1
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Borko V, Friganović T, Weitner T. Preparation and characterization of iron(III) nitrilotriacetate complex in aqueous solutions for quantitative protein binding experiments. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6499-6513. [PMID: 37966722 DOI: 10.1039/d3ay01261a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Various preparations of iron(III) nitrilotriacetate (FeNTA) solution reported in the literature lack a comprehensive method for accurate determination of FeNTA concentration and often result in unstable solutions. A detailed procedure for the preparation of FeNTA solution is presented that includes the standardization of both components of the chelate. The standardization of the components allowed the accurate determination of the molar absorption coefficients for the calculation of the FeNTA concentration in two different buffers at pH 5.6 and 7.4. The variation of pH in this range or ionic strength in the range from 0 M to 3 M (KCl) has little effect on the value of the molar absorption coefficient. The precise concentrations of all species involved in the equilibria between Fe and NTA were determined in the pH range 2-12 using the Jenkins-Traub algorithm to solve the 5th-order polynomial in Microsoft Excel. In view of the experimental observations and the calculated distribution of species, the stability of FeNTA solutions may be affected by the Fe : NTA ratio and the total concentrations, with dilute solutions and those with an excess of NTA over Fe showing higher stability.
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Affiliation(s)
- Valentina Borko
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia.
| | - Tomislav Friganović
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia.
| | - Tin Weitner
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia.
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2
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Barry CJ, Pillay CS, Rohwer JM. Modelling the Decamerisation Cycle of PRDX1 and the Inhibition-like Effect on Its Peroxidase Activity. Antioxidants (Basel) 2023; 12:1707. [PMID: 37760010 PMCID: PMC10525498 DOI: 10.3390/antiox12091707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Peroxiredoxins play central roles in the detoxification of reactive oxygen species and have been modelled across multiple organisms using a variety of kinetic methods. However, the peroxiredoxin dimer-to-decamer transition has been underappreciated in these studies despite the 100-fold difference in activity between these forms. This is due to the lack of available kinetics and a theoretical framework for modelling this process. Using published isothermal titration calorimetry data, we obtained association and dissociation rate constants of 0.050 µM-4·s-1 and 0.055 s-1, respectively, for the dimer-decamer transition of human PRDX1. We developed an approach that greatly reduces the number of reactions and species needed to model the peroxiredoxin decamer oxidation cycle. Using these data, we simulated horse radish peroxidase competition and NADPH-oxidation linked assays and found that the dimer-decamer transition had an inhibition-like effect on peroxidase activity. Further, we incorporated this dimer-decamer topology and kinetics into a published and validated in vivo model of PRDX2 in the erythrocyte and found that it almost perfectly reconciled experimental and simulated responses of PRDX2 oxidation state to hydrogen peroxide insult. By accounting for the dimer-decamer transition of peroxiredoxins, we were able to resolve several discrepancies between experimental data and available kinetic models.
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Affiliation(s)
- Christopher J. Barry
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
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3
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Ma B, Wang R, Chen B, Liu W, Zhou S, Li X, Gong J, Shang S, Li Y, Xu D, Tan Z. Insights into the effect of protein glycosylation on carbohydrate substrate binding. Int J Biol Macromol 2023; 235:123833. [PMID: 36870654 DOI: 10.1016/j.ijbiomac.2023.123833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
The role of glycosylation in the binding of glycoproteins to carbohydrate substrates has not been well understood. The present study addresses this knowledge gap by elucidating the links between the glycosylation patterns of a model glycoprotein, a Family 1 carbohydrate-binding module (TrCBM1), and the thermodynamic and structural properties of its binding to different carbohydrate substrates using isothermal titration calorimetry and computational simulation. The variations in glycosylation patterns cause a gradual transition of the binding to soluble cellohexaose from an entropy-driven process to an enthalpy-driven one, a trend closely correlated with the glycan-induced shift of the predominant binding force from hydrophobic interactions to hydrogen bonding. However, when binding to a large surface of solid cellulose, glycans on TrCBM1 have a more dispersed distribution and thus have less adverse impact on the hydrophobic interaction forces, leading to overall improved binding. Unexpectedly, our simulation results also suggest an evolutionary role of O-mannosylation in transforming the substrate binding features of TrCBM1 from those of type A CBMs to those of type B CBMs. Taken together, these findings provide new fundamental insights into the molecular basis of the role of glycosylation in protein-carbohydrate interactions and are expected to better facilitate further studies in this area.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China
| | - Baoquan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenqiang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Sen Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xue Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinyuan Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiying Shang
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China.
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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4
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Fu X, Yuan S, Yang F, Yu H, Xie Y, Guo Y, Yao W. Characterization of the interaction between boscalid and tannic acid and its effect on the antioxidant properties of tannic acid. J Food Sci 2023; 88:1325-1335. [PMID: 36786363 DOI: 10.1111/1750-3841.16488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
The binding of pesticide residues and fruit components may have a profound impact on pesticide dissipation and the functional characteristics of the corresponding components. Therefore, the interaction between boscalid and tannic acid (TA, a representative phenolic in fruit) was systematically investigated using spectroscopic, thermodynamic, and computational chemistry methods. A separable system was designed to obtain the boscalid-TA complex. Fourier transform infrared and 1 H-NMR spectroscopies indicated the formation of hydrogen bonds in the complex. Isothermal titration calorimetry showed that the complex bound spontaneously through hydrophobic interactions (ΔG < 0, ΔH > 0, ΔS > 0), with a binding constant of 6.0 × 105 M-1 at 298 K. The molecular docking results further confirmed the formation of hydrogen bonds and hydrophobic interactions in the complex at the molecular level, with a binding energy of -8.43 kcal mol-1 . In addition, the binding of boscalid to TA significantly decreased the antioxidant activity of TA. The binding of boscalid residue to TA was characterized at the molecular level, which significantly reduced the in vitro antioxidant properties of TA. PRACTICAL APPLICATION: This study provides a reference for the molecular mechanisms of the interaction between pesticide residues and food matrices, as well as a basis for regulating bound-state pesticide residues in food.
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Affiliation(s)
- Xiaoyan Fu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shaofeng Yuan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Fangwei Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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5
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Dubashynskaya NV, Gasilova ER, Skorik YA. Nano-Sized Fucoidan Interpolyelectrolyte Complexes: Recent Advances in Design and Prospects for Biomedical Applications. Int J Mol Sci 2023; 24:ijms24032615. [PMID: 36768936 PMCID: PMC9916530 DOI: 10.3390/ijms24032615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The marine polysaccharide fucoidan (FUC) is a promising polymer for pharmaceutical research and development of novel drug delivery systems with modified release and targeted delivery. The presence of a sulfate group in the polysaccharide makes FUC an excellent candidate for the formation of interpolyelectrolyte complexes (PECs) with various polycations. However, due to the structural diversity of FUC, the design of FUC-based nanoformulations is challenging. This review describes the main strategies for the use of FUC-based PECs to develop drug delivery systems with improved biopharmaceutical properties, including nanocarriers in the form of FUC-chitosan PECs for pH-sensitive oral delivery, targeted delivery systems, and polymeric nanoparticles for improved hydrophobic drug delivery (e.g., FUC-zein PECs, core-shell structures obtained by the layer-by-layer self-assembly method, and self-assembled hydrophobically modified FUC particles). The importance of a complex study of the FUC structure, and the formation process of PECs based on it for obtaining reproducible polymeric nanoformulations with the desired properties, is also discussed.
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6
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Brown HA, Koropatkin NM. Isothermal Titration Calorimetry for Quantification of Protein-Carbohydrate Interactions. Methods Mol Biol 2023; 2657:129-140. [PMID: 37149527 DOI: 10.1007/978-1-0716-3151-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Isothermal titration calorimetry allows the determination of thermodynamic parameters for the interaction between a protein and mono- or oligosaccharides in solution. For the study of protein-carbohydrate interactions, it is a robust way to determine the stoichiometry and affinity, as well as the enthalpic and entropic contributions to this interaction, without the use of labeled proteins or substrates. Here we describe a standard multiple-injection titration experiment for measuring the binding energetics between a carbohydrate-binding protein and an oligosaccharide.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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7
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3-Thienylboronic Acid as a Receptor for Diol-Containing Compounds: A Study by Isothermal Titration Calorimetry. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The electrochemical activity of 3-thienylboronic acid and its feature to form polymer films makes it a perspective receptor material for sensor applications. The affinity properties of this compound were studied here by isothermal titration calorimetry. A number of different analytes were tested, and the highest binding enthalpy was observed for sorbitol and fructose. An increase of pH in the range of 5.5–10.6 results in the rise of the binding enthalpy with an increase of the binding constant to ~8400 L/mol for sorbitol or ~3400 L/mol for fructose. The dependence of the binding constant on pH has an inflection point at pH 7.6 with a slope that is a ten-fold binding constant per one pH unit. The binding properties of 3-thienylboronic acid were evaluated to be very close to that of the phenylboronic acid, but the electrochemical activity of 3-thienylboronic acid provides a possibility of external electrical control: dependence of the affinity of 3-thienylboronic acid on its redox state defined by the presence of ferro/ferricyanide in different ratios was demonstrated. The results show that 3-thienylboronic acid can be applied in smart chemical sensors with electrochemically controllable receptor affinity.
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8
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Hadži S, Lah J. Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures. Methods Mol Biol 2022; 2516:239-257. [PMID: 35922630 DOI: 10.1007/978-1-0716-2413-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.
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Affiliation(s)
- San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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9
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Liu Y, Zhang L, Guo M, Chen L, Wu B, Huang H. Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2. J Biol Chem 2021; 297:101357. [PMID: 34756887 PMCID: PMC8633003 DOI: 10.1016/j.jbc.2021.101357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022] Open
Abstract
It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.
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Affiliation(s)
- Yanhong Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Linsheng Zhang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Maochao Guo
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Liu Chen
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Hongda Huang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China.
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10
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Tellinghuisen J. A (partial) resolution of binding enthalpy discrepancies in ITC studies of Ba2+crown ether complexation: The importance of calibration. Anal Biochem 2021; 642:114481. [PMID: 34843699 DOI: 10.1016/j.ab.2021.114481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022]
Abstract
By conducting binding experiments at a range of temperatures T using isothermal titration calorimetry (ITC), one can obtain two estimates of the binding enthalpy - calorimetric (ΔH°cal) from the experiments at each T, and van't Hoff (ΔH°vH) from the T dependence of the binding constant K°. From thermodynamics it is clear that these two must be identical, but early efforts to demonstrate this for ITC data indicated significant inconsistency. In an extensive 2004 study of the Ba2+ + 18-crown-6 ether complexation used in prior comparisons, Mizoue and Tellinghuisen found modest (10-20%) but statistically significant differences, which were tentatively attributed to problems converting the calorimetric estimates to their standard state values, as implied by the superscript ° in the notation. In the present work the 2004 results are reanalyzed using results obtained since then from temperature, heat, and volume calibration of the instrument and a better determination of the data variance function required for the weighted least-squares fitting of the data. The new results show consistency for temperatures 5-30 °C but persistent statistically significant differences from 35-46 °C. Several possible explanations for the remaining discrepancies are examined, with methods that include fitting the K and ΔHcal data together.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
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11
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Müller M, Platten F, Dulle M, Fischer B, Hoheisel W, Serno P, Egelhaaf S, Breitkreutz J. Precipitation from amorphous solid dispersions in biorelevant dissolution testing: The polymorphism of regorafenib. Int J Pharm 2021; 603:120716. [PMID: 34015382 DOI: 10.1016/j.ijpharm.2021.120716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/27/2022]
Abstract
Amorphous Solid Dispersions (ASDs) are a major drug formulation technique to achieve higher bioavailability for poorly water-soluble active pharmaceutical ingredients. So far, dissolution tailoring and supersaturation enhancement have been studied in detail, whereas less is known about the importance of formed precipitates with amorphous or crystalline states at the site of drug absorption. Regorafenib monohydrate (RGF MH), a multikinase inhibitor drug categorized as Biopharmaceutics Classification System (BCS) class II compound, was formulated with povidone K25 and hypromellose acetate succinate (HPMCAS) as an ASD. Here, for the first time, the RGF precipitation process as well as the physicochemical properties of the arising precipitates are investigated. The formed precipitates from biorelevant dissolution showed varying drug content and were analyzed offline by scanning electron microscopy (SEM), differential scanning calorimetry (DSC), confocal Raman microscopy (CRM), X-ray powder diffraction (XRPD), and small angle X-ray scattering (SAXS). In addition to different crystalline RGF precipitates, an amorphous co-precipitate of RGF and HPMCAS was identified, which was suppressed in the presence of PVP. Wide angle X-ray scattering (WAXS) and isothermal calorimetry (ITC) were used to track the precipitation process of RGF in-situ. From calorimetric data, the precipitation profile was calculated. RGF forms precipitates in multiple polymorphic states dependent on the environmental conditions, i.e., dissolution media composition and chosen excipients. The engineered formation of defined amorphous structures in-vivo may be a promising future drug formulation strategy.
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Affiliation(s)
- Martin Müller
- Institute of Pharmaceutics and Biopharmaceutics, Heinrich Heine University Düsseldorf, Germany, Universitätsstraße 1, 40225 Düsseldorf, Germany; INVITE GmbH, Formulation Technology, Chempark, Building W 32, 51368 Leverkusen, Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Forschungszentrum Jülich, IBI-4, Wilhelm-Johnen-Straße, 52428 Jülich Jülich, Germany
| | - Martin Dulle
- Forschungszentrum Jülich, JCNS-1/IBI-8, Wilhelm-Johnen-Straße, 52428 Jülich Jülich, Germany
| | - Björn Fischer
- FISCHER GmbH, Raman Spectroscopic Services, Necklenbroicher Str. 22, 40667 Meerbusch, Germany
| | - Werner Hoheisel
- INVITE GmbH, Formulation Technology, Chempark, Building W 32, 51368 Leverkusen, Germany
| | - Peter Serno
- Bayer AG, Research Center Wuppertal-Elberfeld, Friedrich-Ebert-Straße 217-333, 42117 Wuppertal, Germany
| | - Stefan Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jörg Breitkreutz
- Institute of Pharmaceutics and Biopharmaceutics, Heinrich Heine University Düsseldorf, Germany, Universitätsstraße 1, 40225 Düsseldorf, Germany.
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13
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A multi-laboratory benchmark study of isothermal titration calorimetry (ITC) using Ca 2+ and Mg 2+ binding to EDTA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:429-451. [PMID: 33864101 DOI: 10.1007/s00249-021-01523-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
A small-scale ITC benchmarking study was performed involving 9 biophysics laboratories/facilities, to evaluate inter-laboratory and intra-laboratory basal levels of uncertainty. Our prime goal was to assess a number of important factors that can influence both the data gathered by this technique and the thermodynamic parameter values derived therefrom. In its first part, the study involved 5 laboratories and 13 different instruments, working with centrally prepared samples and the same experimental protocol. The second part involved 4 additional laboratories and 6 more instruments, where the users prepared their own samples according to provided instructions and did the experiments following the same protocol as in the first part. The study design comprised: (1) selecting a minimal set of laboratories; (2) providing very stable samples; (3) providing samples not requiring preparation or manipulation; and (4) providing a well-defined and detailed experimental protocol. Thus, we were able to assess: (i) the variability due to instrument and data analysis performed by each user on centrally prepared samples; (ii) the comparability of data retrieved when using 4 different software packages to analyze the same data, besides the data analysis carried out by the different users on their own experimental results; and (iii) the variability due to local sample preparation (second part of the study). Individual values, as well as averages and standard deviations for the binding parameters for EDTA-cation interaction, were used as metrics for comparing the equilibrium association constant (logK), enthalpy of interaction (ΔH), and the so-called "stoichiometry" (n), a concentration-correction factor.
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14
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Wort JL, Ackermann K, Norman DG, Bode BE. A general model to optimise Cu II labelling efficiency of double-histidine motifs for pulse dipolar EPR applications. Phys Chem Chem Phys 2021; 23:3810-3819. [PMID: 33533341 DOI: 10.1039/d0cp06196d] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the dH motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, depending upon pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.
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Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - David G Norman
- School of Life Sciences, University of Dundee, Medical Sciences Institute, Dundee, DD1 5EH, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
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15
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TcpC inhibits toll-like receptor signaling pathway by serving as an E3 ubiquitin ligase that promotes degradation of myeloid differentiation factor 88. PLoS Pathog 2021; 17:e1009481. [PMID: 33788895 PMCID: PMC8041205 DOI: 10.1371/journal.ppat.1009481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/12/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
TcpC is a virulence factor of uropathogenic E. coli (UPEC). It was found that TIR domain of TcpC impedes TLR signaling by direct association with MyD88. It has been a long-standing question whether bacterial pathogens have evolved a mechanism to manipulate MyD88 degradation by ubiquitin-proteasome pathway. Here, we show that TcpC is a MyD88-targeted E3 ubiquitin ligase. Kidney macrophages from mice with pyelonephritis induced by TcpC-secreting UPEC showed significantly decreased MyD88 protein levels. Recombinant TcpC (rTcpC) dose-dependently inhibited protein but not mRNA levels of MyD88 in macrophages. Moreover, rTcpC significantly promoted MyD88 ubiquitination and accumulation in proteasomes in macrophages. Cys12 and Trp106 in TcpC are crucial amino acids in maintaining its E3 activity. Therefore, TcpC blocks TLR signaling pathway by degradation of MyD88 through ubiquitin-proteasome system. Our findings provide not only a novel biochemical mechanism underlying TcpC-medicated immune evasion, but also the first example that bacterial pathogens inhibit MyD88-mediated signaling pathway by virulence factors that function as E3 ubiquitin ligase. Toll/interleukin-1 receptor domain-containing protein encoded by E. coli (TcpC) is an important virulence factor in many strains of uropathogenic E. coli (UPEC). TcpC-mediated evasion of innate immunity plays an important role in the pathogenesis of UPEC caused urinary tract infection (UTI) including pyelonephritis. In the present study, we show TcpC is an E3 ubiquitin ligase that promotes ubiquitination and degradation of MyD88, hereby blocking the TLR signaling pathway. Our findings not only illuminate the novel biochemical mechanisms underlying TcpC-mediated evasion of innate immunity, but also provide the first example that bacterial pathogens can subvert TLR signaling pathway through virulence factors that function as MyD88-targeted E3 ubiquitin ligase.
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16
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Bastos M, Velazquez-Campoy A. Isothermal titration calorimetry (ITC): a standard operating procedure (SOP). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:363-371. [PMID: 33665758 DOI: 10.1007/s00249-021-01509-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/05/2020] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
Isothermal titration calorimetry (ITC) is currently widely used in many applied areas of research, spanning protein-ligand binding, metal-ligand interactions, DNA/DNA or protein/DNA interactions, partition to membranes, and polymer surfactant interactions, to mention just a few. This is due to the availability of commercial instruments, and thus the production and spread of an accepted and widely followed SOP is felt by most users, in an effort to produce results that are scientifically correct and comparable. Therefore, within the efforts of Working Group 4 of the ARBRE-MOBIEU COST Action (CA15126), this ITC SOP was generated, alongside SOPs for several other biophysical techniques. Here, we discuss the factors that are fundamental for good experimental design and that need to be carefully considered, as well as machine calibration, in particular chemical calibration, linked to another outcome of Working Group 4 on ITC benchmarking, to be also published in this Special Issue.
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Affiliation(s)
- Margarida Bastos
- CIQ-UP, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, and Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Fundacion ARAID, Government of Aragon, Zaragoza, Spain
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17
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Abstract
Calorimetry is a classical biophysical method that by definition measures heat. In isothermal titration calorimetry (ITC), the heat is the result of titrating interacting components together and allows direct determination of the thermodynamics for this process. The measured heat reflects the enthalpy change (ΔH), and the prospect of determining this in biological systems where high-resolution structural information is available has led to the possibility of rational thermodynamics-guided design of ligands. Although there are limitations to this approach due to the participation of solvent in the thermodynamics, ITC has become an established technique in many labs providing a valuable tool with which to quantify protein-protein interactions. With careful use, ITC can also provide additional insights into the binding process or be used in increasingly complex systems and where interaction is coupled to other molecular events.
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18
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Ge X, Chen L, Li D, Liu R, Ge G. Estimation of non-constant variance in isothermal titration calorimetry using an ITC measurement model. PLoS One 2020; 15:e0244739. [PMID: 33378411 PMCID: PMC7773272 DOI: 10.1371/journal.pone.0244739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the gold standard for accurate measurement of thermodynamic parameters in solution reactions. In the data processing of ITC, the non-constant variance of the heat requires special consideration. The variance function approach has been successfully applied in previous studies, but is found to fail under certain conditions in this work. Here, an explicit ITC measurement model consisting of main thermal effects and error components has been proposed to quantitatively evaluate and predict the non-constant variance of the heat data under various conditions. Monte Carlo simulation shows that the ITC measurement model provides higher accuracy and flexibility than variance function in high c-value reactions or with additional error components, for example, originated from the fluctuation of the concentrations or other properties of the solutions. The experimental design of basic error evaluation is optimized accordingly and verified by both Monte Carlo simulation and experiments. An easy-to-run Python source code is provided to illustrate the establishment of the ITC measurement model and the estimation of heat variances. The accurate and reliable non-constant variance of heat is helpful to the application of weighted least squares regression, the proper evaluation or selection of the reaction model.
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Affiliation(s)
- Xiujie Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lan Chen
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Dexing Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
| | - Renxiao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Guanglu Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
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19
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Glöckner S, Klebe G. Simultaneous determination of thermodynamic and kinetic data by isothermal titration calorimetry. Biochim Biophys Acta Gen Subj 2020; 1865:129772. [PMID: 33191201 DOI: 10.1016/j.bbagen.2020.129772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Thermodynamic and binding kinetic data increasingly support and guide the drug optimization process. METHODS Because ITC thermograms contain binding thermodynamic and kinetic information, an efficient protocol for the simultaneous extraction of thermodynamic and kinetic data for 1:1 protein ligand reactions from AFFINImeter kinITC in one single experiment are presented. RESULTS The effort to apply this protocol requires the same time as for the standard protocol but increases the precision of both thermodynamic and kinetic data. CONCLUSIONS The protocol enables reliable extraction of both thermodynamic and kinetic data for 1:1 protein-ligand binding reactions with improved precision compared to the 'standard protocol'. GENERAL SIGNIFICANCE Thermodynamic and kinetic data are recorded under exactly the same conditions in solution without any labeling or immobilization from a protein sample that is not 100% active and would otherwise render the extraction of kinetic parameters impossible.
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Affiliation(s)
- Steffen Glöckner
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
| | - Gerhard Klebe
- Philipps-University Marburg, Institute for Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany.
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20
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Kellett K, Slochower DR, Schauperl M, Duggan BM, Gilson MK. Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J Comput Aided Mol Des 2020; 35:95-104. [PMID: 33037548 DOI: 10.1007/s10822-020-00350-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022]
Abstract
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exothermic. Overall, modifications at the 3' position of β-CD, which is at the secondary face, weaken binding by several kJ/mol relative to native β-CD, while modifications at the 6' position (primary face) maintain or somewhat reduce the binding affinity. The variations in binding enthalpy are larger than the variations in binding free energy, so entropy-enthalpy compensation is observed. Characterization of the bound conformations with NOESY NMR shows that the polar groups of the guests may be situated at either face, depending on the host molecule, and, in some cases, both orientations are populated. The present results were used in the SAMPL7 blinded prediction challenge whose results are detailed in the same special issue of JCAMD.
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Affiliation(s)
- K Kellett
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - D R Slochower
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M Schauperl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - B M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA.
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21
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Monti A, Sturlese M, Caporale A, Roger JDA, Mascanzoni F, Ruvo M, Doti N. Design, synthesis, structural analysis and biochemical studies of stapled AIF(370-394) analogues as ligand of CypA. Biochim Biophys Acta Gen Subj 2020; 1864:129717. [PMID: 32861757 DOI: 10.1016/j.bbagen.2020.129717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/28/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The neuronal apoptotic process requires the nuclear translocation of Apoptosis Inducing Factor (AIF) in complex with Cyclophilin A (CypA) with consequent chromatin condensation and DNA degradation events. Targeting CypA by delivering an AIF-blocking peptide (AIF(370-394)) provides a significant neuroprotection, demonstrating the biological relevance of the AIF/CypA complex. To date pharmaceutical compounds targeting this complex are missing. METHODS We designed and synthesized a set of mono and bicyclic AIF(370-394) analogs containing both disulfide and 1,2,3-triazole bridges, in the attempt to both stabilize the peptide conformation and improve its binding affinity to CypA. Peptide structures in solution and in complex with CypA have been studied by circular dichroism (CD), Nuclear Magnetic Resonance (NMR) and molecular modeling. The ability of stapled peptides to interact with CypA was evaluated by using Epic Corning label free technique and Isothermal Titration Calorimetry experiments. RESULTS We identified a stapled peptide analogue of AIF(370-394) with a ten-fold improved affinity for CypA. Molecular modeling studies reveal that the new peptide acquires β-turn/β-fold structures and shares with the parent molecule the same binding region on CypA. CONCLUSIONS Data obtained provide invaluable assistance in designing new ligand of CypA for therapeutic approaches in neurodegenerative diseases. GENERAL SIGNIFICANCE Due to the crucial role of AIF/CypA complex formation in neurodegeneration, identification of selective inhibitors is of high importance for targeted therapies. We describe new bicyclic peptide inhibitors with improved affinity for CypA, investigating the kinetic, thermodynamic and structural effects of conformational constraints on the protein-ligand interaction, and their utility for drug design.
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Affiliation(s)
- Alessandra Monti
- Istituto di Biostrutture e Bioimmagini-CNR; Via Mezzocannone, 16, 80134 Napoli, Italy; DISTABIF, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, CE, Italy
| | - Mattia Sturlese
- Molecular Modeling Section, Dipartimento di Scienze del Farmaco, Università di Padova, via F. Marzolo 5, 35131 Padova, Italy
| | - Andrea Caporale
- Istituto di Biostrutture e Bioimmagini-CNR; Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Jessica De Almeida Roger
- Molecular Modeling Section, Dipartimento di Scienze del Farmaco, Università di Padova, via F. Marzolo 5, 35131 Padova, Italy
| | - Fabiola Mascanzoni
- Istituto di Biostrutture e Bioimmagini-CNR; Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini-CNR; Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini-CNR; Via Mezzocannone, 16, 80134 Napoli, Italy.
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22
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Maruno T, Ohkubo T, Uchiyama S. Stirring rate affects thermodynamics and unfolding kinetics in isothermal titration calorimetry. J Biochem 2020; 168:53-62. [PMID: 32134445 DOI: 10.1093/jb/mvaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
Isothermal titration calorimetry (ITC) directly provides thermodynamic parameters depicting the energetics of intermolecular interactions in solution. During ITC experiments, a titration syringe with a paddle is continuously rotating to promote a homogeneous mixing. Here, we clarified that the shape of the paddles (flat, corkscrew and small-pitched corkscrew) and the stirring rates influence on the thermodynamic parameters of protein-ligand interaction. Stirring with the flat paddle at lower and higher rate both yielded a lower exothermic heat due to different reasons. The complete reaction with no incompetent fractions was achieved only when the stirring was performed at 500 or 750 rpm using the small-pitched corkscrew paddle. The evaluation of the protein solution after 1,500 rpm stirring indicated that proteins in the soluble fraction decreased to 94% of the initial amount, among which 6% was at an unfolded state. In addition, a significant increase of micron aggregates was confirmed. Furthermore, a new approach for the determination of the unfolding kinetics based on the time dependence of the total reaction heat was developed. This study demonstrates that a proper stirring rate and paddle shape are essential for the reliable estimation of thermodynamic parameters in ITC experiments.
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Affiliation(s)
- Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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23
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Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W. Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140404. [DOI: 10.1016/j.bbapap.2020.140404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/25/2020] [Indexed: 01/31/2023]
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24
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Samuelsen L, Holm R, Lathuile A, Schönbeck C. Determination of acidity constants for weak acids and bases by isothermal titration calorimetry. J Pharm Biomed Anal 2020; 184:113206. [PMID: 32126458 DOI: 10.1016/j.jpba.2020.113206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 10/24/2022]
Abstract
The advantage of isothermal titration calorimetry (ITC) to determine the acid dissociation constant (pKa value) is the simultaneous determination of the binding constant and binding enthalpy, as well as being precise and easy to use. The pKa can be calculated from the binding constant, and the temperature dependency of the pKa can be calculated from the binding enthalpy. The use of ITC to study protonation reactions is less common compared to its more conventional use of studying macromolecules and ligands. Water will influence the equilibrium due to autoionization, meaning that both the conjugate base and acid will exist in the sample cell at the beginning of the experiment. These differences are accounted for by optimizing the theoretical model used to estimate the binding constant and binding enthalpy. Through simulations and experimental measurements, we show that ITC can be used to determine the pKa for ibuprofen, ascorbic acid, 2-morpholin-4-ylethanesulfonic acid and paracetamol. The pKa values were consistent with potentiometric or spectrophotometric determinations as well as literature values. Optimizing the theoretical model does not lead to an improved determination, so the "one set of sites" model is adequate for the determination of pKa values.
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Affiliation(s)
- Lisa Samuelsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - René Holm
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark; Drug Product Development, Janssen Research and Development, Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Audrey Lathuile
- Drug Product Development, Janssen Research and Development, Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Christian Schönbeck
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
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25
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Krishnamoorthy GK, Alluvada P, Hameed Mohammed Sherieff S, Kwa T, Krishnamoorthy J. Isothermal titration calorimetry and surface plasmon resonance analysis using the dynamic approach. Biochem Biophys Rep 2020; 21:100712. [PMID: 31890903 PMCID: PMC6926116 DOI: 10.1016/j.bbrep.2019.100712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/24/2022] Open
Abstract
Biophysical techniques such as isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are routinely used to ascertain the global binding mechanisms of protein-protein or protein-ligand interaction. Recently, Dumas etal, have explicitly modelled the instrument response of the ligand dilution and analysed the ITC thermogram to obtain kinetic rate constants. Adopting a similar approach, we have integrated the dynamic instrument response with the binding mechanism to simulate the ITC profiles of equivalent and independent binding sites, equivalent and sequential binding sites and aggregating systems. The results were benchmarked against the standard commercial software Origin-ITC. Further, the experimental ITC chromatograms of 2′-CMP + RNASE and BH3I-1 + hBCLXL interactions were analysed and shown to be comparable with that of the conventional analysis. Dynamic approach was applied to simulate the SPR profiles of a two-state model, and could reproduce the experimental profile accurately. Incorporated instrument response within the kinetic framework using dynamic approach to analyse ITC and SPR data. Different modelling approaches for instrument response such as lumped and kinetic modelling were compared and their equivalence were shown. (1) equivalent single site, (2) equivalent sequential sites, (3) equivalent parallel sites and (4) aggregating molecular system were modelled using dynamic approach.
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26
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Zhan YY, Jiang QC, Ishii K, Koide T, Kobayashi O, Kojima T, Takahashi S, Tachikawa M, Uchiyama S, Hiraoka S. Polarizability and isotope effects on dispersion interactions in water. Commun Chem 2019. [DOI: 10.1038/s42004-019-0242-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractTrue understanding of dispersion interaction in solution remains elusive because of difficulty in the precise evaluation of its interaction energy. Here, the effect of substituents with different polarizability on dispersion interactions in water is discussed based on the thermodynamic parameters determined by isothermal titration calorimetry for the formation of discrete aggregates from gear-shaped amphiphiles (GSAs). The substituents with higher polarizability enthalpically more stabilize the nanocube, which is due to stronger dispersion interactions and to the hydrophobic effect. The differences in the thermodynamic parameters for the nanocubes from the GSAs with CH3 and CD3 groups are also discussed to lead to the conclusion that the H/D isotope effect on dispersion interactions is negligibly small, which is due to almost perfect entropy-enthalpy compensation between the two isotopomers.
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27
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Hansen LD, Quinn C. Obtaining precise and accurate results by ITC. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2019; 48:825-835. [PMID: 31555842 DOI: 10.1007/s00249-019-01399-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Acquisition of precise and accurate results by isothermal titration calorimetry (ITC) can be achieved through thoughtful experimental design and modeling and careful experimental operations. Large reported errors in ITC results in determinations of stoichiometries, equilibrium constants and enthalpy changes for ligand binding to proteins are the consequence of poor experiment design, failure to properly calibrate and test instruments and protocols, lack of controls, errors in solution preparation, and incorrect data analyses. Analysis of a recent report that claimed to have determined the "repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein-ligand binding reaction" by ITC is used to illustrate how to improve ITC operations and results. The analysis shows that the reported results are misleading because calorimeters were not calibrated, operating parameters were not optimized, errors were made in solution preparations, and data analysis was not optimized. As a consequence, the results do not provide a valid comparison of the capabilities of the calorimeters included in the study. A proposal that reaction of acetazolamide with carbonic anhydrase II be used as a comparison standard for testing ITCs and procedures is problematic because the binding constant is too large and for several other reasons discussed in the paper. Requirements for obtaining precise and accurate results by ITC are discussed and experimental results are presented to illustrate the precision and accuracy attainable with low volume ITCs. The problem of the blank correction is identified as the limiting factor in obtaining accurate results by ITC.
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Affiliation(s)
- Lee D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
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28
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Fernandes CAH, Perez AM, Barros AC, Dreyer TR, da Silva MS, Morea EGO, Fontes MRM, Cano MIN. Dual cellular localization of the Leishmania amazonensis Rbp38 (LaRbp38) explains its affinity for telomeric and mitochondrial DNA. Biochimie 2019; 162:15-25. [PMID: 30930281 DOI: 10.1016/j.biochi.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Rbp38 is a protein exclusively found in trypanosomatid parasites, including Leishmania amazonensis, the etiologic agent of tegumentar leishmaniasis in the Americas. The protein was first described as a Leishmania tarentolae mitochondrial RNA binding protein. Later, it was shown that the trypanosomes Rbp38 orthologues were exclusively found in the mitochondria and involved in the stabilization and replication of kinetoplast DNA (kDNA). In contrast, L. amazonensis Rbp38 (LaRbp38), co-purifies with telomerase activity and interacts not only with kDNA but also with telomeric DNA, although shares with its counterparts high sequence identity and a putative N-terminal mitochondrial targeting signal (MTS). To understand how LaRbp38 interacts both with nuclear and kDNA, we have first investigated its subcellular localization. Using hydroxy-urea synchronized L. amazonensis promastigotes we could show that LaRbp38 shuttles from mitochondria to the nucleus at late S and G2 phases. Further, we identified a non-classical nuclear localization signal (NLS) at LaRbp38 C-terminal that binds with importin alpha, a protein involved in the nuclear transport of several proteins. Also, we obtained LaRbp38 truncated forms among which, some of them also showed an affinity for both telomeric DNA and kDNA. Analysis of these truncated forms showed that LaRbp38 DNA-binding region is located between amino acid residues 95-235. Together, our findings strongly suggest that LaRbp38 is multifunctional with dual subcellular localization.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil; Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Arina M Perez
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Andrea C Barros
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcelo S da Silva
- Laboratório Especial de Ciclo Cellular, (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
| | - Edna Gicela O Morea
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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29
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Song Z, Liu J, Hou Y, Yuan W, Yang B. Study on the interaction between pyridoxal and CopC by multi-spectroscopy and docking methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 208:214-221. [PMID: 30321861 DOI: 10.1016/j.saa.2018.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
The interaction between pyridoxal hydrochloride (HQ) and apoCopC was investigated using Fourier transform infrared spectroscopy (FTIR), isothermal titration calorimetry (ITC), circular dichroism (CD), fluorescence spectroscopy, three-dimensional (3D) fluorescence spectroscopy, fluorescence lifetime, TNS fluorescence and docking methods. FTIR, CD, TNS fluorescence and fluorescence lifetime experiments suggested that the apoCopC conformation was altered by HQ with an increase in the random coil content and a reduction in the β-sheet content. In addition, the data from fluorescence spectroscopy, 3D fluorescence spectroscopy and molecular docking revealed that the binding site of HQ was located in the hydrophobic area of apoCopC, and a redshift of the HQ fluorescence spectra was observed. Furthermore, ITC and fluorescence quenching data manifested that the binding ratio of HQ and apoCopC was 1:1, and the forming constant was calculated to be (7.06 ± 0.21) × 105 M-1. The thermodynamic parameters ΔH and ΔS suggested that the formation of a CopC-HQ complex depended on the hydrophobic force. Furthermore, the average binding distance between tryptophan in apoCopC and HQ was determined by means of Förster non-radioactive resonance energy transfer and molecular docking. The results agreed well with each other. As a redox switch in the modulation of copper, the interaction of apoCopC with small molecules will affect the action of the redox switch. These findings could provide useful information to illustrate the copper regulation mechanism.
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Affiliation(s)
- Zhen Song
- Taiyuan Normal University Department of Chemistry, Jinzhong 030619, China
| | - Jin Liu
- Hubei Provincial Corps Hospital, Chinese People's Armed Police Forces, Wuhan 430061, China
| | - Yuxin Hou
- Taiyuan Normal University Department of Chemistry, Jinzhong 030619, China
| | - Wen Yuan
- Taiyuan Normal University Department of Chemistry, Jinzhong 030619, China
| | - Binsheng Yang
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China.
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Song Y, Song Z, Yang B. Spectral Study on the Interactions Among Cu(II), Doxorubicin and CopC. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-8284-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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vWA proteins of Leptospira interrogans induce hemorrhage in leptospirosis by competitive inhibition of vWF/GPIb-mediated platelet aggregation. EBioMedicine 2018; 37:428-441. [PMID: 30337247 PMCID: PMC6284457 DOI: 10.1016/j.ebiom.2018.10.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUD Leptospira interrogans is the major causative agent of leptospirosis, a worldwide zoonotic disease. Hemorrhage is a typical pathological feature of leptospirosis. Binding of von Willebrand factor (vWF) to platelet glycoprotein-Ibα (GPIbα) is a crucial step in initiation of platelet aggregation. The products of L. interrogans vwa-I and vwa-II genes contain vWF-A domains, but their ability to induce hemorrhage has not been determined. METHODS Human (Hu)-platelet- and Hu-GPIbα-binding abilities of the recombinant proteins expressed by L. interrogans strain Lai vwa-I and vwa-II genes (rLep-vWA-I and rLep-vWA-II) were detected by flowcytometry, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Hu-platelet aggregation and its signaling kinases and active components were detected by lumiaggregometry, Western analysis, spectrophotometry and confocal microscopy. Hu-GPIbα-binding sites in rLep-vWA-I and rLep-vWA-II were identified by SPR/ITC measurements. FINDINGS Both rLep-vWA-I and rLep-vWA-II were able to bind to Hu-platelets and inhibit rHu-vWF/ristocetin-induced Hu-platelet aggregation, but Hu-GPIbα-IgG, rLep-vWA-I-IgG and rLep-vWA-II-IgG blocked this binding or inhibition. SPR and ITC revealed a tight interaction between Hu-GPIbα and rLep-vWA-I/rLep-vWA-II with KD values of 3.87 × 10-7-8.65 × 10-8 M. Hu-GPIbα-binding of rL-vWA-I/rL-vWA-II neither activated the PI3K/AKT-ERK and PLC/PKC kinases nor affected the NO, cGMP, ADP, Ca2+ and TXA2 levels in Hu-platelets. G13/R36/G47 in Lep-vWA-I and G76/Q126 in Lep-vWA-II were confirmed as the Hu-GPIbα-binding sites. Injection of rLep-vWA-I or rLep-vWA-II in mice resulted in diffuse pulmonary and focal renal hemorrhage but this hemorrhage was blocked by rLep-vWA-I-IgG or rLep-vWA-II-IgG. INTERPRETATION The products of L. interrogans vwa-I and vwa-II genes induce hemorrhage by competitive inhibition of vWF-mediated Hu-platelet aggregation.
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Tellinghuisen J. Critique of methods for estimating heats in isothermal titration calorimetry. Anal Biochem 2018; 563:79-86. [PMID: 30149027 DOI: 10.1016/j.ab.2018.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Abstract
Isothermal titration calorimetry data recorded on a MicroCal/Malvern VP-ITC instrument for water-water blanks and for dilution of aqueous solutions of BaCl2 and Ba(NO3)2 are analyzed using Origin software, the freeware NITPIC program, and in-house algorithms, to compare precisions for estimating the heat per injection q. The data cover temperatures 6-47 °C, injection volumes 4-40 μL, and average heats 0-200 μcal. For water-water blanks, where baseline noise limits precision, NITPIC and the in-house algorithm achieve precisions of 0.05 μcal, which is better than Origin by a factor of 4. The precision differences decrease with increasing |q|, becoming insignificant for |q| > 200 μcal. In its default mode, NITPIC underestimates |q| for peaks with incomplete return to baseline, but the shortfall can be largely corrected by overriding the default injection time parameter. The variance estimates from 26 dilution experiments are used to assess the data variance function. The results determine the conditions under which weighted least squares should be used to estimate thermodynamic parameters from ITC data.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
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A novel Fas-binding outer membrane protein and lipopolysaccharide of Leptospira interrogans induce macrophage apoptosis through the Fas/FasL-caspase-8/-3 pathway. Emerg Microbes Infect 2018; 7:135. [PMID: 30061622 PMCID: PMC6066479 DOI: 10.1038/s41426-018-0135-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/18/2018] [Accepted: 06/23/2018] [Indexed: 02/08/2023]
Abstract
Leptospira interrogans is the major causative agent of leptospirosis, an emerging, globally spreading zoonotic infectious disease. The pathogen induces macrophage apoptosis, but the molecular basis and mechanism remain unknown. In the present study, we found that L. interrogans caused apoptosis of phagocytosis-inhibited macrophages, and the product of the L. interrogans LB047 gene (Lep-OMP047) was the unique protein captured by mouse and human Fas proteins. The recombinant expressed Lep-OMP047 (rLep-OMP047) strongly bound mouse and human Fas proteins with equilibrium association constant (KD) values of 5.20 × 10−6 to 2.84 × 10−9 M according to surface plasmon resonance measurement and isothermal titration calorimetry. Flow-cytometric examination showed that 5 μg rLep-OMP047 or 1 μg lipopolysaccharide of L. interrogans (Lep-LPS) caused 43.70% or 21.90% early apoptosis in mouse J774A.1 macrophages and 28.41% or 15.80% for PMA-differentiated human THP-1 macrophages, respectively, but the apoptosis was blocked by Fas-antagonizing IgGs, Fas siRNAs, and caspase-8/-3 inhibitors. Moreover, Lep-OMP047 was significantly upregulated during infection of macrophages. Lep-LPS promoted the expression and cytomembrane translocation of Fas and FasL in macrophages. The JNK and p38 MAPK but not ERK signaling pathways, as well as the transcription factors c-Jun and ATF2 but not CHOP, mediated Lep-LPS-induced Fas/FasL expression and translocation. TLR2 but not TLR4 mediated Lep-LPS-induced JNK/p38 MAPK activation. Therefore, we demonstrated that a novel Fas-binding OMP and LPS of L. interrogans induce macrophage apoptosis through the Fas/FasL-caspase-8/-3 pathway.
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Zhuo W, Peng X, Lin X. Insights into the interaction mechanism between tiagabine hydrochloride and two serum albumins. RSC Adv 2018; 8:24953-24960. [PMID: 35542170 PMCID: PMC9082336 DOI: 10.1039/c8ra04153a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/29/2018] [Indexed: 12/03/2022] Open
Abstract
Tiagabine hydrochloride (TGB) is a widely used anticonvulsive drug for the treatment of epilepsy. To better understand the interactions of TGB with plasma proteins, human serum albumin (HSA) and bovine serum albumin (BSA) were selected as model proteins. TGB slightly increased thermal stability of the proteins as confirmed by VP-capillary differential scanning calorimetric (DSC) measurements. Isothermal titration calorimeter (ITC) results showed that TGB could be combined with HSA and BSA moderately, which was also corroborated by fluorescence analysis. Besides, the thermodynamic parameters (ΔH > 0, ΔS > 0) indicated that hydrophobic forces played a major role in the formulation of TGB-HSA and TGB-BSA complexes. Moreover, the main binding sites of TGB to HSA and BSA were also examined by classical fluorescent probe (dansylsarcosine and dansylamide) experiments, showing that TGB and dansylsarcosine competitively interacted with HSA and BSA at the same binding sites. Additionally, TGB had no obvious effect on the conformation change of HSA and BSA as indicated by spectroscopic analyses. This study provides useful information about the interaction mechanism of TGB and serum albumins, which could help to better utilize TGB in biomedical field.
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Affiliation(s)
- Weiling Zhuo
- School of Chemical Engineering, Sichuan University Chengdu 610065 People's Republic of China +86 028 85990908 +86 02885990908
| | - Xilin Peng
- Sinopharm Chuankang Pharmaceutical Co., Ltd. Chengdu 611731 People's Republic of China
| | - Xiang Lin
- School of Chemical Engineering, Sichuan University Chengdu 610065 People's Republic of China +86 028 85990908 +86 02885990908
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Tellinghuisen J. Can you trust the parametric standard errors in nonlinear least squares? Yes, with provisos. Biochim Biophys Acta Gen Subj 2017; 1862:886-894. [PMID: 29289616 DOI: 10.1016/j.bbagen.2017.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 12/14/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND Questions about the reliability of parametric standard errors (SEs) from nonlinear least squares (LS) algorithms have led to a general mistrust of these precision estimators that is often unwarranted. METHODS The importance of non-Gaussian parameter distributions is illustrated by converting linear models to nonlinear by substituting eA, ln A, and 1/A for a linear parameter a. Monte Carlo (MC) simulations characterize parameter distributions in more complex cases, including when data have varying uncertainty and should be weighted, but weights are neglected. This situation leads to loss of precision and erroneous parametric SEs, as is illustrated for the Lineweaver-Burk analysis of enzyme kinetics data and the analysis of isothermal titration calorimetry data. RESULTS Non-Gaussian parameter distributions are generally asymmetric and biased. However, when the parametric SE is <10% of the magnitude of the parameter, both the bias and the asymmetry can usually be ignored. Sometimes nonlinear estimators can be redefined to give more normal distributions and better convergence properties. CONCLUSION Variable data uncertainty, or heteroscedasticity, can sometimes be handled by data transforms but more generally requires weighted LS, which in turn require knowledge of the data variance. GENERAL SIGNIFICANCE Parametric SEs are rigorously correct in linear LS under the usual assumptions, and are a trustworthy approximation in nonlinear LS provided they are sufficiently small - a condition favored by the abundant, precise data routinely collected in many modern instrumental methods.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University Nashville, TN 37235, USA.
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Kantonen SA, Henriksen NM, Gilson MK. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta Gen Subj 2017; 1862:692-704. [PMID: 29221984 DOI: 10.1016/j.bbagen.2017.11.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/15/2017] [Accepted: 11/28/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND In theory, binding enthalpies directly obtained from calorimetry (such as ITC) and the temperature dependence of the binding free energy (van't Hoff method) should agree. However, previous studies have often found them to be discrepant. METHODS Experimental binding enthalpies (both calorimetric and van't Hoff) are obtained for two host-guest pairs using ITC, and the discrepancy between the two enthalpies is examined. Modeling of artificial ITC data is also used to examine how different sources of error propagate to both types of binding enthalpies. RESULTS For the host-guest pairs examined here, good agreement, to within about 0.4kcal/mol, is obtained between the two enthalpies. Additionally, using artificial data, we find that different sources of error propagate to either enthalpy uniquely, with concentration error and heat error propagating primarily to calorimetric and van't Hoff enthalpies, respectively. CONCLUSIONS With modern calorimeters, good agreement between van't Hoff and calorimetric enthalpies should be achievable, barring issues due to non-ideality or unanticipated measurement pathologies. Indeed, disagreement between the two can serve as a flag for error-prone datasets. A review of the underlying theory supports the expectation that these two quantities should be in agreement. GENERAL SIGNIFICANCE We address and arguably resolve long-standing questions regarding the relationship between calorimetric and van't Hoff enthalpies. In addition, we show that comparison of these two quantities can be used as an internal consistency check of a calorimetry study.
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Affiliation(s)
- Samuel A Kantonen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736, USA.
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