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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: 1.0] [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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2
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Prozeller D, Morsbach S, Landfester K. Isothermal titration calorimetry as a complementary method for investigating nanoparticle-protein interactions. NANOSCALE 2019; 11:19265-19273. [PMID: 31549702 DOI: 10.1039/c9nr05790k] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Isothermal titration calorimetry (ITC) is a complementary technique that can be used for investigations of protein adsorption on nanomaterials, as it quantifies the thermodynamic parameters of intermolecular interactions in situ. As soon as nanomaterials enter biological media, a corona of proteins forms around the nanomaterials, which influences the surface properties and therefore the behavior of nanomaterials tremendously. ITC enhances our understanding of nanoparticle-protein interactions, as it provides information on binding affinity (in form of association constant Ka), interaction mechanism (in form of binding enthalpy ΔH, binding entropy ΔS and Gibbs free energy ΔG) and binding stoichiometry n. Therefore, as a complementary method, ITC enhances our mechanistic understanding of the protein corona. In this minireview, the information obtained from a multitude of ITC studies regarding different nanomaterials and proteins are gathered and relations between nanomaterials' properties and their resulting interactions undergone with proteins are deduced. Nanomaterials formed of a hydrophilic material without strongly charged surface and steric stabilization experience the weakest interactions with proteins. As a result, such nanomaterials undergo the least unspecific protein-interactions and are most promising for allowing an engineering of the protein corona.
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Affiliation(s)
- Domenik Prozeller
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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3
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Alniss HY, Witzel II, Semreen MH, Panda PK, Mishra YK, Ahuja R, Parkinson JA. Investigation of the Factors That Dictate the Preferred Orientation of Lexitropsins in the Minor Groove of DNA. J Med Chem 2019; 62:10423-10440. [DOI: 10.1021/acs.jmedchem.9b01534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hasan Y. Alniss
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Ini-Isabée Witzel
- Core Technology Platform, New York University of Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
| | - Yogendra Kumar Mishra
- Functional Nanomaterials, Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Rajeev Ahuja
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
- Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-10044 Stockholm Sweden
| | - John A. Parkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
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5
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
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Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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6
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Affiliation(s)
- Hasan Y. Alniss
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
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7
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Affiliation(s)
- Liora Werber
- Department of Chemistry and the Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
| | - Yitzhak Mastai
- Department of Chemistry and the Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
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Amartely H, David A, Shamir M, Lebendiker M, Izraeli S, Friedler A. Differential effects of zinc binding on structured and disordered regions in the multidomain STIL protein. Chem Sci 2016; 7:4140-4147. [PMID: 30155058 PMCID: PMC6014068 DOI: 10.1039/c6sc00115g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/01/2016] [Indexed: 11/24/2022] Open
Abstract
Here we show that simultaneous binding of Zn2+ ions has different effects on structured and disordered domains in the same multidomain protein.
Binding of metal ions is an important regulatory mechanism in proteins. Specifically, Zn2+ binding to disordered regions commonly induces a disorder to order transition and gain of structure or oligomerization. Here we show that simultaneous binding of Zn2+ ions has different effects on structured and disordered domains in the same multidomain protein. The centrosomal STIL protein bound Zn2+ ions via both its structured N-terminal domain (NTD) and disordered central region (IDR). Zn2+ binding induced structural rearrangement of the structured NTD but promoted oligomerization of the IDR. We suggest that by binding Zn2+ STIL acquires a different conformation, which allows its oligomerization and induces its activity. Sequence alignment of the oligomerization region revealed a new suggested motif, SxKxS/SxHxS/SxLxS, which may participate in STIL oligomerization. Binding of the same metal ion through a disordered and a structured domain in the same protein is a property that may have implications in regulating the protein activity. By doing so, the protein achieves two parallel outcomes: structural changes and oligomerization that can take place together. Our results describe a new important role of the delicate interplay between structure and intrinsic disorder in proteins.
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Affiliation(s)
- Hadar Amartely
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Ahuvit David
- Sheba Cancer Research Center and the Edmond and Lily Safra Children Hospital , Sheba Medical Center , Tel-Hashomer 52621 , Israel.,Department of Molecular Genetics and Biochemistry , Faculty of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Mai Shamir
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
| | - Shai Izraeli
- Sheba Cancer Research Center and the Edmond and Lily Safra Children Hospital , Sheba Medical Center , Tel-Hashomer 52621 , Israel.,Department of Molecular Genetics and Biochemistry , Faculty of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Assaf Friedler
- Institute of Chemistry , Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel
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9
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Falconer RJ. Applications of isothermal titration calorimetry - the research and technical developments from 2011 to 2015. J Mol Recognit 2016; 29:504-15. [PMID: 27221459 DOI: 10.1002/jmr.2550] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry is a widely used biophysical technique for studying the formation or dissociation of molecular complexes. Over the last 5 years, much work has been published on the interpretation of isothermal titration calorimetry (ITC) data for single binding and multiple binding sites. As over 80% of ITC papers are on macromolecules of biological origin, this interpretation is challenging. Some researchers have attempted to link the thermodynamics constants to events at the molecular level. This review highlights work carried out using binding sites characterized using x-ray crystallography techniques that allow speculation about individual bond formation and the displacement of individual water molecules during ligand binding and link these events to the thermodynamic constants for binding. The review also considers research conducted with synthetic binding partners where specific binding events like anion-π and π-π interactions were studied. The revival of assays that enable both thermodynamic and kinetic information to be collected from ITC data is highlighted. Lastly, published criticism of ITC research from a physical chemistry perspective is appraised and practical advice provided for researchers unfamiliar with thermodynamics and its interpretation. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Robert J Falconer
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK.
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10
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Lin K, Yu Z, Yu Y, Liao X, Huang P, Guo C, Lin D. Distinct effects of Cu2+-binding on oligomerization of human and rabbit prion proteins. Acta Biochim Biophys Sin (Shanghai) 2015; 47:842-50. [PMID: 26350098 DOI: 10.1093/abbs/gmv081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/12/2015] [Indexed: 11/13/2022] Open
Abstract
The cellular prion protein (PrP(C)) is a kind of cell-surface Cu(2+)-binding glycoprotein. The oligomerization of PrP(C) is highly related to transmissible spongiform encephalopathies (TSEs). Cu(2+) plays a vital role in the oligomerization of PrP(C), and participates in the pathogenic process of TSE diseases. It is expected that Cu(2+)-binding has different effects on the oligomerization of TSE-sensitive human PrP(C) (HuPrP(C)) and TSE-resistant rabbit PrP(C) (RaPrP(C)). However, the details of the distinct effects remain unclear. In the present study, we measured the interactions of Cu(2+) with HuPrP(C) (91-230) and RaPrP(C) (91-228) by isothermal titration calorimetry, and compared the effects of Cu(2+)-binding on the oligomerization of both PrPs. The measured dissociation constants (Kd) of Cu(2+) were 11.1 ± 2.1 μM for HuPrP(C) and 21.1 ± 3.1 μM for RaPrP(C). Cu(2+)-binding promoted the oligomerization of HuPrP(C) more significantly than that of RaPrP(C). The far-ultraviolet circular dichroism spectroscopy experiments showed that Cu(2+)-binding induced more significant secondary structure change and increased more β-sheet content for HuPrP(C) compared with RaPrP(C). Moreover, the urea-induced unfolding transition experiments indicated that Cu(2+)-binding decreased the conformational stability of HuPrP(C) more distinctly than that of RaPrP(C). These results suggest that RaPrP(C) possesses a low susceptibility to Cu(2+), potentially weakening the risk of Cu(2+)-induced TSE diseases. Our work sheds light on the Cu(2+)-promoted oligomerization of PrP(C), and may be helpful for further understanding the TSE-resistance of rabbits.
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Affiliation(s)
- Kejiang Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Ziyao Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China
| | - Yuanhui Yu
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinli Liao
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Arijaje EO, Jayanthi S, Kumar TKS, Wang Y. Linear starch and hexanoic acid complexation evaluated by isothermal titration calorimetry. STARCH-STARKE 2015. [DOI: 10.1002/star.201500030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Srinivas Jayanthi
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleARUSA
| | | | - Ya‐Jane Wang
- Department of Food ScienceUniversity of ArkansasFayettevilleARUSA
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12
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Microcalorimetric study of adsorption and disassembling of virus-like particles on anion exchange chromatography media. J Chromatogr A 2015; 1388:195-206. [PMID: 25744549 DOI: 10.1016/j.chroma.2015.02.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/14/2015] [Accepted: 02/16/2015] [Indexed: 11/24/2022]
Abstract
Chromatographic purification of virus-like particles (VLPs) is important to the development of modern vaccines. However, disassembly of the VLPs on the solid-liquid interface during chromatography process could be a serious problem. In this study, isothermal titration calorimetric (ITC) measurements, together with chromatography experiments, were performed on the adsorption and disassembling of multi-subunits hepatitis B virus surface antigen virus-like particles (HB-VLPs). Two gigaporous ion-exchange chromatography (IEC) media, DEAE-AP-280 nm and DEAE-POROS, were used. The application of gigaporous media with high ligand density led to significantly increased irreversible disassembling of HB-VLPs and consequently low antigen activity recovery during IEC process. To elucidate the thermodynamic mechanism of the effect of ligand density on the adsorption and conformational change of VLPs, a thermodynamic model was proposed. With this model, one can obtain the intrinsic molar enthalpy changes related to the binding of VLPs and the accompanying conformational change on the liquid-solid interface during its adsorption. This model assumes that, when intact HB-VLPs interact with the IEC media, the total adsorbed proteins contain two states, the intact formation and the disassembled formation; accordingly, the apparent adsorption enthalpy, ΔappH, which can be directly measured from ITC experiments, presents the sum of three terms: (1) the intrinsic molar enthalpy change associated to the binding of intact HB-VLPs (ΔbindHintact), (2) the intrinsic molar enthalpy change associated to the binding of HB-VLPs disassembled formation (ΔbindHdis), and (3) the enthalpy change accompanying the disassembling of HB-VLPs (ΔconfHdis). The intrinsic binding of intact HB-VLPs and the disassembled HB-VLPs to both kinds of gigaporous media (each of which has three different ligand densities), were all observed to be entropically driven as indicated by positive values of ΔbindHintact and ΔbindHdis; while the nagative ΔconfHdis values suggested a spontenous enthalpy-driven process for the forming of HB-VLPs disassembled formation at all conditions studied. As ligand density increases, ΔconfHdis became more negative, which was in agreement with the findings from chromatography experiments, that higher ligand density leads to more serious disassembling of HB-VLPs. Results from thermodynamic studies provided us insight understanding on the mechanism of adsorption and conformational change of VLPs, as well as the effect of ligand densities on the structural stability of VLPs during IEC process.
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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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14
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Wenz G. Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives. Beilstein J Org Chem 2012; 8:1890-5. [PMID: 23209527 PMCID: PMC3511027 DOI: 10.3762/bjoc.8.218] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/16/2012] [Indexed: 01/01/2023] Open
Abstract
Various heptasubstituted derivatives of β-cyclodextrin (β-CD) bearing 1, 2 and 3 methyl substituents per glucose unit were synthesized by regioselective methods. Binding free energies and binding enthalpies of these hosts towards 4-tert-butylbenzoate and adamantane-1-carboxylate were determined by isothermal titration microcalorimetry (ITC). It was found that methyl substituents at the secondary positions of β-CD lead to a tremendous reduction of the binding potential, while methylation at the primary positions significantly improved binding. Stabilizing intramolecular hydrogen bonds between the glucose units were made responsible for the high binding potentials of those β-CD derivatives that possess secondary hydroxy groups.
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Affiliation(s)
- Gerhard Wenz
- Organic Macromolecular Chemistry, Saarland University, Campus Saarbrücken C4.2, 66123 Saarbrücken, Germany
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15
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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: 123] [Impact Index Per Article: 9.5] [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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17
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Demarse NA, Quinn CF, Eggett DL, Russell DJ, Hansen LD. Calibration of nanowatt isothermal titration calorimeters with overflow reaction vessels. Anal Biochem 2011; 417:247-55. [DOI: 10.1016/j.ab.2011.06.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/07/2011] [Indexed: 11/29/2022]
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18
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Freiburger LA, Mittermaier AK, Auclair K. Collecting variable-concentration isothermal titration calorimetry datasets in order to determine binding mechanisms. J Vis Exp 2011:2529. [PMID: 21505408 DOI: 10.3791/2529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is commonly used to determine the thermodynamic parameters associated with the binding of a ligand to a host macromolecule. ITC has some advantages over common spectroscopic approaches for studying host/ligand interactions. For example, the heat released or absorbed when the two components interact is directly measured and does not require any exogenous reporters. Thus the binding enthalpy and the association constant (Ka) are directly obtained from ITC data, and can be used to compute the entropic contribution. Moreover, the shape of the isotherm is dependent on the c-value and the mechanistic model involved. The c-value is defined as c = n[P]tKa, where [P]t is the protein concentration, and n is the number of ligand binding sites within the host. In many cases, multiple binding sites for a given ligand are non-equivalent and ITC allows the characterization of the thermodynamic binding parameters for each individual binding site. This however requires that the correct binding model be used. This choice can be problematic if different models can fit the same experimental data. We have previously shown that this problem can be circumvented by performing experiments at several c-values. The multiple isotherms obtained at different c-values are fit simultaneously to separate models. The correct model is next identified based on the goodness of fit across the entire variable-c dataset. This process is applied here to the aminoglycoside resistance-causing enzyme aminoglycoside N-6'-acetyltransferase-Ii (AAC(6')-Ii). Although our methodology is applicable to any system, the necessity of this strategy is better demonstrated with a macromolecule-ligand system showing allostery or cooperativity, and when different binding models provide essentially identical fits to the same data. To our knowledge, there are no such systems commercially available. AAC(6')-Ii, is a homo-dimer containing two active sites, showing cooperativity between the two subunits. However ITC data obtained at a single c-value can be fit equally well to at least two different models a two-sets-of-sites independent model and a two-site sequential (cooperative) model. Through varying the c-value as explained above, it was established that the correct binding model for AAC(6')-Ii is a two-site sequential binding model. Herein, we describe the steps that must be taken when performing ITC experiments in order to obtain datasets suitable for variable-c analyses.
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Lemeski ET, Behbehani GR, Saboury AA, Monajjemi M, Mehrabian RZ, Golsefidi MA, Rajabzadeh H, Baei MT, Hasanzadeh S. Thermodynamic Study of the Binding of Mercury Ion to Human Growth Hormone at Different Temperatures. J SOLUTION CHEM 2011; 40:575-586. [DOI: 10.1007/s10953-011-9668-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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20
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Davies P, Wang X, Sarell CJ, Drewett A, Marken F, Viles JH, Brown DR. The synucleins are a family of redox-active copper binding proteins. Biochemistry 2010; 50:37-47. [PMID: 21117662 DOI: 10.1021/bi101582p] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thermodynamic studies in conjunction with EPR confirm that α-synuclein, β-synuclein, and γ-synuclein bind copper(II) in a high affinity 1:1 stoichiometry. γ-Synuclein demonstrates the highest affinity, in the picomolar range, while α-synuclein and β-synuclein both bind copper(II) with nanomolar affinity. The copper center on all three proteins demonstrates reversible or partly reversible redox cycling. Various mutations show that the primary coordinating ligand for copper(II) is located within the N-terminal regions between residues 2-9. There is also a contribution from the C-terminus in conjunction with the histidine at position 50 in α-synuclein and position 65 in β-synuclein, although these regions appear to have little effect on overall coordination stability. These histidines and the C-terminus, however, appear to be critical to the redox engine of the proteins.
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Affiliation(s)
- Paul Davies
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA27AY, UK
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Hansen LD, Fellingham GW, Russell DJ. Simultaneous determination of equilibrium constants and enthalpy changes by titration calorimetry: Methods, instruments, and uncertainties. Anal Biochem 2010; 409:220-9. [PMID: 21073852 DOI: 10.1016/j.ab.2010.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/28/2010] [Accepted: 11/03/2010] [Indexed: 11/16/2022]
Abstract
Calorimetric methods have been used to determine equilibrium constants since 1937, but no comprehensive review of the various calorimeters and methods has been done previously. This article reports methods for quantitative comparison of the capabilities of calorimeters for simultaneous determination of equilibrium constants and enthalpy changes, for determining optimal experimental conditions, and for assessing the effects of systematic and random errors on the accuracy and precision of equilibrium constants and enthalpy changes determined by this method.
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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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22
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Edink E, Jansen C, Leurs R, de Esch IJ. The heat is on: thermodynamic analysis in fragment-based drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e147-e202. [PMID: 24103770 DOI: 10.1016/j.ddtec.2010.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Abstract
Calorimetric measurements on biological systems from small molecules to whole organisms lead to a new conception of the nature of live matter that has profound consequences for our understanding of biology. The data show that the differences in Gibbs energy (ΔG) and enthalpy (ΔH) are near zero or negative and the difference in entropy (ΔS) is near zero between a random mixture of molecules and live matter of the same composition. A constant input of energy is required to maintain ion gradients, ATP production, and the other functions of living matter, but because cells are organized in a spontaneous process, no energy input is required to maintain the structure or organization of cells. Thus, the origin of life and evolution of complex life forms occurs by thermodynamically spontaneous processes, carbon-based life should be common throughout the universe, and because there is no energy cost, evolution can occur relatively rapidly.
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24
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Hota PK, Buck M. Thermodynamic characterization of two homologous protein complexes: associations of the semaphorin receptor plexin-B1 RhoGTPase binding domain with Rnd1 and active Rac1. Protein Sci 2009; 18:1060-71. [PMID: 19388051 DOI: 10.1002/pro.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Plexin receptors function in response to semaphorin guidance cues in a variety of developmental processes involving cell motility. Interactions with Rho, as well as Ras family small GTPases are critical events in the cell signaling mechanism. We have recently determined the structure of a cytoplasmic domain (RBD) of plexin-B1 and mapped its binding interface with several Rho-GTPases, Rac1, Rnd1, and RhoD. All three GTPases associate with a similar region of this plexin domain, but show different functional behavior in cells. To understand whether thermodynamic properties of the GTPase-RBD interaction contribute to such different behavior, we have examined the interaction at different temperatures, buffer, and pH conditions. Although the binding affinity of both Rnd1 and Rac1 with the plexin-B1 RBD is similar, the detailed thermodynamic properties of the interactions are considerably different. These data suggest that on Rac1 binding to the plexin-B1 RBD, the proteins become more rigid in the complex. By contrast, Rnd1 binding is consistent with unchanged or slightly increased flexibility in one or both proteins. Both GTPases show an appreciable reduction in affinity for the dimeric plexin-B1 RBD indicating that GTPase binding is not cooperative with dimer formation, but that a partial steric hindrance destabilizes the dimer. However, a reduced affinity binding mode to a disulphide stabilized model for the dimeric RBD is also possible. Consistent with cellular studies, the interaction thermodynamics imply that further levels of regulation involving additional binding partners and/or regions outside of the RhoGTPase binding domain are required for receptor activation.
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Affiliation(s)
- Prasanta K Hota
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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25
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Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
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Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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26
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Dieterle M, Blaschke T, Hasse H. Microcalorimetric study of adsorption of human monoclonal antibodies on cation exchange chromatographic materials. J Chromatogr A 2008; 1205:1-9. [DOI: 10.1016/j.chroma.2008.07.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/02/2008] [Accepted: 07/09/2008] [Indexed: 10/21/2022]
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Buurma NJ, Haq I. Calorimetric and spectroscopic studies of Hoechst 33258: self-association and binding to non-cognate DNA. J Mol Biol 2008; 381:607-21. [PMID: 18617189 DOI: 10.1016/j.jmb.2008.05.073] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 05/04/2008] [Accepted: 05/30/2008] [Indexed: 10/22/2022]
Abstract
Sequence and structure-specific molecular recognition of DNA by small molecules is an important goal in biophysical chemistry and drug discovery. Many candidate ligands possess flat aromatic surfaces and other molecular features that allow them to self-associate. In addition, non-specific binding to the target is a complicating feature of these interactions. Therefore, multiple equilibria are present and need to be accounted for in data analysis in order to obtain meaningful thermodynamic parameters. In order to address these issues we have systematically examined the bis-benzimidazole dye Hoechst 33258 (H33258) in terms of self-aggregation and binding to DNA oligonucleotides lacking any cognate minor groove A.T sites. This model system has been interrogated using isothermal titration calorimetry (ITC), circular dichroism (CD), fluorescence spectroscopy and pulsed gradient spin echo NMR. Three distinct binding events and ligand self-aggregation have been identified and, where possible, quantified. H33258 self-aggregation involves a step-wise aggregation mechanism, driven by stacking interactions. The DNA binding process includes two specific binding modes and non-specific DNA-templated H33258 stacking. We have written novel ITC data-fitting software (IC-ITC; freely available to the biophysics community), which simultaneously fits ligand aggregation and ligand-DNA binding. Here, this numerical analysis, which uses simulated annealing of complex calorimetric data representing multiple coupled equilibria, is described.
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Affiliation(s)
- Niklaas J Buurma
- Centre for Chemical Biology, The Department of Chemistry, The University of Sheffield, Dainton Building, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Buurma NJ, Haq I. Advances in the analysis of isothermal titration calorimetry data for ligand-DNA interactions. Methods 2007; 42:162-72. [PMID: 17472898 DOI: 10.1016/j.ymeth.2007.01.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 12/20/2006] [Accepted: 01/08/2007] [Indexed: 11/22/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is a well established technique for the study of biological interactions. The strength of ITC is that it directly measures enthalpy changes associated with interactions. Experiments can also yield binding isotherms allowing quantification of equilibrium binding constants, hence an almost complete thermodynamic profile can be established. Principles and application of ITC have been well documented over recent years, experimentally the technique is simple to use and in ideal scenarios data analysis is trivial. However, ITC experiments can be designed such that previously inaccessible parameters can be evaluated. We outline some of these advances, including (1) exploiting different experimental conditions; (2) low affinity systems; (3) high affinity systems and displacement assays. In addition we ask the question: What if data cannot be fit using the fitting functions incorporated in the data-analysis software that came with your ITC? Examples where such data might be generated include systems following non 1:n binding patterns and systems where binding is coupled to other events such as ligand dissociation. Models dealing with such data are now appearing in literature and we summarise examples relevant for the study of ligand-DNA interactions.
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Isin EM, Guengerich FP. Multiple Sequential Steps Involved in the Binding of Inhibitors to Cytochrome P450 3A4. J Biol Chem 2007; 282:6863-74. [PMID: 17200113 DOI: 10.1074/jbc.m610346200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) 3A4 is an extensively studied human enzyme involved in the metabolism of >50% of drugs. The mechanism of the observed homotropic and heterotropic cooperativity in P450 3A4-catalyzed oxidations is not well understood, and together with the cooperative behavior, a detailed understanding of interaction of drug inhibitors with P450 3A4 is important in predicting clinical drug-drug interactions. The interactions of P450 3A4 with several structurally diverse inhibitors were investigated using both kinetic and thermodynamic approaches to resolve the steps involved in binding of these ligands. The results of pre-steady-state absorbance and fluorescence experiments demonstrate that inhibitor binding is clearly a multistep process, even more complex than the binding of substrates. Based on spectrophotometric equilibrium binding titrations as well as isothermal titration calorimetry experiments, the stoichiometry of binding appears to be 1:1 in the concentration ranges studied. Using a sequential-mixing stopped-flow approach, we were also able to show that the observed multiphasic binding kinetics is the result of sequential events as opposed to the existence of multiple enzyme populations in dynamic equilibrium that interact with ligands at different rates. We propose a three-step minimal model for inhibitor binding, developed with kinetic simulations, consistent with our previously reported model for the binding of substrates, although it is possible that even more steps are involved.
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Affiliation(s)
- Emre M Isin
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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31
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Ababou A, Ladbury JE. Survey of the year 2005: literature on applications of isothermal titration calorimetry. J Mol Recognit 2007; 20:4-14. [PMID: 17006876 DOI: 10.1002/jmr.803] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of an interaction. Its usage does not suffer from constraints of molecular size, shape or chemical constitution. Neither is there any need for chemical modification or attachment to solid support. This ease of use has made it an invaluable instrumental resource and led to its appearance in many laboratories. Despite this, the value of the thermodynamic parameterization has, only quite recently, become widely appreciated. Although our understanding of the correlation between thermodynamic data and structural details continues to be somewhat naïve, a large number of publications have begun to improve the situation. In this overview of the literature for 2005, we have attempted to highlight works of interest and novelty. Furthermore, we draw attention to those works which we feel have provided a route to better analysis and increased our ability to understand the meaning of thermodynamic change on binding.
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Affiliation(s)
- Adessamad Ababou
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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32
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Cooper MA. Non-optical screening platforms: the next wave in label-free screening? Drug Discov Today 2006; 11:1068-74. [PMID: 17129825 DOI: 10.1016/j.drudis.2006.10.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 08/17/2006] [Accepted: 10/04/2006] [Indexed: 11/15/2022]
Abstract
The use of optical biosensors for compound screening was first demonstrated in the mid-1990s, but there has been limited uptake in the market owing to issues of limited throughput and a lack of applications for key receptor classes. Recently, several start-up and established tools companies have exploited non-optical detection modalities that seek to address the shortcomings of more established optical approaches. Platforms based on acoustic resonance, electrical impedance, microcantilevers, nanowires and differential calorimetry are beginning to appear with commercially available products targeted at post-high-throughput screening hit confirmation and mode-of-action studies. This article highlights key advances in commercial label-free analysis platforms, which complement more traditional optical system and which also allow novel assay formats for the analysis of previously intractable targets.
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Affiliation(s)
- Matthew A Cooper
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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Sun DZ, Li L, Qiu XM, Liu M, Yin BL. Cyclodextrins Binding to Paeonol and Two of Its Isomers in Aqueous Solution. Isothermal Titration Calorimetry and 1H NMR Investigations of Molecular Recognition. J SOLUTION CHEM 2006. [DOI: 10.1007/s10953-006-9075-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Isin EM, Guengerich FP. Kinetics and Thermodynamics of Ligand Binding by Cytochrome P450 3A4. J Biol Chem 2006; 281:9127-36. [PMID: 16467307 DOI: 10.1074/jbc.m511375200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) 3A4, the major catalyst involved in human drug oxidation, displays substrate- and reaction-dependent homotropic and heterotropic cooperative behavior. Although several models have been proposed, these mainly rely on steady-state kinetics and do not provide information on the contribution of the individual steps of P450 catalytic cycle to the observed cooperativity. In this work, we focused on the kinetics of substrate binding, and the fluorescent properties of bromocriptine and alpha-naphthoflavone allowed analysis of an initial ligand-P450 3A4 interaction that does not cause a perturbation of the heme spectrum. The binding stoichiometry for bromocriptine was determined to be unity using isothermal titration calorimetry and equilibrium dialysis methods, suggesting that the ligand bound to the peripheral site during the initial encounter dissociates subsequently. A three-step substrate binding model is proposed, based on absorbance and fluorescence stopped-flow kinetic data and equilibrium binding data obtained with bromocriptine, and evaluated using kinetic modeling. The results are consistent with the substrate molecule binding at a site peripheral to the active site and subsequently moving toward the active site to bind to the heme and resulting in a low to high spin iron shift. The last step is attributed to a conformational change in the enzyme active site. The later steps of binding were shown to have rate constants comparable with the subsequent steps of the catalytic cycle. The P450 3A4 binding process is more complex than a two-state system, and the overlap of rates of some of the events with subsequent steps is proposed to underlie the observed cooperativity.
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Affiliation(s)
- Emre M Isin
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Madrid K, Jardim A. Peroxin 5-peroxin 14 association in the protozoan Leishmania donovani involves a novel protein-protein interaction motif. Biochem J 2006; 391:105-14. [PMID: 15929724 PMCID: PMC1237144 DOI: 10.1042/bj20050328] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Import of proteins with a PTS1 (peroxisomal targeting signal 1) into the Leishmania glycosomal organelle involves docking of a PTS1-laden LdPEX5 [Leishmania donovani PEX5 (peroxin 5)] receptor to LdPEX14 on the surface of the glycosomal membrane. In higher eukaryotes, the PEX5-PEX14 interaction is mediated by a conserved diaromatic WXXXY/F motif. Site-directed and deletion mutageneses of the three WXXXY/F repeats in LdPEX5 did not abolish the LdPEX5-LdPEX14 association. Analysis of the equilibrium dissociation constant (K(d)) revealed that ldpex5-W53A (Trp53-->Ala), ldpex5-W293A, ldpex5-W176,293A and ldpex5-W53,176,293A mutant receptors were capable of binding LdPEX14 with affinities comparable with wild-type LdPEX5. That the diaromatic motifs were not required for the LdPEX5-LdPEX14 interaction was further verified by deletion analysis that showed that ldpex5 deletion mutants or ldpex5 fragments lacking the WXXXY/F motifs retained LdPEX14 binding activity. Mapping studies of LdPEX5 indicated that the necessary elements required for LdPEX14 association were localized to a region between residues 290 and 323. Finally, mutational analysis of LdPEX14 confirmed that residues 23-63, which encompass the conserved signature sequence AX2FLX7SPX6FLKGKGL/V present in all PEX14 proteins, are essential for LdPEX5 binding.
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Affiliation(s)
- Kleber P. Madrid
- Institute of Parasitology, McGill University, Macdonald Campus, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
| | - Armando Jardim
- Institute of Parasitology, McGill University, Macdonald Campus, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
- To whom correspondence should be addressed (email )
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Abstract
Ultra-high-resolution X-ray crystallography of macromolecules (i.e. resolution better than 0.8 Angstroms) is a rising field that promises to provide new insight into the structure-function relationships of biomacromolecules. The picture emerging from macromolecular structures at this resolution is far more complex than previously understood, requiring for its study improved tools for structure refinement, analysis and annotation. Some of these problems were highlighted during the recent High Resolution Drug Design Meeting (Bischenberg-Strasbourg, France, 13-16 May 2004). We will review here some of the results and discussions that took place during that meeting and elaborate on the trends and challenges ahead in this emerging new field of research.
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Ladbury JE, Williams MA. The extended interface: measuring non-local effects in biomolecular interactions. Curr Opin Struct Biol 2004; 14:562-9. [PMID: 15465316 DOI: 10.1016/j.sbi.2004.08.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Improvements in the sensitivity and availability of biophysical techniques for the detection of the formation of complexes in solution are revealing that the effects of binding are not restricted to the direct contacts between the biomolecules or even to a localised site. Rather, information about the binding event is transmitted throughout the biomolecules and the surrounding solution through changes in the hydrogen bonding, hydration and electrostatic field as the complex is formed. Calorimetric, volumetric and NMR methods are beginning to provide a quantitative view of the nature and thermodynamic consequences of this extended interface, and the resulting data pose a major challenge for computational models of binding.
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Affiliation(s)
- John E Ladbury
- Department of Biochemistry and Molecular Biology, Institute for Structural Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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38
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Madrid KP, De Crescenzo G, Wang S, Jardim A. Modulation of the Leishmania donovani peroxin 5 quaternary structure by peroxisomal targeting signal 1 ligands. Mol Cell Biol 2004; 24:7331-44. [PMID: 15314146 PMCID: PMC506994 DOI: 10.1128/mcb.24.17.7331-7344.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 04/28/2004] [Accepted: 06/03/2004] [Indexed: 11/20/2022] Open
Abstract
The import of proteins containing the peroxisomal targeting signal 1 (PTS1) into the Leishmania glycosome is dependent on the docking of the PTS1-loaded LdPEX5 cytosolic receptor with LdPEX14 on the glycosome surface. Here we show that, in the absence of PTS1, LdPEX5 is a tetramer that is stabilized by two distinct interaction domains; the first is a coiled-coil motif encompassing residues 277 to 310, whereas the second domain is localized to residues 1 to 202. By using microcalorimetry, surface plasmon resonance, and size exclusion chromatography techniques, we show that PTS1 peptide binding to LdPEX5 tetramers promotes their dissociation into dimeric structures, which are stabilized by a coiled-coil interaction. Moreover, we demonstrated that the resulting LdPEX5-PTS1 complex is remarkably stable and exhibits extremely slow dissociation kinetics. However, binding of LdPEX14 to LdPEX5 modulates the LdPEX5-PTS1 affinity as it decreases the thermodynamic dissociation constant for this latter complex by 10-fold. These changes in the oligomeric state of LdPEX5 and in its affinity for PTS1 ligand upon LdPEX14 binding may explain how, under physiological conditions, LdPEX5 can function to deliver and unload its cargo to the protein translocation machinery on the glycosomal membrane.
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Affiliation(s)
- Kleber P Madrid
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
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Cliff MJ, Gutierrez A, Ladbury JE. A survey of the year 2003 literature on applications of isothermal titration calorimetry. J Mol Recognit 2004; 17:513-23. [PMID: 15384176 DOI: 10.1002/jmr.714] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the last decade isothermal titration calorimetry (ITC) has developed from a specialist method which was largely restricted in its use to dedicated experts, to a major, commercially available tool in the arsenal directed at understanding molecular interactions. The number of those proficient in this field has multiplied dramatically, as has the range of experiments to which this method has been applied. This has led to an overwhelming amount of new data and novel applications to be assessed. With the increasing number of publications in this field comes a need to highlight works of interest and impact. In this overview of the literature we have attempted to draw attention to papers and issues for which both the experienced calorimetrist and the interested dilettante hopefully will share our enthusiasm.
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Affiliation(s)
- Matthew J Cliff
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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