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Affiliation(s)
- Sachin Singh
- Amorphous Semiconductor Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, India; (S.S.); (P.K.S.)
| | - Pravin Kumar Singh
- Amorphous Semiconductor Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, India; (S.S.); (P.K.S.)
| | - Ahmad Umar
- Department of Chemistry, Faculty of Science and Arts, Najran University, Najran 11001, Saudi Arabia
- Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran 11001, Saudi Arabia;
| | - Pooja Lohia
- Department of Electronics and Communication Engineering, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, India;
| | - Hasan Albargi
- Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran 11001, Saudi Arabia;
- Department of Physics, Faculty of Science and Arts, Najran University, Najran 11001, Saudi Arabia
| | - L. Castañeda
- Sección de Estudios de Posgrado e Investigación de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico;
| | - D. K. Dwivedi
- Amorphous Semiconductor Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur 273010, India; (S.S.); (P.K.S.)
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15
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Abstract
Quantitative measurements of biomolecule associations are central to biological understanding and are needed to build and test predictive and mechanistic models. Given the advances in high-throughput technologies and the projected increase in the availability of binding data, we found it especially timely to evaluate the current standards for performing and reporting binding measurements. A review of 100 studies revealed that in most cases essential controls for establishing the appropriate incubation time and concentration regime were not documented, making it impossible to determine measurement reliability. Moreover, several reported affinities could be concluded to be incorrect, thereby impacting biological interpretations. Given these challenges, we provide a framework for a broad range of researchers to evaluate, teach about, perform, and clearly document high-quality equilibrium binding measurements. We apply this framework and explain underlying fundamental concepts through experimental examples with the RNA-binding protein Puf4.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Ishraq AlSadhan
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
- Stanford ChEM-H, Stanford UniversityStanfordUnited States
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16
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Ke H, Du X, Wang L, Wang X, Zhu J, Gao Y, Peng B, Hao H, Cai N. Detection of morphine in urine based on a surface plasmon resonance imaging immunoassay. Anal Methods 2020; 12:3038-3044. [PMID: 32930164 DOI: 10.1039/d0ay00648c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Based on the surface plasmon resonance imaging (SPRi) technique, a new detection method for morphine in urine samples was developed. Sample labelling was not required, and qualitative and quantitative analysis could be completed in 20 minutes. According to an indirect competitive immunoassay, the mixture of morphine at different concentrations and morphine antibody at a certain concentration as the mobile phase was reacted with morphine BSA fixed on a chip surface in a competitive way. A calibration curve was obtained by correlating the signals generated from SPRi with the concentrations of morphine. By the addition of morphine to a blank urine sample, this method was confirmed to be feasible for the detection of morphine in actual urine. The limit of detection was as low as 9.59 ng mL-1. This method is fast and sensitive and can be applied in many fields.
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Affiliation(s)
- Haokun Ke
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, China.
| | - Xianchao Du
- State Key Laboratory of Luminescent Materials and Device, Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, Center for Aggregation-Induced Emission, South China University of Technology, China
| | - Ling Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, China.
| | - Xiao Wang
- Northwest University of Political Science and Law, China
| | | | - Yuan Gao
- Plexera Biotechnology Co., Ltd., China
| | - Bo Peng
- Plexera Biotechnology Co., Ltd., China
| | - Hongxia Hao
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, China.
- Collaborative Innovation Center of Judicial Civilization, China
| | - Nengbin Cai
- Shanghai Key Laboratory of Criminal Scene Evidence, China
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17
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Affiliation(s)
- Qiuquan Cai
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Xiaodong Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Weipu Zhu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
- Key Laboratory of Adsorption and Separation Materials & Technologies of Zhejiang Province, Hangzhou 310027, China
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18
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Shibata H, Nemoto J, Shiba S, Yamane Y, Kawai G, Hashimoto K. Immobilization of DNA on Quartz Crystal Microbalance Sensor Modified with Self-Assembled Monolayer of Thiol Derivative. J Oleo Sci 2020; 69:271-276. [PMID: 32051359 DOI: 10.5650/jos.ess19317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we investigated the direct detection of DNA, without pretreatment, using a quartz crystal microbalance (QCM) sensor. This sensor is modified by a self-assembled monolayer of a thiol derivative that has an amino group as the terminal functional group. Contact angle values and the attenuated total reflectance Fourier transform infrared (ATR/FT-IR) spectra of the QCM sensors after immersion into an ethanol solution of thiol derivatives clearly showed that self-assembled monolayers of the derivatives were formed on the QCM sensors. Although QCM measurements using unmodified and carboxylic group-modified sensors could not detect DNA-Na salt, the sensor modified with amino groups could detect the DNA. This system can be used for the analysis of the interaction between DNA and DNAbinding proteins.
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Affiliation(s)
- Hirobumi Shibata
- Faculty of Engineering, Chiba Institute of Technology.,Photocatalysis International Research Center, Tokyo University of Science
| | - Junpei Nemoto
- Faculty of Engineering, Chiba Institute of Technology
| | - Shota Shiba
- Faculty of Engineering, Chiba Institute of Technology
| | - Yusuke Yamane
- Faculty of Engineering, Chiba Institute of Technology
| | - Gota Kawai
- Faculty of Advanced Engineering, Chiba Institute of Technology
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19
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Singh V, Singh K, Nand A, Dai H, Wang J, Zhang L, Merino A, Zhu J. Small molecule microarray screening methodology based on surface plasmon resonance imaging. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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20
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Yablokov EO, Sushko TA, Ershov PV, Florinskaya AV, Gnedenko OV, Shkel TV, Grabovec IP, Strushkevich NV, Kaluzhskiy LA, Usanov SA, Gilep AA, Ivanov AS. A large-scale comparative analysis of affinity, thermodynamics and functional characteristics of interactions of twelve cytochrome P450 isoforms and their redox partners. Biochimie 2019; 162:156-66. [DOI: 10.1016/j.biochi.2019.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/24/2019] [Indexed: 12/16/2022]
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21
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Yang M, Moroz P, Jin Z, Budkina DS, Sundrani N, Porotnikov D, Cassidy J, Sugiyama Y, Tarnovsky AN, Mattoussi H, Zamkov M. Delayed Photoluminescence in Metal-Conjugated Fluorophores. J Am Chem Soc 2019; 141:11286-11297. [DOI: 10.1021/jacs.9b04697] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Zhicheng Jin
- Department of Chemistry, Biochemistry, Florida State University, Tallahassee, Florida 32303, United States
| | | | | | | | | | - Yuya Sugiyama
- Asahi-Kasei Corporation, Healthcare R&D Center, 2-1 Samejima, Fuji City, Shizuoka 416-8501 Japan
| | | | - Hedi Mattoussi
- Department of Chemistry, Biochemistry, Florida State University, Tallahassee, Florida 32303, United States
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22
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. Plant Cell Environ 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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23
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Abolhasan R, Mehdizadeh A, Rashidi MR, Aghebati-Maleki L, Yousefi M. Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis. Biosens Bioelectron 2019; 129:164-74. [PMID: 30708263 DOI: 10.1016/j.bios.2019.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/09/2018] [Accepted: 01/03/2019] [Indexed: 01/12/2023]
Abstract
Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.
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24
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Vorauer-Uhl K, Lhota G. Quantification of Recombinant Products in Yeast. Methods Mol Biol 2019; 1923:385-428. [PMID: 30737753 DOI: 10.1007/978-1-4939-9024-5_20] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantification of various proteins expressed in yeast can be performed by different methods. In this respect, classical as well as advanced techniques can be applied, where the analysis of crude supernatants is of special interest in screening but also manufacturing.The following chapter addresses the analytical background of the introduced methods followed by specific recommendations for the quantification of different products of industrial interest. The method portfolio includes electrophoresis, chromatography, and ELISA as classical techniques, but also biosensor-based, microfluidic and automated, miniaturized methods are introduced. Furthermore, individual strengths and perceived limitations are summarized.Although prominent examples are described, it should be noted that individual modifications are required according to host and cultivation mode.
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Affiliation(s)
- Karola Vorauer-Uhl
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.
| | - Gabriele Lhota
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
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25
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Wang K, Wang Z, Cui R, Chu H. Polysaccharopeptide from Trametes versicolor blocks inflammatory osteoarthritis pain-morphine tolerance effects via activating cannabinoid type 2 receptor. Int J Biol Macromol 2019; 126:805-10. [PMID: 30584942 DOI: 10.1016/j.ijbiomac.2018.12.212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022]
Abstract
Analgesia with opioids such as morphine is an effective clinical strategy for the treatment of cancer pain and chronic inflammatory pain. However, long-term use of morphine can cause morphine tolerance (MT), which limits the clinical application of opioids. Polysaccharopeptide from Trametes versicolor (TPSP) is a biologically active macromolecule that exerts anti-tumor, immune-enhancing and pain-relieving effects. In order to address the clinical problem of MT, herein, we investigated the inhibitory effect and mechanism of TPSP in rats with inflammatory pain-morphine tolerance. A chronic inflammatory osteoarthritis pain-morphine tolerance model was simulated by injection of complete Freund's adjuvant (CFA) through the ankle joint cavity and continuous intrathecal administration of morphine. Different doses of TPSP (50 μg/kg, 100 μg/kg and 200 μg/kg) were intrathecally administered for consecutive 3 weeks. Our results indicate that TPSP can significantly inhibit the development of morphine dependence and acute withdrawal in rats, alleviate the decrease of paw withdrawal mechanical threshold and heat stimulation retraction latency. In addition, mechanistically at the molecular level, these effects are elicited via up-regulation of the cannabinoid type 2 receptor, up-regulating the level of β-endorphin, and reducing the levels of IL-1, NO and PGE2. In summary, we report for the first time the application of TPSP as an adjunctive therapy strategy for the relief of MT in clinic.
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26
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Seo M, Lei L, Egli M. Label-Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein-RNA Complexes. ACTA ACUST UNITED AC 2018; 76:e70. [PMID: 30461222 DOI: 10.1002/cpnc.70] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The electrophoretic mobility shift assay (EMSA) is a well-established method to detect formation of complexes between proteins and nucleic acids and to determine, among other parameters, equilibrium constants for the interaction. Mixtures of protein and nucleic acid solutions of various ratios are analyzed via polyacrylamide gel electrophoresis (PAGE) under native conditions. In general, protein-nucleic acid complexes will migrate more slowly than the free nucleic acid. From the distributions of the nucleic acid components in the observed bands in individual gel lanes, quantitative parameters such as the dissociation constant (Kd ) of the interaction can be measured. This article describes a simple and rapid EMSA that relies either on precast commercial or handcast polyacrylamide gels and uses unlabeled protein and nucleic acid. Nucleic acids are instead detected with SYBR Gold stain and band intensities established with a standard gel imaging system. We used this protocol specifically to determine Kd values for complexes between the PAZ domain of Argonaute 2 (Ago2) enzyme and native and chemically modified RNA oligonucleotides. EMSA-based equilibrium constants are compared to those determined with isothermal titration calorimetry (ITC). Advantages and limitations of this simple EMSA are discussed by comparing it to other techniques used for determination of equilibrium constants of protein-RNA interactions, and a troubleshooting guide is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Minguk Seo
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
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27
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Mujahid A, Mustafa G, Dickert FL. Label-Free Bioanalyte Detection from Nanometer to Micrometer Dimensions-Molecular Imprinting and QCMs †. Biosensors 2018; 8:E52. [PMID: 29865200 PMCID: PMC6022876 DOI: 10.3390/bios8020052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 12/13/2022]
Abstract
Modern diagnostic tools and immunoassay protocols urges direct analyte recognition based on its intrinsic behavior without using any labeling indicator. This not only improves the detection reliability, but also reduces sample preparation time and complexity involved during labeling step. Label-free biosensor devices are capable of monitoring analyte physiochemical properties such as binding sensitivity and selectivity, affinity constants and other dynamics of molecular recognition. The interface of a typical biosensor could range from natural antibodies to synthetic receptors for example molecular imprinted polymers (MIPs). The foremost advantages of using MIPs are their high binding selectivity comparable to natural antibodies, straightforward synthesis in short time, high thermal/chemical stability and compatibility with different transducers. Quartz crystal microbalance (QCM) resonators are leading acoustic devices that are extensively used for mass-sensitive measurements. Highlight features of QCM devices include low cost fabrication, room temperature operation, and most importantly ability to monitor extremely low mass shifts, thus potentially a universal transducer. The combination of MIPs with quartz QCM has turned out as a prominent sensing system for label-free recognition of diverse bioanalytes. In this article, we shall encompass the potential applications of MIP-QCM sensors exclusively label-free recognition of bacteria and virus species as representative micro and nanosized bioanalytes.
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Affiliation(s)
- Adnan Mujahid
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria.
- Institute of Chemistry, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan.
| | - Ghulam Mustafa
- Center for Interdisciplinary Research in Basic Sciences, International Islamic University, H-10, Islamabad 44000, Pakistan.
| | - Franz L Dickert
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria.
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28
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Taghipour P, Zakariazadeh M, Sharifi M, Ezzati Nazhad Dolatabadi J, Barzegar A. Bovine serum albumin binding study to erlotinib using surface plasmon resonance and molecular docking methods. J Photochem Photobiol B 2018; 183:11-15. [PMID: 29679689 DOI: 10.1016/j.jphotobiol.2018.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Bovine serum albumin (BSA) is the most abundant protein in the blood circulation and it is commonly used for drug delivery in blood. Therefore, we aim to study BSA interaction with erlotinib as an anticancer drug using surface plasmon resonance (SPR) and molecular modeling methods under physiological conditions (pH = 7.4). BSA immobilized on carboxymethyl dextran hydrogel Au chip (CMD) after activation with N-hydroxysuccinimide and N-ethyl-N-(3-diethylaminopropyl) carbodiimide and then the erlotinib binding to BSA at different concentrations was evaluated. Increasing of erlotinib concentration led to dose-response sensorgrams of BSA. The amount of equilibrium constant (KD) at 25 °C (4.25 × 10-9) showed the high affinity of erlotinib to BSA. Thermodynamic parameters were attained at four different temperatures. The positive value of enthalpy and entropy showed that hydrophobic forces play major role in the interaction of erlotinib with BSA. Besides, the positive value of Gibbs free energy demonstrated that the interaction of erlotinib with BSA was nonspontaneous and enthalpy driven and the complexion of drug were dependent on endothermic process. According to the molecular docking study, the most favorable binding sites of erlotinib on the BSA were subdomain IIIA and IB. Moreover, molecular docking study results showed that hydrogen binding has a role in intermolecular force that stabilize erlotinib-BSA complex.
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Affiliation(s)
- Parvin Taghipour
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mostafa Zakariazadeh
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Maryam Sharifi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Ezzati Nazhad Dolatabadi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.
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29
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Wielgus-Kutrowska B, Grycuk T, Bzowska A. Part-of-the-sites binding and reactivity in the homooligomeric enzymes - facts and artifacts. Arch Biochem Biophys 2018; 642:31-45. [PMID: 29408402 DOI: 10.1016/j.abb.2018.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/13/2018] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
For a number of enzymes composed of several subunits with the same amino acid sequence, it was documented, or suggested, that binding of a ligand, or catalysis, is carried out by a single subunit. This phenomenon may be the result of a pre-existent asymmetry of subunits or a limiting case of the negative cooperativity, and is sometimes called "half-of-the-sites binding (or reactivity)" for dimers and could be called "part-of-the-sites binding (or reactivity)" for higher oligomers. In this article, we discuss molecular mechanisms that may result in "part-of-the-sites binding (and reactivity)", offer possible explanations why it may have a beneficial role in enzyme function, and point to experimental problems in documenting this behaviour. We describe some cases, for which such a mechanism was first reported and later disproved. We also give several examples of enzymes, for which this mechanism seems to be well documented, and profitable. A majority of enzymes identified in this study as half-of-the-sites binding (or reactive) use it in the flip-flop version, in which "half-of-the-sites" refers to a particular moment in time. In general, the various variants of the mechanism seems to be employed often by oligomeric enzymes for allosteric regulation to enhance the efficiency of enzymatic reactions in many key metabolic pathways.
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Affiliation(s)
- Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
| | - Tomasz Grycuk
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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Wang Y, Ali MA, Chow EKC, Dong L, Lu M. An optofluidic metasurface for lateral flow-through detection of breast cancer biomarker. Biosens Bioelectron 2018; 107:224-9. [PMID: 29475186 DOI: 10.1016/j.bios.2018.02.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 11/20/2022]
Abstract
The rapid growth of point-of-care tests demands for biosensors with high sensitivity and small size. This paper demonstrates an optofluidic metasurface that combines silicon-on-insulator (SOI) nanophotonics and nanofluidics to realize a high-performance, lateral flow-through biosensor. The metasurface is made of a periodic array of silicon nanoposts on an SOI substrate, and functionalized with specific receptor molecules. Bonding of a polydimethylsiloxane slab directly onto the surface results in an ultracompact biosensor, where analyte solutions are restricted to flow only in the space between the nanoposts. No flow exists above the nanoposts. This sensor design overcomes the issue with diffusion-limited detection of many other biosensors. The lateral flow-through feature, in conjunction with high-Q resonance modes associated with optical bound states of the metasurface, offers an improved sensitivity to subtle molecule-bonding induced changes in refractive index. The device exhibits a resonance mode around 1550 nm wavelength and provides an index sensitivity of 720 nm/RIU. Biosensing is conducted to detect the epidermal growth factor receptor 2 (ErbB2), a protein biomarker for early-stage breast cancer screening, by monitoring resonance wavelength shifts in response to specific analyte-ligand binding events at the metasurface. The limit of detection of the device is 0.7 ng mL-1 for ErbB2.
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Abstract
The dissociation constant describes the interaction between two partners in the binding equilibrium and is a measure of their affinity. It is a crucial parameter to compare different ligands, e.g., competitive inhibitors, protein isoforms and mutants, for their binding strength to a binding partner. Dissociation constants are determined by plotting concentrations of bound versus free ligand as binding curves. In contrast, titration curves, in which a signal that is proportional to the concentration of bound ligand is plotted against the total concentration of added ligand, are much easier to record. The signal can be detected spectroscopically and by enzyme-linked immunosorbent assay (ELISA). This is exemplified in a protocol for a titration ELISA that measures the binding of the snake venom-derived rhodocetin to its immobilized target domain of α2β1 integrin. Titration ELISAs are versatile and widely used. Any pair of interacting proteins can be used as immobilized receptor and soluble ligand, provided that both proteins are pure, and their concentrations are known. The difficulty so far has been to determine the dissociation constant from a titration curve. In this study, a mathematical function underlying titration curves is introduced. Without any error-prone graphical estimation of a saturation yield, this algorithm allows processing of the raw data (signal intensities at different concentrations of added ligand) directly by mathematical evaluation via non-linear regression. Thus, several titration curves can be recorded simultaneously and transformed into a set of characteristic parameters, among them the dissociation constant and the concentration of binding-active receptor, and they can be evaluated statistically. When combined with this algorithm, titration ELISAs gain the advantage of directly presenting the dissociation constant. Therefore, they may be used more efficiently in the future.
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Affiliation(s)
- Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster;
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Oh JM, Kalimuthu S, Gangadaran P, Baek SH, Zhu L, Lee HW, Rajendran RL, Hong CM, Jeong SY, Lee SW, Lee J, Ahn BC. Reverting iodine avidity of radioactive-iodine refractory thyroid cancer with a new tyrosine kinase inhibitor (K905-0266) excavated by high-throughput NIS (sodium iodide symporter) enhancer screening platform using dual reporter gene system. Oncotarget 2018; 9:7075-87. [PMID: 29467951 DOI: 10.18632/oncotarget.24159] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/21/2017] [Indexed: 11/25/2022] Open
Abstract
Radioactive-iodine (RAI) therapy is typically unprevailing as anaplastic thyroid cancer (ATC) management, owing to the decrease in the endogenous sodium iodide symporter (NIS) expression. Therefore, new strategies for NIS re-induction are required to improve the efficacy of RAI therapy in ATC. In this study, we developed a novel high-throughput NIS enhancer screening platform using a dual reporter gene system to identify a potent tyrosine kinase inhibitor (TKI) and selected a new hit compound, K905-0266 TKI. The effects of K905-0266 TKI treatment was validated as RAI accumulation, changes in signalling pathway related to thyroid pathogenesis, and cytotoxicity of RAI depending on re-induction of endogenous NIS expression in ATC. Furthermore, we evaluated enhancement of NIS promoter and therapeutic efficacy of RAI in ATC tumour xenograft mice. After K905-0266 TKI treatment, the expression of endogenous NIS was significantly increased, while phosphorylated-ERK was decreased. In addition, the thyroid-metabolising protein expressions were upregulated and increased of RAI accumulation and its therapeutic effects in ATC. Moreover, K905-0266 TKI increased therapeutic efficacy of RAI in ATC tumour in vivo. In conclusion, we successfully established a novel high-throughput NIS enhancer screening platform to excavate a NIS enhancer and identified K905-0266 TKI among TKI candidates and it's proven to increase the endogenous NIS expression and therapeutic efficacy of RAI in ATC. These findings suggest that a novel high-throughput NIS enhancer screening platform is useful for selecting of NIS promoter enhancers. In addition, K905-0266 TKI can be used to re-induce endogenous NIS expression and recover RAI therapy in ATC.
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Li M, Guo X, Li H, Zuo X, Hao R, Song H, Aldalbahi A, Ge Z, Li J, Li Q, Song S, Li S, Shao N, Fan C, Wang L. Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor. ACS Appl Mater Interfaces 2018; 10:341-349. [PMID: 29241329 DOI: 10.1021/acsami.7b17324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.
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Affiliation(s)
- Min Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xudong Guo
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shaohua Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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Camunas-Soler J, Alemany A, Ritort F. Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems. Science 2017; 355:412-415. [PMID: 28126820 DOI: 10.1126/science.aah4077] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022]
Abstract
Thermodynamic bulk measurements of binding reactions rely on the validity of the law of mass action and the assumption of a dilute solution. Yet, important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, or misfolded molecules may not follow these assumptions and may require a particular reaction model. Here we introduce a fluctuation theorem for ligand binding and an experimental approach using single-molecule force spectroscopy to determine binding energies, selectivity, and allostery of nucleic acids and peptides in a model-independent fashion. A similar approach could be used for proteins. This work extends the use of fluctuation theorems beyond unimolecular folding reactions, bridging the thermodynamics of small systems and the basic laws of chemical equilibrium.
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Affiliation(s)
- Joan Camunas-Soler
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Alemany
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain. .,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
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35
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Kamaruddin NH, Bakar AAA, Mobarak NN, Zan MSD, Arsad N. Binding Affinity of a Highly Sensitive Au/Ag/Au/Chitosan-Graphene Oxide Sensor Based on Direct Detection of Pb 2+ and Hg 2+ Ions. Sensors (Basel) 2017; 17:s17102277. [PMID: 28984826 PMCID: PMC5677024 DOI: 10.3390/s17102277] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022]
Abstract
The study of binding affinity is essential in surface plasmon resonance (SPR) sensing because it allows researchers to quantify the affinity between the analyte and immobilised ligands of an SPR sensor. In this study, we demonstrate the derivation of the binding affinity constant, K, for Pb2+ and Hg2+ ions according to their SPR response using a gold/silver/gold/chitosan-graphene oxide (Au/Ag/Au/CS-GO) sensor for the concentration range of 0.1-5 ppm. The higher affinity of Pb2+ to binding with the CS-GO sensor explains the outstanding sensitivity of 2.05 °ppm-1 against 1.66 °ppm-1 of Hg2+. The maximum signal-to-noise ratio (SNR) upon detection of Pb2+ is 1.53, and exceeds the suggested logical criterion of an SNR. The Au/Ag/Au/CS-GO SPR sensor also exhibits excellent repeatability in Pb2+ due to the strong bond between its functional groups and this cation. The adsorption data of Pb2+ and Hg2+ on the CS-GO sensor fits well with the Langmuir isotherm model where the affinity constant, K, of Pb2+ and Hg2+ ions is computed. The affinity of Pb2+ ions to the Au/Ag/Au/CS-GO sensor is significantly higher than that of Hg2+ based on the value of K, 7 × 10⁵ M-1 and 4 × 10⁵ M-1, respectively. The higher shift in SPR angles due to Pb2+ and Hg2+ compared to Cr3+, Cu2+ and Zn2+ ions also reveals the greater affinity of the CS-GO SPR sensor to them, thus supporting the rationale for obtaining K for these two heavy metals. This study provides a better understanding on the sensing performance of such sensors in detecting heavy metal ions.
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Affiliation(s)
- Nur Hasiba Kamaruddin
- Department of Electric, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Ahmad Ashrif A Bakar
- Department of Electric, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Nadhratun Naiim Mobarak
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Mohd Saiful Dzulkefly Zan
- Department of Electric, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Norhana Arsad
- Department of Electric, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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Kim K, Lee W, Chung K, Lee H, Son T, Oh Y, Xiao YF, Ha Kim D, Kim D. Molecular overlap with optical near-fields based on plasmonic nanolithography for ultrasensitive label-free detection by light-matter colocalization. Biosens Bioelectron 2017; 96:89-98. [PMID: 28463741 DOI: 10.1016/j.bios.2017.04.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 01/19/2023]
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37
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38
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Badie Bostan H, Danesh NM, Karimi G, Ramezani M, Mousavi Shaegh SA, Youssefi K, Charbgoo F, Abnous K, Taghdisi SM. Ultrasensitive detection of ochratoxin A using aptasensors. Biosens Bioelectron 2017; 98:168-179. [PMID: 28672192 DOI: 10.1016/j.bios.2017.06.055] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/22/2017] [Accepted: 06/25/2017] [Indexed: 12/28/2022]
Abstract
Regarding teratogenic, carcinogenic, and immunotoxic nature of ochratoxin A (OTA), selective and sensitive monitoring of this molecule in food samples is of great importance. In recent years, various methods have been introduced for detection of OTA. However, they are usually time-consuming, labor-intensive and expensive. Therefore, these parameters limited their usage. The emerging method of detection, aptasensor, has attracted more attention for OTA detection, due to distinctive advantages including high sensitivity, selectivity and simplicity. In this review, the new developed aptasensors for detection of OTA have been investigated. We also highlighted advantages and disadvantages of different types of OTA aptasensors. This review also takes into consideration the goal to find out which designs are the most rational ones for highly sensitive detection of OTA.
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Affiliation(s)
- Hasan Badie Bostan
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Noor Mohammad Danesh
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Research Institute of Sciences and New Technology, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Kazem Youssefi
- Department of English, Tabaran Institute of Higher Education, Mashhad, Iran
| | - Fahimeh Charbgoo
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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39
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Sharifi M, Ezzati Nazhad Dolatabadi J, Fathi F, Zakariazadeh M, Barzegar A, Rashidi M, Tajalli H, Rashidi MR. Surface plasmon resonance and molecular docking studies of bovine serum albumin interaction with neomycin: kinetic and thermodynamic analysis. ACTA ACUST UNITED AC 2017; 7:91-97. [PMID: 28752073 PMCID: PMC5524990 DOI: 10.15171/bi.2017.12] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 12/25/2016] [Revised: 05/20/2017] [Accepted: 05/24/2017] [Indexed: 11/09/2022]
Abstract
Introduction: The interactions between biomacromolecules such as serum albumin (SA) and various drugs have attracted increasing research attention in recent years. However, the study of SA with those drugs that have relatively high hydrophilicity and a lower affinity for SA could be a challenging issue. At the present study, the interaction of bovine SA (BSA) with neomycin as a hydrophilic drug has been investigated using surface plasmon resonance (SPR) and molecular docking methods. Methods: BSA was immobilized on the carboxymethyl dextran hydrogel sensor chip after activation of carboxylic groups through NHS/EDC and, then, the neomycin interaction with BSA at different concentrations (1-128 µM) was investigated. Results: Dose-response sensorgrams of BSA upon increasing concentration of neomycin has been shown through SPR analysis. The small KD value (4.96 e-7 at 40°C) demonstrated high affinity of neomycin to BSA. Thermodynamic parameters were calculated through van't Hoff equation at 4 different temperatures. The results showed that neomycin interacts with BSA via Van der Waals interactions and hydrogen bonds and increase of KD with temperature rising indicated that the binding process was entropy driven. Molecular docking study confirmed that hydrogen bond was the major intermolecular force stabilizing neomycin-BSA complex. Conclusion: The attained results showed that neomycin molecules can efficiently distribute within the body after interaction with BSA in spite of having hydrophilic properties. Besides, SPR can be considered as a useful instrument for study of the interaction of hydrophilic drugs with SA.
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Affiliation(s)
- Maryam Sharifi
- Research Institute for Applied Physics and Astronomy, University of Tabriz, Tabriz, Iran
| | - Jafar Ezzati Nazhad Dolatabadi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Fathi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mostafa Zakariazadeh
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Mohammad Rashidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib Tajalli
- Research Institute for Applied Physics and Astronomy, University of Tabriz, Tabriz, Iran
| | - Mohammad-Reza Rashidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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40
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Nazmul Islam M, Yadav S, Hakimul Haque M, Munaz A, Islam F, Al Hossain MS, Gopalan V, Lam AK, Nguyen N, Shiddiky MJ. Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 92:668-78. [DOI: 10.1016/j.bios.2016.10.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 11/23/2022]
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41
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Abstract
Modern techniques for quantifying blood group antibody-antigen interactions are very limited, especially for weaker interactions which result from low antigen expression and/or partial expression of the antigen structure. Surface plasmon resonance (SPR) detection is often used to monitor and quantify bio-interactions. Previously, a regenerable, multi-fucntional platform for quantitative RBC phenotyping of normal antigen expression using SPR detection was reported. However, detection of weaker variants were not explored. Here, this sensitivity study used anti-human IgG antibodies immobilized to a gold sensor surface to two clinically important types of weaker D variants using SPR; weak D and partial D. Positive pre-sensitised cells bind to the anti-human IgG monolayer, and the response unit (RU) is reported (>100 RU). Unbound negative cells are directly eluted (<100 RU). Weak D cells were detected between a range of 180–580 RU, due to a lower expression of antigens. Partial D cells, category D VI, were also positively identified (352–1147 RU), similar to that of normal D antigens. The detection of two classes of weaker D variants was achieved for the first time using this fully regenerable SPR platform, opening up a new avenue to replace the current subjective and arbitrary methods for quantifying blood group antibody-antigen interactions.
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Affiliation(s)
- Whui Lyn Then
- Bioresource Research Institute of Australia (BioPRIA), Australian Pulp and Paper Institute (APPI), Department of Chemical Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Marie-Isabel Aguilar
- Monash biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Heath Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Gil Garnier
- Bioresource Research Institute of Australia (BioPRIA), Australian Pulp and Paper Institute (APPI), Department of Chemical Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia.
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42
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Callaway DJE, Matsui T, Weiss T, Stingaciu LR, Stanley CB, Heller WT, Bu Z. Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics. J Mol Biol 2017; 429:987-998. [PMID: 28285124 DOI: 10.1016/j.jmb.2017.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/04/2017] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
Abstract
The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The "tip of the whip" that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the binding of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.
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Affiliation(s)
- David J E Callaway
- Department of Chemistry and Biochemistry, City College of New York, CUNY, New York, NY 10031, USA.
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, Menlo Park, CA 94025, USA
| | - Thomas Weiss
- Stanford Synchrotron Radiation Light Source, Menlo Park, CA 94025, USA
| | - Laura R Stingaciu
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, Outstation at SNS, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Christopher B Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William T Heller
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zimei Bu
- Department of Chemistry and Biochemistry, City College of New York, CUNY, New York, NY 10031, USA.
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43
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Sharifi M, Dolatabadi JEN, Fathi F, Rashidi M, Jafari B, Tajalli H, Rashidi MR. Kinetic and thermodynamic study of bovine serum albumin interaction with rifampicin using surface plasmon resonance and molecular docking methods. J Biomed Opt 2017; 22:37002. [PMID: 28253382 DOI: 10.1117/1.jbo.22.3.037002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
The interaction of bovine serum albumin (BSA) with various drugs, such as antibiotics, due to the importance of BSA in drug delivery has attracted increasing research attention at present. Therefore, the aim of this study was investigation of BSA interaction with rifampicin using surface plasmon resonance (SPR) and molecular docking methods under the imitated physiological conditions ( pH = 7.4 ). BSA immobilization on carboxymethyl dextran hydrogel chip has been carried out after activation with N-hydroxysuccinimide/N-ethyl-N-(3-diethylaminopropyl) carbodiimide. The dose-response sensorgrams of BSA upon increasing concentration of refampicin were attained in SPR analysis. The high affinity of rifampicin to BSA was demonstrated by a low equilibrium constants ( K D ) value ( 3.46 × 10 ? 5 at 40°C). The process of kinetic values changing shows that affinity of BSA to rifampicin decreased with rising temperature. The positive value of both enthalpy change ( ? H ) and entropy change ( ? S ) showed that hydrophobic force plays major role in the BSA interaction with rifampicin. The positive value of ? G was indicative of nonspontaneous and enthalpy-driven binding process. In addition, according to the molecular docking study, hydrogen binding has some contributions in the interaction of rifampicin with BSA.
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Affiliation(s)
- Maryam Sharifi
- University of Tabriz, Research Institute for Applied Physics and Astronomy, Tabriz, Iran
| | - Jafar Ezzati Nazhad Dolatabadi
- Tabriz University of Medical Sciences, Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz, Iran
| | - Farzaneh Fathi
- Tabriz University of Medical Sciences, Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz, IrancTabriz University of Medical Sciences, Student Research Committee, Tabriz, Iran
| | - Mohammad Rashidi
- Tabriz University of Medical Sciences, Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz, Iran
| | - Behzad Jafari
- Tabriz University of Medical Sciences, Biotechnology Research Center, Tabriz, Iran
| | - Habib Tajalli
- University of Tabriz, Research Institute for Applied Physics and Astronomy, Tabriz, Iran
| | - Mohammad-Reza Rashidi
- Tabriz University of Medical Sciences, Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz, Iran
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Abstract
A flow chart of the screening of lead compounds.
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Affiliation(s)
- Li Wang
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
- State Key Laboratory of Veterinary Etiological Biology
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Shuai Wang
- State Key Laboratory of Veterinary Etiological Biology
- Lanzhou Veterinary Research Institute
- Chinese Academy of Agricultural Sciences
- Lanzhou 730046
- China
| | - Xichen Zhang
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
| | - Xuepeng Cai,
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
- State Key Laboratory of Veterinary Etiological Biology
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45
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Abstract
There have been many trials to visualize smell using various techniques in order to objectively express the smell because information obtained from the sense of smell in human is very subjective. So far, well-trained experts such as a perfumer, complex and large-scale equipment such as GC-MS, and an electronic nose have played major roles in objectively detecting and recognizing odors. Recently, an optoelectronic nose was developed to achieve this purpose, but some limitations regarding the sensitivity and the number of smells that can be visualized still persist. Since the elucidation of the olfactory mechanism, numerous researches have been accomplished for the development of a sensing device by mimicking human olfactory system. Engineered olfactory cells were constructed to mimic the human olfactory system, and the use of engineered olfactory cells for smell visualization has been attempted with the use of various methods such as calcium imaging, CRE reporter assay, BRET, and membrane potential assay; however, it is not easy to consistently control the condition of cells and it is impossible to detect low odorant concentration. Recently, the bioelectronic nose was developed, and much improved along with the improvement of nano-biotechnology. The bioelectronic nose consists of the following two parts: primary transducer and secondary transducer. Biological materials as a primary transducer improved the selectivity of the sensor, and nanomaterials as a secondary transducer increased the sensitivity. Especially, the bioelectronic noses using various nanomaterials combined with human olfactory receptors or nanovesicles derived from engineered olfactory cells have a potential which can detect almost all of the smells recognized by human because an engineered olfactory cell might be able to express any human olfactory receptor as well as can mimic human olfactory system. Therefore, bioelectronic nose will be a potent tool for smell visualization, but only if two technologies are completed. First, a multi-channel array-sensing system has to be applied for the integration of all of the olfactory receptors into a single chip for mimicking the performance of human nose. Second, the processing technique of the multi-channel system signals should be simultaneously established with the conversion of the signals to visual images. With the use of this latest sensing technology, the realization of a proper smell-visualization technology is expected in the near future.
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Affiliation(s)
- Hwi Jin Ko
- Bio-MAX Institute, Seoul, 151-742 Republic of Korea
| | - Tai Hyun Park
- Bio-MAX Institute, Seoul, 151-742 Republic of Korea ; School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-742 Republic of Korea ; Advanced Institutes of Convergence Technology, Suwon, Gyeonggido 443-270 Republic of Korea
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46
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Abstract
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol). We also report on the protocol for the affinity screening of a panel of anti-thrombin RNA aptamers with a single phosphorodithioate (PS2) modification, whereby the position of the modification along the RNA backbone is varied systematically (Support Protocol). The PS2 modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphodiester backbone linkage. The PS2-modified RNAs are nuclease resistant and several in vitro and in vivo assays have demonstrated their biological activity. For example, combining the PS2 with the 2'-OMe modification affords increased loading of modified small interfering RNA (siRNA) duplexes into the RNA-induced silencing complex (RISC) as well as enhanced gene-silencing antitumor activity. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
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47
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Ansari MH, Hassan S, Qurashi A, Khanday FA. Microfluidic-integrated DNA nanobiosensors. Biosens Bioelectron 2016; 85:247-260. [DOI: 10.1016/j.bios.2016.05.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 11/28/2022]
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48
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49
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Xu GK, Hu J, Lipowsky R, Weikl TR. Binding constants of membrane-anchored receptors and ligands: A general theory corroborated by Monte Carlo simulations. J Chem Phys 2016; 143:243136. [PMID: 26723621 DOI: 10.1063/1.4936134] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Adhesion processes of biological membranes that enclose cells and cellular organelles are essential for immune responses, tissue formation, and signaling. These processes depend sensitively on the binding constant K2D of the membrane-anchored receptor and ligand proteins that mediate adhesion, which is difficult to measure in the "two-dimensional" (2D) membrane environment of the proteins. An important problem therefore is to relate K2D to the binding constant K3D of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in three dimensions (3D). In this article, we present a general theory for the binding constants K2D and K3D of rather stiff proteins whose main degrees of freedom are translation and rotation, along membranes and around anchor points "in 2D," or unconstrained "in 3D." The theory generalizes previous results by describing how K2D depends both on the average separation and thermal nanoscale roughness of the apposing membranes, and on the length and anchoring flexibility of the receptors and ligands. Our theoretical results for the ratio K2D/K3D of the binding constants agree with detailed results from Monte Carlo simulations without any data fitting, which indicates that the theory captures the essential features of the "dimensionality reduction" due to membrane anchoring. In our Monte Carlo simulations, we consider a novel coarse-grained model of biomembrane adhesion in which the membranes are represented as discretized elastic surfaces, and the receptors and ligands as anchored molecules that diffuse continuously along the membranes and rotate at their anchor points.
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Affiliation(s)
- Guang-Kui Xu
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jinglei Hu
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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50
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Weikl TR, Hu J, Xu GK, Lipowsky R. Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory. Cell Adh Migr 2016; 10:576-589. [PMID: 27294442 PMCID: PMC5079412 DOI: 10.1080/19336918.2016.1180487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022] Open
Abstract
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant [Formula: see text] and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between [Formula: see text] and the binding constant [Formula: see text] of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D).
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Affiliation(s)
- Thomas R. Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
| | - Jinglei Hu
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
| | - Guang-Kui Xu
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi'an Jiaotong University, Xi'an, China
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
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