1
|
Inhibitory Activity and Mechanism Investigation of Hypericin as a Novel α-Glucosidase Inhibitor. Molecules 2021; 26:molecules26154566. [PMID: 34361714 PMCID: PMC8348433 DOI: 10.3390/molecules26154566] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/20/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
α-glucosidase is a major enzyme that is involved in starch digestion and type 2 diabetes mellitus. In this study, the inhibition of hypericin by α-glucosidase and its mechanism were firstly investigated using enzyme kinetics analysis, real-time interaction analysis between hypericin and α-glucosidase by surface plasmon resonance (SPR), and molecular docking simulation. The results showed that hypericin was a high potential reversible and competitive α-glucosidase inhibitor, with a maximum half inhibitory concentration (IC50) of 4.66 ± 0.27 mg/L. The binding affinities of hypericin with α-glucosidase were assessed using an SPR detection system, which indicated that these were strong and fast, with balances dissociation constant (KD) values of 6.56 × 10−5 M and exhibited a slow dissociation reaction. Analysis by molecular docking further revealed that hydrophobic forces are generated by interactions between hypericin and amino acid residues Arg-315 and Tyr-316. In addition, hydrogen bonding occurred between hypericin and α-glucosidase amino acid residues Lys-156, Ser-157, Gly-160, Ser-240, His-280, Asp-242, and Asp-307. The structure and micro-environment of α-glucosidase enzymes were altered, which led to a decrease in α-glucosidase activity. This research identified that hypericin, an anthracene ketone compound, could be a novel α-glucosidase inhibitor and further applied to the development of potential anti-diabetic drugs.
Collapse
|
2
|
Tiwari PB, Bencheqroun C, Lemus M, Shaw T, Kouassi-Brou M, Alaoui A, Üren A. SPRD: a surface plasmon resonance database of common factors for better experimental planning. BMC Mol Cell Biol 2021; 22:17. [PMID: 33676410 PMCID: PMC7937274 DOI: 10.1186/s12860-021-00354-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Background Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surface plasmon resonance is a very powerful tool in different stages of small molecule drug development and antibody characterization. Both academic institutions and pharmaceutical industry extensively utilize this method for screening and validation studies involving direct molecular interactions. In most applications of the surface plasmon resonance technology, one of the studied molecules is immobilized on a microchip, while the second molecule is delivered through a microfluidic system over the immobilized molecules. Changes in total mass on the chip surface is recorded in real time as an indicator of the molecular interactions. Main body Quality and accuracy of the surface plasmon resonance data depend on experimental variables, including buffer composition, type of sensor chip, coupling chemistry of molecules on the sensor surface, and surface regeneration conditions. These technical details are generally included in materials and methods sections of published manuscripts and are not easily accessible using the common internet browser search engines or PubMed. Herein, we introduce a surface plasmon resonance database, www.sprdatabase.info that contains technical details extracted from 5140 publications with surface plasmon resonance data. We also provide an analysis of experimental conditions preferred by different laboratories. These experimental variables can be searched within the database and help future users of this technology to design better experiments. Conclusion Amine coupling and CM5 chips were the most common methods used for immobilizing proteins in surface plasmon resonance experiments. However, number of different chips, capture methods and buffer conditions were used by multiple investigators. We predict that the database will significantly help the scientific community using this technology and hope that users will provide feedback to improve and expand the database indefinitely. Publicly available information in the database can save a great amount of time and resources by assisting initial optimization and troubleshooting of surface plasmon resonance experiments.
Collapse
Affiliation(s)
| | - Camelia Bencheqroun
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Mario Lemus
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Taryn Shaw
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Marilyn Kouassi-Brou
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.,Geisel School of Medicine, Dartmouth College, NH, 03755, Hanover, USA
| | - Adil Alaoui
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.
| |
Collapse
|
3
|
Li P, Huang Z, She Y, Qin S, Gao W, Cao Y, Liu X. An assessment of the interaction for three Chrysanthemum indicum flavonoids and α-amylase by surface plasmon resonance. Food Sci Nutr 2020; 8:620-628. [PMID: 31993185 PMCID: PMC6977516 DOI: 10.1002/fsn3.1349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 11/23/2022] Open
Abstract
This study evaluated the interaction of Chrysanthemum indicum (CI) flavonoids (luteolin, acacetin, and buddleoside) with α-amylase. Surface plasmon resonance (SPR) assay showed their equilibrium dissociation constants (KD ) are 1.9695 ± 0.12, 2.9240 ± 0.20, and 3.2966 ± 0.08 mM at pH 6.0, respectively. Furthermore, their binding affinities were influenced by KCl, MgCl2, and CaCl2. Enzymatic kinetic studies revealed that three flavonoids exhibited noncompetitive α-amylase inhibitory activity. The inhibitory sequence is luteolin > acacetin > buddleoside, which was in accordance with the results of binding affinity from SPR. 1,1-diphenyl-2-picryl hydrazyl radical assay demonstrated that antioxidant activities of three flavonoids were inhibited significantly with α-amylase. Meanwhile, the study reveals that hydroxyl on C'-4, C'-5, and C-7 of flavonoids play an important role on the interaction of three flavonoids with α-amylase. Also, SPR could be used as sensor for rapid screening inhibitors of α-amylase and provide useful information for the application of C. indicum flavonoids in food and pharmaceutical area.
Collapse
Affiliation(s)
- Pao Li
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Zhao Huang
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Yin She
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Si Qin
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
- Hunan Co‐Innovation Center for Utilization of Botanical Functional IngredientsChangshaChina
| | - Wanru Gao
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Yanan Cao
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
| | - Xia Liu
- College of Food Science and TechnologyHunan Provincial Key Laboratory of Food Science and BiotechnologyHunan Agricultural UniversityChangshaChina
- Hunan Co‐Innovation Center for Utilization of Botanical Functional IngredientsChangshaChina
| |
Collapse
|
4
|
Wang Y, Rakela S, Chambers JW, Hua ZC, Muller MT, Nitiss JL, Tse-Dinh YC, Leng F. Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching. ACS OMEGA 2019; 4:18413-18422. [PMID: 31720544 PMCID: PMC6844113 DOI: 10.1021/acsomega.9b02676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
DNA topoisomerases are essential enzymes for all living organisms and important targets for anticancer drugs and antibiotics. Although DNA topoisomerases have been studied extensively, steady-state kinetics has not been systematically investigated because of the lack of an appropriate assay. Previously, we demonstrated that newly synthesized, fluorescently labeled plasmids pAB1_FL905 and pAB1_FL924 can be used to study DNA topoisomerase-catalyzed reactions by fluorescence resonance energy transfer (FRET) or supercoiling-dependent fluorescence quenching (SDFQ). With the FRET or SDFQ method, we performed steady-state kinetic studies for six different DNA topoisomerases including two type IA enzymes (Escherichia coli and Mycobacterium smegmatis DNA topoisomerase I), two type IB enzymes (human and variola DNA topoisomerase I), and two type IIA enzymes (E. coli DNA gyrase and human DNA topoisomerase IIα). Our results show that all DNA topoisomerases follow the classical Michaelis-Menten kinetics and have unique steady-state kinetic parameters, K M, V max, and k cat. We found that k cat for all topoisomerases are rather low and that such low values may stem from the tight binding of topoisomerases to DNA. Additionally, we confirmed that novobiocin is a competitive inhibitor for adenosine 5'-triphosphate binding to E. coli DNA gyrase, demonstrating the utility of our assay for studying topoisomerase inhibitors.
Collapse
Affiliation(s)
- Yunke Wang
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
- School
of Life Sciences, Nanjing University, Nanjing, Jiangsu Province 210023, P. R. China
| | - Samantha Rakela
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Jeremy W. Chambers
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Zi-Chun Hua
- School
of Life Sciences, Nanjing University, Nanjing, Jiangsu Province 210023, P. R. China
- Changzhou
High-Tech Research Institute of Nanjing University and Jiangsu TargetPharma
Laboratories Inc., Changzhou, Jiangsu 213164, P. R. China
| | - Mark T. Muller
- TopoGEN,
Inc., Buena Vista, Colorado 81211, United
States
| | - John L. Nitiss
- Pharmaceutical
Sciences Department, College of Pharmacy at Rockford, University of Illinois at Chicago, 1601 Parkview Avenue, N310, Rockford, Illinois 61107, United States
| | - Yuk-Ching Tse-Dinh
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
5
|
Quantitative investigation of the direct interaction between Hemagglutinin and fusion proteins of Peste des petits ruminant virus using surface Plasmon resonance. Virol J 2018; 15:21. [PMID: 29357882 PMCID: PMC5778702 DOI: 10.1186/s12985-018-0933-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/15/2018] [Indexed: 11/30/2022] Open
Abstract
Background The specific and dynamic interaction between the hemagglutinin (H) and fusion (F) proteins of morbilliviruses is a prerequisite for the conformational rearrangements and membrane fusion during infection process. The two heptad repeat regions (HRA and HRB) of F protein are both important for the triggering of F protein. Methods In this study, the direct interactions of Peste des petits ruminants virus (PPRV) H with F, HRA and HRB were quantitatively evaluated using biosensor surface plasmon resonance (SPR). Results The binding affinities of immobilized pCMV-HA-H (HA-H) interacted with proteins pCMV-HA-F (HA-F) and pCMV-HA-HRB (HA-HRB) (KD = 1.91 × 10− 8 M and 2.60 × 10− 7 M, respectively) reacted an order of magnitude more strongly than that of pCMV-HA-HRA (HA-HRA) and pCMV-HA-Tp IGFR-LD (HA) (KD = 1.08 × 10− 4 M and 1.43 × 10− 4 M, respectively). Conclusions The differences of the binding affinities suggested that HRB is involved in functionally important intermolecular interaction in the fusion process.
Collapse
|
6
|
Liu X, Luo F, Li P, She Y, Gao W. Investigation of the interaction for three Citrus flavonoids and α-amylase by surface plasmon resonance. Food Res Int 2017; 97:1-6. [PMID: 28578029 DOI: 10.1016/j.foodres.2017.03.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/26/2017] [Accepted: 03/10/2017] [Indexed: 02/01/2023]
Abstract
Flavonoids, a class of natural drugs with broad biological activity, exhibit inhibitory effect on α-amylase. Citrus peel is a good source of flavonoids. The real-time interactions between three Citrus flavonoids (naringin, neohesperidin, hesperidin) and α-amylase were investigated by surface plasmon resonance biosensor, and were compared with the α-amylase inhibitors, acarbose. These results showed the binding affinities of naringin, neohesperidin and hesperidin with α-amylase reach the highest at pH6 with KD values of 2.27±0.18mM, 3.09±0.20mM and 3.51±0.09mM, and can be reinforced with 0.2M NaCl and 0.1M CaCl2, respectively. The results of 1, 1-diphenyl-2-picryl hydrazyl radical assay indicate that the antioxidant activities of naringin, neohesperidin and hesperidin are significantly inhibited by interacting with α-amylase, and the inhibition percentage are 47.61±0.034%, 22.81±0.037% and 21.01±0.051%, respectively. Additionally, it is found that both the number and the position of hydroxyl group play an important role in the interaction of three Citrus flavonoids and α-amylase. These results provide useful information for rapid screening inhibitors of α-amylase from plant-based food.
Collapse
Affiliation(s)
- Xia Liu
- College of Food Science and Technology, Hunan Agricultural University, Hunan Province Key Laboratory of Food Science and Biotechnology, Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, PR China.
| | - Fang Luo
- College of Food Science and Technology, Hunan Agricultural University, Hunan Province Key Laboratory of Food Science and Biotechnology, Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, PR China
| | - Pao Li
- College of Food Science and Technology, Hunan Agricultural University, Hunan Province Key Laboratory of Food Science and Biotechnology, Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, PR China
| | - Yin She
- College of Food Science and Technology, Hunan Agricultural University, Hunan Province Key Laboratory of Food Science and Biotechnology, Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, PR China
| | - Wanru Gao
- College of Food Science and Technology, Hunan Agricultural University, Hunan Province Key Laboratory of Food Science and Biotechnology, Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, PR China
| |
Collapse
|
7
|
Tiwari PB, Chapagain PP, Banda S, Darici Y, Üren A, Tse-Dinh YC. Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations. FEBS Lett 2016; 590:2844-51. [PMID: 27448274 DOI: 10.1002/1873-3468.12321] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022]
Abstract
Escherichia coli topoisomerase I (EctopoI), a type IA DNA topoisomerase, relaxes the negative DNA supercoiling generated by RNA polymerase (RNAP) during transcription elongation. Due to the lack of structural information on the complex, the exact nature of the RNAP-EctopoI interactions remains unresolved. Herein, we report for the first time, the structure-based modeling of the RNAP-EctopoI interactions using computational methods. Our results predict that the salt bridge as well as hydrogen bond interactions are responsible for the formation and stabilization of the RNAP-EctopoI complex. Our investigations provide molecular insights for understanding how EctopoI interacts with RNAP, a critical step for preventing hypernegative DNA supercoiling during transcription.
Collapse
Affiliation(s)
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Srikanth Banda
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Yesim Darici
- Department of Physics, Florida International University, Miami, FL, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| |
Collapse
|
8
|
Banda S, Tiwari PB, Darici Y, Tse-Dinh YC. Investigating direct interaction between Escherichia coli topoisomerase I and RecA. Gene 2016; 585:65-70. [PMID: 27001450 PMCID: PMC4838544 DOI: 10.1016/j.gene.2016.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/12/2016] [Indexed: 01/14/2023]
Abstract
Protein-protein interactions are of special importance in cellular processes, including replication, transcription, recombination, and repair. Escherichia coli topoisomerase I (EcTOP1) is primarily involved in the relaxation of negative DNA supercoiling. E. coli RecA, the key protein for homologous recombination and SOS DNA-damage response, has been shown to stimulate the relaxation activity of EcTOP1. The evidence for their direct protein-protein interaction has not been previously established. We report here the direct physical interaction between E. coli RecA and topoisomerase I. We demonstrated the RecA-topoisomerase I interaction via pull-down assays, and surface plasmon resonance measurements. Molecular docking supports the observation that the interaction involves the topoisomerase I N-terminal domains that form the active site. Our results from pull-down assays showed that ATP, although not required, enhances the RecA-EcTOP1 interaction. We propose that E. coli RecA physically interacts with topoisomerase I to modulate the chromosomal DNA supercoiling.
Collapse
Affiliation(s)
- Srikanth Banda
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | | | - Yesim Darici
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| |
Collapse
|
9
|
Zuccaro L, Tesauro C, Kurkina T, Fiorani P, Yu HK, Knudsen BR, Kern K, Desideri A, Balasubramanian K. Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene. ACS NANO 2015; 9:11166-76. [PMID: 26445172 DOI: 10.1021/acsnano.5b05709] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.
Collapse
Affiliation(s)
- Laura Zuccaro
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
- Department of Molecular Biology & Genetics, Aarhus University , DK-8000 Aarhus, Denmark
| | - Tetiana Kurkina
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata , I-00133 Rome, Italy
- Institute of Translational Pharmacology , National Research Council CNR, I-00133 Rome, Italy
| | - Hak Ki Yu
- Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Birgitta R Knudsen
- Department of Molecular Biology & Genetics, Aarhus University , DK-8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University , DK-8000 Aarhus, Denmark
| | - Klaus Kern
- Max Planck Institute for Solid State Research , D-70569 Stuttgat, Germany
- Institut de Physique de la Matière Condensée, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | | | | |
Collapse
|
10
|
Tiwari PB, Üren A, He J, Darici Y, Wang X. Note: Model identification and analysis of bivalent analyte surface plasmon resonance data. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:106107. [PMID: 26521004 PMCID: PMC4617740 DOI: 10.1063/1.4933318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Surface plasmon resonance (SPR) is a widely used, affinity based, label-free biophysical technique to investigate biomolecular interactions. The extraction of rate constants requires accurate identification of the particular binding model. The bivalent analyte model involves coupled non-linear differential equations. No clear procedure to identify the bivalent analyte mechanism has been established. In this report, we propose a unique signature for the bivalent analyte model. This signature can be used to distinguish the bivalent analyte model from other biphasic models. The proposed method is demonstrated using experimentally measured SPR sensorgrams.
Collapse
Affiliation(s)
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, District of Columbia 20057, USA
| | - Jin He
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Yesim Darici
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Xuewen Wang
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| |
Collapse
|
11
|
Tiwari PB, Wang X, He J, Darici Y. Analyzing surface plasmon resonance data: choosing a correct biphasic model for interpretation. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:035001. [PMID: 25832266 DOI: 10.1063/1.4914027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Surface plasmon resonance (SPR) has been widely used as a label-free biophysical technique to quantitatively study biochemical processes. For the SPR data fitting using a single exponential function, the procedure to extract the rate constants is straightforward. However, there is no simple procedure for SPR data fitting with double exponential functions. A highly non-linear fitting procedure is, therefore, used to fit the biphasic SPR data with numerical solutions of the rate equations. This procedure requires some prior knowledge of the underlying interaction mechanism, and the extracted rate constants often have large uncertainties. In this report, we propose a new method of analyzing the biphasic SPR data using the three commonly employed biphasic models. Our method is based on a general analytical solution of the biphasic rate equations, which is much more transparent and straightforward than the highly non-linear numerical integration approach. Our method can be used to determine the underlying biphasic interaction mechanism from the analysis of the SPR data and to extract the rate constants with high confidence levels. We have illustrated the procedures with examples of the data analysis on simulated SPR profiles, and the results are discussed.
Collapse
Affiliation(s)
| | - Xuewen Wang
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Jin He
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| | - Yesim Darici
- Department of Physics, Florida International University, Miami, Florida 33199, USA
| |
Collapse
|