1
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Vernon TN, Terrell JR, Albrecht AV, Germann MW, Wilson WD, Poon GMK. Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors. Structure 2024; 32:83-96.e4. [PMID: 38042148 DOI: 10.1016/j.str.2023.11.003] [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: 08/08/2023] [Revised: 10/12/2023] [Accepted: 11/07/2023] [Indexed: 12/04/2023]
Abstract
Nucleobases such as inosine have been extensively utilized to map direct contacts by proteins in the DNA groove. Their deployment as targeted probes of dynamics and hydration, which are dominant thermodynamic drivers of affinity and specificity, has been limited by a paucity of suitable experimental models. We report a joint crystallographic, thermodynamic, and computational study of the bidentate complex of the arginine side chain with a Watson-Crick guanine (Arg×GC), a highly specific configuration adopted by major transcription factors throughout the eukaryotic branches in the Tree of Life. Using the ETS-family factor PU.1 as a high-resolution structural framework, inosine substitution for guanine resulted in a sharp dissection of conformational dynamics and hydration and elucidated their role in the DNA specificity of PU.1. Our work suggests an under-exploited utility of modified nucleobases in untangling the structural thermodynamics of interactions, such as the Arg×GC motif, where direct and indirect readout are tightly integrated.
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Affiliation(s)
- Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
| | - J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
| | - Amanda V Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; Department of Biology, Georgia State University, Atlanta, GA 30302, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, USA.
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2
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Chen J, Qu C, Lu M, Zhang M, Wu Y, Gao C, Huang Q, Cai P. Extracellular polymeric substances and mineral interfacial reactions control the simultaneous immobilization and reduction of arsenic (As(V)). JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131651. [PMID: 37245361 DOI: 10.1016/j.jhazmat.2023.131651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 05/14/2023] [Indexed: 05/30/2023]
Abstract
Extracellular polymeric substances (EPS) play a crucial role in controlling the mobility and bioavailability of heavy metal(loid)s in water, soils, and sediments. The formation of EPS-mineral complex changes the reactivity of the end-member materials. However, little is known about the adsorption and redox mechanisms of arsenate (As(V)) in EPS and EPS-mineral complexes. Here we examined the reaction sites, valence state, thermodynamic parameters and distribution of As in the complexes using potentiometric titration, isothermal titration calorimetry (ITC), FTIR, XPS, and SEM-EDS. The results showed that ∼54% of As(V) was reduced to As(III) by EPS, potentially driven by an enthalpy change (ΔH) of - 24.95 kJ/mol. The EPS coating on minerals clearly affected the reactivity to As(V). The strong masking of functional sites between EPS and goethite inhibited both the adsorption and reduction of As. In contrast, the weak binding of EPS onto montmorillonite retained more reactive sites for the reaction with As. Meanwhile, montmorillonite facilitated the immobilization of As to EPS through the formation of As-organic bounds. Our findings deepen the understanding of EPS-mineral interfacial reactions in controlling the redox and mobility of As, and the knowledge is important for predicting the behavior of As in natural environments.
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Affiliation(s)
- Jinzhao Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenchen Qu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
| | - Man Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yichao Wu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunhui Gao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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3
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Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 2023; 14:714. [PMID: 36759615 PMCID: PMC9911696 DOI: 10.1038/s41467-023-36184-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
RNA flexibility is reflected in its heterogeneous conformation. Through direct visualization using atomic force microscopy (AFM) and the adenosylcobalamin riboswitch aptamer domain as an example, we show that a single RNA sequence folds into conformationally and architecturally heterogeneous structures under near-physiological solution conditions. Recapitulated 3D topological structures from AFM molecular surfaces reveal that all conformers share the same secondary structural elements. Only a population-weighted cohort, not any single conformer, including the crystal structure, can account for the ensemble behaviors observed by small-angle X-ray scattering (SAXS). All conformers except one are functionally active in terms of ligand binding. Our findings provide direct visual evidence that the sequence-structure relationship of RNA under physiologically relevant solution conditions is more complex than the one-to-one relationship for well-structured proteins. The direct visualization of conformational and architectural ensembles at the single-molecule level in solution may suggest new approaches to RNA structural analyses.
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4
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Lee YT, Fan L, Ding J, Wang YX. Combining Biophysical Methods for Structure-Function Analyses of RNA in Solution. Methods Mol Biol 2023; 2568:165-177. [PMID: 36227568 DOI: 10.1007/978-1-0716-2687-0_11] [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: 06/16/2023]
Abstract
RNA-level regulation by riboswitches relies on the specific binding of small metabolites to the aptamer domain to trigger substantial conformational changes that affect transcription or translation. Although several biophysical methods have been employed to study such RNAs, the utility of any one single method is limited. Hybrid approaches, therefore, are essential to better characterize these intrinsically dynamic molecules and elucidate their regulatory mechanisms driven by ligand-induced conformational changes. This chapter outlines procedures for biochemical and biophysical characterization of RNA that employs a combination of solution-based methods: isothermal titration calorimetry (ITC), small-angle X-ray scattering (SAXS), and atomic force microscopy (AFM). Collectively, these tools provide a semi-quantitative assessment of the thermodynamics associated with ligand binding and subsequent conformational changes.
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Affiliation(s)
- Yun-Tzai Lee
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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5
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Dumas P. Isothermal titration calorimetry in the single-injection mode with imperfect mixing. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:77-84. [PMID: 34999938 DOI: 10.1007/s00249-021-01588-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/19/2021] [Accepted: 12/24/2021] [Indexed: 05/23/2023]
Abstract
Isothermal titration calorimetry (ITC) is now a method of choice to obtain thermodynamic information about the interaction between two molecular partners. Most often, the method in use is the so-called multiple-injection method (MIM) consisting in distinct short-time injections of the titrant separated by sufficient delay to reach equilibrium before each new injection. However, an alternative single-injection method (SIM) exists. It consists in a unique continuous injection and, despite the fact that it is quite simple and generally faster than MIM, it is very little used. The goal of this work is to reconsider its theoretical basis. A new equation taking into account the effect of dilution resulting from the continuous titration process is obtained. It allows to consider efficiently the continuum of possibilities from perfect to imperfect mixing of the cell content. It is shown that, to good approximation, imperfect mixing can be accounted for by considering the cell volume as an adjustable parameter. Most likely, this should lead to an artificial increase of it, although one cannot reject the possibility of a decrease. The processing of experimental data on the interaction of Ba++ with 18-crown-6 from led to an increase by 6.9%, which resulted in a much better fit of the titration curve and improved results on the association constant Ka and enthalpy variation ∆H. A criterion is also obtained on the maximum injection rate to be used for maintaining quasi-equilibrium during the whole titration for the association-dissociation mechanism [Formula: see text].
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Affiliation(s)
- Philippe Dumas
- Department of Integrative Structural Biology, IGBMC, Strasbourg University, ESBS, 1 rue Laurent Fries, 67404, Illkirch CEDEX, France.
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6
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Chang JW, Armaou A, Rioux RM. Continuous Injection Isothermal Titration Calorimetry for In Situ Evaluation of Thermodynamic Binding Properties of Ligand-Receptor Binding Models. J Phys Chem B 2021; 125:8075-8087. [PMID: 34259524 DOI: 10.1021/acs.jpcb.1c01821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We utilize a continuous injection approach (CIA) rather than the traditional incremental injection approach (IIA) to deliver ligand (or receptor) to the calorimeter cell to evaluate thermodynamic binding parameters for three common ligand-receptor binding models-single independent, competitive, and two independent binding sites-using isothermal titration calorimetry (ITC). A general mathematical expression for the binding isotherm for any binding stoichiometry under continuous delivery of ligand (or receptor) resulting in an analytical solution for the thermodynamic binding parameters is presented. The advantages of CIA include reduction in experimental time, estimation of thermodynamic binding parameter values, and automation of the experiment since thermodynamic parameters are estimated in situ. We demonstrate the inherent advantages of CIA over IIA for the three binding models. For the single independent site model, we utilized the binding of Ba2+ ions to ethylenediaminetetraacetic acid (EDTA), while competitive binding was captured by titration of Ca2+ ions into a buffered solution of Ba2+ and EDTA. We experimentally simulated a two independent binding site system by injecting Ca2+ into a solution of EDTA and 1,3-diaminopropane-N,N,N',N'-tetraacetic acid (DPTA). The results demonstrate estimation of thermodynamic parameters with greater confidence and simultaneous reduction in the experimental time of 83% and titrating reagent of 50%, as compared to IIA.
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Affiliation(s)
- Ji Woong Chang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemical Engineering, Kumoh National Institute of Technology, Gumi-si, Gyeongsangbuk-do 39177, South Korea
| | - Antonios Armaou
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,FORTH Institute of Chemical Engineering Sciences, Rio 26504, Greece
| | - Robert M Rioux
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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7
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He T, Wang K, Zhao L, Chen Y, Zhou W, Liu F, Hu Z. Interaction with longan seed polyphenols affects the structure and digestion properties of maize starch. Carbohydr Polym 2021; 256:117537. [PMID: 33483053 DOI: 10.1016/j.carbpol.2020.117537] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/01/2022]
Abstract
This study investigated effects of longan seed polyphenols (LSPs) on the structure and digestion properties of starch, and discussed the interaction mechanism between starch and LSPs. The results showed cooking with 20 % LSPs did not change amylopectin chain length distribution of normal maize starch, however, the amylose content was reduced from 21.60 to 14.03 %. This suggests LSPs may interact with starch via non-covalent bond. Isothermal titration microcalorimetry and XRD results confirmed the existence of non-covalent interaction, and indicated that LSPs may enter the hydrophobic cavity of amylose, forming V-type inclusion complex. LSPs did not affect gelatinization temperatures of maize starch, whereas 20 % LSPs decreased the enthalpy change by about 26 %. The digestion results indicate significant inhibition effect of LSPs on the digestion of cooked starch, attributing to the interaction of LSPs with starch. These suggest potential applications of LSPs as functional ingredients in modulating postprandial glycemic response of starchy food.
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Affiliation(s)
- Ting He
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Wang
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Zhao
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Chen
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxia Zhou
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Fangmei Liu
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Tea and Tourism Industry Development Service Center of Anhua County, Yiyang, Hunan, 413500, China
| | - Zhuoyan Hu
- College of Food Science, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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8
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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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9
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Esaki S, Evich MG, Erlitzki N, Germann MW, Poon GMK. Multiple DNA-binding modes for the ETS family transcription factor PU.1. J Biol Chem 2017; 292:16044-16054. [PMID: 28790174 DOI: 10.1074/jbc.m117.798207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/07/2017] [Indexed: 01/17/2023] Open
Abstract
The eponymous DNA-binding domain of ETS (E26 transformation-specific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level.
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Affiliation(s)
| | | | | | | | - Gregory M K Poon
- From the Departments of Chemistry and .,the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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10
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Lounis FM, Chamieh J, Leclercq L, Gonzalez P, Geneste A, Prelot B, Cottet H. Interactions between Oppositely Charged Polyelectrolytes by Isothermal Titration Calorimetry: Effect of Ionic Strength and Charge Density. J Phys Chem B 2017; 121:2684-2694. [DOI: 10.1021/acs.jpcb.6b11907] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Feriel Meriem Lounis
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC
1706, 34095 Montpellier
Cedex 5, France
| | - Joseph Chamieh
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC
1706, 34095 Montpellier
Cedex 5, France
| | - Laurent Leclercq
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC
1706, 34095 Montpellier
Cedex 5, France
| | - Philippe Gonzalez
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC
1706, 34095 Montpellier
Cedex 5, France
| | - Amine Geneste
- Institut
Charles Gerhardt de Montpellier, UMR 5253 CNRS-UM-ENSCM, Université de Montpellier, CC1502, Place Eugène Bataillon, 34095 Montpellier, France
| | - Benedicte Prelot
- Institut
Charles Gerhardt de Montpellier, UMR 5253 CNRS-UM-ENSCM, Université de Montpellier, CC1502, Place Eugène Bataillon, 34095 Montpellier, France
| | - Hervé Cottet
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, Place Eugène Bataillon, CC
1706, 34095 Montpellier
Cedex 5, France
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11
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Herrera I, Winnik MA. Differential Binding Models for Direct and Reverse Isothermal Titration Calorimetry. J Phys Chem B 2016; 120:2077-86. [PMID: 26889710 DOI: 10.1021/acs.jpcb.5b09202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Isothermal titration calorimetry (ITC) is a technique to measure the stoichiometry and thermodynamics from binding experiments. Identifying an appropriate mathematical model to evaluate titration curves of receptors with multiple sites is challenging, particularly when the stoichiometry or binding mechanism is not available. In a recent theoretical study, we presented a differential binding model (DBM) to study calorimetry titrations independently of the interaction among the binding sites (Herrera, I.; Winnik, M. A. J. Phys. Chem. B 2013, 117, 8659-8672). Here, we build upon our DBM and show its practical application to evaluate calorimetry titrations of receptors with multiple sites independently of the titration direction. Specifically, we present a set of ordinary differential equations (ODEs) with the general form d[S]/dV that can be integrated numerically to calculate the equilibrium concentrations of free and bound species S at every injection step and, subsequently, to evaluate the volume-normalized heat signal (δQ(V) = δq/dV) of direct and reverse calorimetry titrations. Additionally, we identify factors that influence the shape of the titration curve and can be used to optimize the initial concentrations of titrant and analyte. We demonstrate the flexibility of our updated DBM by applying these differentials and a global regression analysis to direct and reverse calorimetric titrations of gadolinium ions with multidentate ligands of increasing denticity, namely, diglycolic acid (DGA), citric acid (CIT), and nitrilotriacetic acid (NTA), and use statistical tests to validate the stoichiometries for the metal-ligand pairs studied.
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Affiliation(s)
- Isaac Herrera
- Chemistry Department, University of Toronto , 80 St. George Street, Toronto ON, Canada , M5S 3H6
| | - Mitchell A Winnik
- Chemistry Department, University of Toronto , 80 St. George Street, Toronto ON, Canada , M5S 3H6
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12
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Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site. J Bacteriol 2015; 197:3601-15. [PMID: 26350131 DOI: 10.1128/jb.00612-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 08/28/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Streptococcus mutans is the causative agent of dental caries, a significant concern for human health, and therefore an attractive target for therapeutics development. Previous work in our laboratory has identified a homodimeric, manganese-dependent repressor protein, SloR, as an important regulator of cariogenesis and has used site-directed mutagenesis to map functions to specific regions of the protein. Here we extend those studies to better understand the structural interaction between SloR and its operator and its effector metal ions. The results of DNase I assays indicate that SloR protects a 42-bp region of DNA that overlaps the sloABC promoter on the S. mutans UA159 chromosome, while electrophoretic mobility shift and solution binding assays indicate that each of two SloR dimers binds to this region. Real-time semiquantitative reverse transcriptase PCR (real-time semi-qRT-PCR) experiments were used to determine the individual base pairs that contribute to SloR-DNA binding specificity. Solution studies indicate that Mn(2+) is better than Zn(2+) at specifically activating SloR to bind DNA, and yet the 2.8-Å resolved crystal structure of SloR bound to Zn(2+) provides insight into the means by which selective activation by Mn(2+) may be achieved and into how SloR may form specific interactions with its operator. Taken together, these experimental observations are significant because they can inform rational drug design aimed at alleviating and/or preventing S. mutans-induced caries formation. IMPORTANCE This report focuses on investigating the SloR protein as a regulator of essential metal ion transport and virulence gene expression in the oral pathogen Streptococcus mutans and on revealing the details of SloR binding to its metal ion effectors and binding to DNA that together facilitate this expression. We used molecular and biochemical approaches to characterize the interaction of SloR with Mn(2+) and with its SloR recognition element to gain a clearer picture of the regulatory networks that optimize SloR-mediated metal ion homeostasis and virulence gene expression in S. mutans. These experiments can have a significant impact on caries treatment and/or prevention by revealing the S. mutans SloR-DNA binding interface as an appropriate target for the development of novel therapeutic interventions.
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Olesen NE, Westh P, Holm R. Determination of thermodynamic potentials and the aggregation number for micelles with the mass-action model by isothermal titration calorimetry: A case study on bile salts. J Colloid Interface Sci 2015; 453:79-89. [PMID: 25978555 DOI: 10.1016/j.tca.2014.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 05/28/2023]
Abstract
The aggregation number (n), thermodynamic potentials (ΔG, ΔH, ΔS) and critical micelle concentration (CMC) for 6 natural bile salts were determined on the basis of both original and previously published isothermal titration calorimetry (ITC) data. Different procedures to estimate parameters of micelles with ITC were compared to a mass-action model (MAM) of reaction type: n⋅S⇌Mn. This analysis can provide guidelines for future ITC studies of systems behaving in accordance with this model such as micelles and proteins that undergo self-association to oligomers. Micelles with small aggregation numbers, as those of bile salts, are interesting because such small aggregates cannot be characterized as a separate macroscopic phase and the widely applied pseudo-phase model (PPM) is inaccurate. In the present work it was demonstrated that the aggregation number of micelles was constant at low concentrations enabling determination of the thermodynamic potentials by the MAM. A correlation between the aggregation number and the heat capacity was found, which implies that the dehydrated surface area of bile salts increases with the aggregation number. This is in accordance with Tanford's principles of opposing forces where neighbouring molecules in the aggregate are better able to shield from the surrounding hydrophilic environment when the aggregation number increases.
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Affiliation(s)
- Niels Erik Olesen
- Biologics and Pharmaceutical Science, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark; NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - René Holm
- Biologics and Pharmaceutical Science, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark.
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Olesen NE, Westh P, Holm R. Determination of thermodynamic potentials and the aggregation number for micelles with the mass-action model by isothermal titration calorimetry: A case study on bile salts. J Colloid Interface Sci 2015; 453:79-89. [PMID: 25978555 DOI: 10.1016/j.jcis.2015.03.069] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 01/04/2023]
Abstract
The aggregation number (n), thermodynamic potentials (ΔG, ΔH, ΔS) and critical micelle concentration (CMC) for 6 natural bile salts were determined on the basis of both original and previously published isothermal titration calorimetry (ITC) data. Different procedures to estimate parameters of micelles with ITC were compared to a mass-action model (MAM) of reaction type: n⋅S⇌Mn. This analysis can provide guidelines for future ITC studies of systems behaving in accordance with this model such as micelles and proteins that undergo self-association to oligomers. Micelles with small aggregation numbers, as those of bile salts, are interesting because such small aggregates cannot be characterized as a separate macroscopic phase and the widely applied pseudo-phase model (PPM) is inaccurate. In the present work it was demonstrated that the aggregation number of micelles was constant at low concentrations enabling determination of the thermodynamic potentials by the MAM. A correlation between the aggregation number and the heat capacity was found, which implies that the dehydrated surface area of bile salts increases with the aggregation number. This is in accordance with Tanford's principles of opposing forces where neighbouring molecules in the aggregate are better able to shield from the surrounding hydrophilic environment when the aggregation number increases.
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Affiliation(s)
- Niels Erik Olesen
- Biologics and Pharmaceutical Science, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark; NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - René Holm
- Biologics and Pharmaceutical Science, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark.
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15
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Zhao H, Piszczek G, Schuck P. SEDPHAT--a platform for global ITC analysis and global multi-method analysis of molecular interactions. Methods 2015; 76:137-148. [PMID: 25477226 PMCID: PMC4380758 DOI: 10.1016/j.ymeth.2014.11.012] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 01/02/2023] Open
Abstract
Isothermal titration calorimetry experiments can provide significantly more detailed information about molecular interactions when combined in global analysis. For example, global analysis can improve the precision of binding affinity and enthalpy, and of possible linkage parameters, even for simple bimolecular interactions, and greatly facilitate the study of multi-site and multi-component systems with competition or cooperativity. A pre-requisite for global analysis is the departure from the traditional binding model, including an 'n'-value describing unphysical, non-integral numbers of sites. Instead, concentration correction factors can be introduced to account for either errors in the concentration determination or for the presence of inactive fractions of material. SEDPHAT is a computer program that embeds these ideas and provides a graphical user interface for the seamless combination of biophysical experiments to be globally modeled with a large number of different binding models. It offers statistical tools for the rigorous determination of parameter errors, correlations, as well as advanced statistical functions for global ITC (gITC) and global multi-method analysis (GMMA). SEDPHAT will also take full advantage of error bars of individual titration data points determined with the unbiased integration software NITPIC. The present communication reviews principles and strategies of global analysis for ITC and its extension to GMMA in SEDPHAT. We will also introduce a new graphical tool for aiding experimental design by surveying the concentration space and generating simulated data sets, which can be subsequently statistically examined for their information content. This procedure can replace the 'c'-value as an experimental design parameter, which ceases to be helpful for multi-site systems and in the context of gITC.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Role of Self-Association and Supersaturation in Oral Absorption of a Poorly Soluble Weakly Basic Drug. Pharm Res 2015; 32:2579-94. [DOI: 10.1007/s11095-015-1645-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/02/2015] [Indexed: 10/23/2022]
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17
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Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods 2014; 76:99-115. [PMID: 25305413 DOI: 10.1016/j.ymeth.2014.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023] Open
Abstract
Isothermal titration calorimetry (ITC) has become the gold-standard technique for studying binding processes due to its high precision and sensitivity, as well as its capability for the simultaneous determination of the association equilibrium constant, the binding enthalpy and the binding stoichiometry. The current widespread use of ITC for biological systems has been facilitated by technical advances and the availability of commercial calorimeters. However, the complexity of data analysis for non-standard models is one of the most significant drawbacks in ITC. Many models for studying macromolecular interactions can be found in the literature, but it looks like each biological system requires specific modeling and data analysis approaches. The aim of this article is to solve this lack of unity and provide a unified methodological framework for studying binding interactions by ITC that can be applied to any experimental system. The apparent complexity of this methodology, based on the binding polynomial, is overcome by its easy generalization to complex systems.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; IIS Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Spain.
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18
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Keeler C, Poon G, Kuo IY, Ehrlich BE, Hodsdon ME. An explicit formulation approach for the analysis of calcium binding to EF-hand proteins using isothermal titration calorimetry. Biophys J 2014; 105:2843-53. [PMID: 24359756 DOI: 10.1016/j.bpj.2013.11.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 11/28/2022] Open
Abstract
We present an improved and extended version of a recently proposed mathematical approach for modeling isotherms of ligand-to-macromolecule binding from isothermal titration calorimetry. Our approach uses ordinary differential equations, solved implicitly and numerically as initial value problems, to provide a quantitative description of the fraction bound of each competing member of a complex mixture of macromolecules from the basis of general binding polynomials. This approach greatly simplifies the formulation of complex binding models. In addition to our generalized, model-free approach, we have introduced a mathematical treatment for the case where ligand is present before the onset of the titration, essential for data analysis when complete removal of the binding partner may disrupt the structural and functional characteristics of the macromolecule. Demonstration programs playable on a freely available software platform are provided. Our method is experimentally validated with classic calcium (Ca(2+)) ion-selective potentiometry and isotherms of Ca(2+) binding to a mixture of chelators with and without residual ligand present in the reaction vessel. Finally, we simulate and compare experimental data fits for the binding isotherms of Ca(2+) binding to its canonical binding site (EF-hand domain) of polycystin 2, a Ca(2+)-dependent channel with relevance to polycystic kidney disease.
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Affiliation(s)
- Camille Keeler
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Gregory Poon
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington
| | - Ivana Y Kuo
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Barbara E Ehrlich
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Michael E Hodsdon
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut.
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19
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Wang S, Linde MH, Munde M, Carvalho VD, Wilson WD, Poon GMK. Mechanistic heterogeneity in site recognition by the structurally homologous DNA-binding domains of the ETS family transcription factors Ets-1 and PU.1. J Biol Chem 2014; 289:21605-16. [PMID: 24952944 DOI: 10.1074/jbc.m114.575340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a "dry" mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1 · DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
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Affiliation(s)
- Shuo Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Miles H Linde
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - Manoj Munde
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Victor D Carvalho
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - W David Wilson
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Gregory M K Poon
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
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20
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Petrović PV, Grimme S, Zarić SD, Pfeffer M, Djukic JP. Experimental and theoretical investigations of the self-association of oxaliplatin. Phys Chem Chem Phys 2014; 16:14688-98. [DOI: 10.1039/c4cp01500b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The issue of self-aggregation of oxaliplatin in water as well as in the gas phase is investigated analytically and analyzed by state-of-the-art DFT-D methods.
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Affiliation(s)
- Predrag V. Petrović
- Institut de Chimie de Strasbourg
- Université de Strasbourg
- 67000 Strasbourg, France
- Faculty of Chemistry
- University of Belgrade
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- University of Bonn
- D-53115 Bonn, Germany
| | - Snežana D. Zarić
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
| | - Michel Pfeffer
- Institut de Chimie de Strasbourg
- Université de Strasbourg
- 67000 Strasbourg, France
| | - Jean-Pierre Djukic
- Institut de Chimie de Strasbourg
- Université de Strasbourg
- 67000 Strasbourg, France
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21
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Turcu I, Mic M. Size Dependence of Molecular Self-Assembling in Stacked Aggregates. 2. Heat Exchange Effects. J Phys Chem B 2013; 117:9083-93. [DOI: 10.1021/jp403768x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ioan Turcu
- Department of Molecular and Biomolecular Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
| | - Mihaela Mic
- Department of Molecular and Biomolecular Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
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22
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Herrera I, Winnik MA. Differential binding models for isothermal titration calorimetry: moving beyond the Wiseman isotherm. J Phys Chem B 2013; 117:8659-72. [PMID: 23841823 DOI: 10.1021/jp311812a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present a set of model-independent differential equations to analyze isothermal titration calorimetry (ITC) experiments. In contrast with previous approaches that begin with specific assumptions about the number of binding sites and the interactions among them (e.g., sequential, independent, cooperative), our derivation makes more general assumptions, such that a receptor with multiple sites for one type of ligand species (homotropic binding) can be studied with the same analytical expression. Our approach is based on the binding polynomial formalism, and the resulting analytical expressions can be extended to account for any number of binding sites and any type of binding interaction among them. We refer to the set of model-independent differential equations to study ITC experiments as a differential binding model (DBM). To demonstrate the flexibility of our DBM, we present the analytical expressions to study receptors with one or two binding sites. The DBM for a receptor with one site is equivalent to the Wiseman isotherm but with a more intuitive representation that depends on the binding polynomial and the dimensionless parameter c = K·MT, where K is the binding constant and MT the total receptor concentration. In addition, we show how to constrain the general DBM for a receptor with two sites to represent sequential, independent, or cooperative binding interactions between the sites. We use the sequential binding model to study the binding interaction between Gd(III) and citrate anions. In addition, we simulate calorimetry titrations of receptors with positive, negative, and noncooperative interactions between the two binding sites. Finally, we derive a DBM for titrations of receptors with n-independent binding sites.
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Affiliation(s)
- Isaac Herrera
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON Canada M5S 3H6
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23
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Moschetta EG, Gans KM, Rioux RM. Characterization of sites of different thermodynamic affinities on the same metal center via isothermal titration calorimetry. J Catal 2013. [DOI: 10.1016/j.jcat.2013.02.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Turcu I, Bogdan M. Size Dependence of Molecular Self-Assembling in Stacked Aggregates. 1. NMR Investigation of Ciprofloxacin Self-Association. J Phys Chem B 2012; 116:6488-98. [DOI: 10.1021/jp3034215] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ioan Turcu
- Department of Molecular and Biomolecular
Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
| | - Mircea Bogdan
- Department of Molecular and Biomolecular
Physics, National Institute of Isotopic and Molecular Technology, 400293 Cluj-Napoca, Romania
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25
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Poon GMK. DNA Binding Regulates the Self-Association of the ETS Domain of PU.1 in a Sequence-Dependent Manner. Biochemistry 2012; 51:4096-107. [DOI: 10.1021/bi300331v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Gregory M. K. Poon
- Department of Pharmaceutical
Sciences, Washington State University,
Pullman, Washington 99164-6534, United States
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26
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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27
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28
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Narang AS, Yamniuk AP, Zhang L, Comezoglu SN, Bindra DS, Varia S, Doyle ML, Badawy S. Reversible and pH-dependent weak drug-excipient binding does not affect oral bioavailability of high dose drugs. J Pharm Pharmacol 2012; 64:553-65. [DOI: 10.1111/j.2042-7158.2011.01435.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract
Objectives
Drug-excipient binding can affect in-vitro drug release. Literature suggests that drug-excipient ionic binding interaction that is not disrupted by physiological salt concentration in the dissolution medium can impact a drug's oral bioavailability. We investigated whether nondisruption of interaction by physiological salt concentration was an adequate predictor of its biorelevance using the binding of a model amine high dose drug brivanib alaninate (BA) to croscarmellose sodium (CCS) as an example.
Methods
BA was formulated into an immediate release tablet using CCS as disintegrant by a wet granulation process. In-vitro drug release was carried out as a function of pH and buffer concentration of the medium. BA-CCS binding was studied in buffer solution and data fitted to a Langmuir isotherm. A simulation model and an isothermal titration calorimetry method were developed to assess the bioavailability risk and strength of drug-excipient binding interaction, independent of physiological salt concentration consideration.
Key findings
BA-CCS binding was pH-dependent, reversible, ionic, and not disrupted by increasing the buffer concentration in the dissolution medium. Absorption simulation predictions of no effect of CCS binding on BA's bioavailability were confirmed by a monkey pharmacokinetic study.
Conclusions
A pH-dependent and reversible weak drug-excipient binding interaction is unlikely to affect the oral bioavailability of high dose drugs.
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Affiliation(s)
- Ajit S Narang
- Drug Product Science and Technology, Bristol-Myers Squibb, Co., New Brunswick, USA
| | - Aaron P Yamniuk
- Protein Science and Structure, Bristol-Myers Squibb, Co., Princeton, NJ, USA
| | - Limin Zhang
- Analytical and Bioanalytical Development, Bristol-Myers Squibb, Co., New Brunswick, USA
| | - S Nilgun Comezoglu
- Biotransformation Department, Bristol-Myers Squibb, Co., Princeton, NJ, USA
| | - Dilbir S Bindra
- Drug Product Science and Technology, Bristol-Myers Squibb, Co., New Brunswick, USA
| | - Sailesh Varia
- Drug Product Science and Technology, Bristol-Myers Squibb, Co., New Brunswick, USA
| | - Michael L Doyle
- Protein Science and Structure, Bristol-Myers Squibb, Co., Princeton, NJ, USA
| | - Sherif Badawy
- Drug Product Science and Technology, Bristol-Myers Squibb, Co., New Brunswick, USA
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29
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Tellinghuisen J. Designing isothermal titration calorimetry experiments for the study of 1:1 binding: problems with the "standard protocol". Anal Biochem 2012; 424:211-20. [PMID: 22306472 DOI: 10.1016/j.ab.2011.12.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 12/17/2011] [Accepted: 12/22/2011] [Indexed: 11/18/2022]
Abstract
Literature recommendations for designing isothermal titration calorimetry (ITC) experiments to study 1:1 binding, M+X -->/<-- MX, are not consistent and have persisted through time with little quantitative justification. In particular, the "standard protocol" employed by most workers involves 20 to 30 injections of titrant to a final titrant/titrand mole ratio (R(m)) of ~ 2-a scheme that can be far from optimal and can needlessly limit applicability of the ITC technique. These deficiencies are discussed here along with other misconceptions. Whether a specific binding process can be studied by ITC is determined less by c (the product of binding constant K and titrand concentration [M](0)) than by the total detectable heat q(tot) and the extent to which M can be converted to MX. As guidelines, with 90% conversion to MX, K can be estimated within 5% over the range 10 to 10(8)M(-1) when q(tot)/σ(q)≈700, where σ(q) is the standard deviation for estimation of q. This ratio drops to ~150 when the stoichiometry parameter n is treated as known. A computer application for modeling 1:1 binding yields realistic estimates of parameter standard errors for use in protocol design and feasibility assessment.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
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