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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: 7.1] [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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52
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Brautigam CA, Zhao H, Vargas C, Keller S, Schuck P. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions. Nat Protoc 2016; 11:882-94. [PMID: 27055097 PMCID: PMC7466939 DOI: 10.1038/nprot.2016.044] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - 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, U.S.A
| | - Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Germany
| | - 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, U.S.A
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53
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Affiliation(s)
- Jonathan B Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
| | - Lee D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - 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, 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, USA.
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54
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Scheuermann TH, Padrick SB, Gardner KH, Brautigam CA. On the acquisition and analysis of microscale thermophoresis data. Anal Biochem 2015; 496:79-93. [PMID: 26739938 DOI: 10.1016/j.ab.2015.12.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 01/30/2023]
Abstract
A comprehensive understanding of the molecular mechanisms underpinning cellular functions is dependent on a detailed characterization of the energetics of macromolecular binding, often quantified by the equilibrium dissociation constant, KD. While many biophysical methods may be used to obtain KD, the focus of this report is a relatively new method called microscale thermophoresis (MST). In an MST experiment, a capillary tube filled with a solution containing a dye-labeled solute is illuminated with an infrared laser, rapidly creating a temperature gradient. Molecules will migrate along this gradient, causing changes in the observed fluorescence. Because the net migration of the labeled molecules will depend on their liganded state, a binding curve as a function of ligand concentration can be constructed from MST data and analyzed to determine KD. Herein, simulations demonstrate the limits of KD that can be measured in current instrumentation. They also show that binding kinetics is a major concern in planning and executing MST experiments. Additionally, studies of two protein-protein interactions illustrate challenges encountered in acquiring and analyzing MST data. Combined, these approaches indicate a set of best practices for performing and analyzing MST experiments. Software for rigorous data analysis is also introduced.
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Affiliation(s)
- Thomas H Scheuermann
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
| | - Shae B Padrick
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA.
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55
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Use of isothermal titration calorimetry to study surfactant aggregation in colloidal systems. Biochim Biophys Acta Gen Subj 2015; 1860:999-1016. [PMID: 26459003 DOI: 10.1016/j.bbagen.2015.10.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/23/2015] [Accepted: 10/07/2015] [Indexed: 02/01/2023]
Abstract
BACKGROUND Isothermal titration calorimetry (ITC) is a general technique that allows for precise and highly sensitive measurements. These measurements may provide a complete and accurate thermodynamic description of association processes in complex systems such as colloidal mixtures. SCOPE OF THE REVIEW This review will address uses of ITC for studies of surfactant aggregation to form micelles, with emphasis on the thermodynamic studies of homologous surfactant series. We will also review studies on surfactant association with polymers of different molecular characteristics and with colloidal particles. GENERAL SIGNIFICANCE ITC studies on the association of different homologous series of surfactants provide quantitative information on independent contribution from their apolar hydrocarbon chains and polar headgroups to the different thermodynamic functions associated with micellization (Gibbs energy, enthalpy and entropy). Studies on surfactant association to polymers by ITC provide a comprehensive description of the association process, including examples in which particular features revealed by ITC were elucidated by using ancillary techniques such as light or X-ray scattering measurements. Examples of uses of ITC to follow surfactant association to biomolecules such as proteins or DNA, or nanoparticles are also highlighted. Finally, recent theoretical models that were proposed to analyze ITC data in terms of binding/association processes are discussed. MAJOR CONCLUSIONS This review stresses the importance of using direct calorimetric measurements to obtain and report accurate thermodynamic data, even in complex systems. These data, whenever possible, should be confirmed and associated with other ancillary techniques that allow elucidation of the nature of the transformations detected by calorimetric results, providing a complete description of the process under scrutiny.
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Johnson RA, Manley OM, Spuches AM, Grossoehme NE. Dissecting ITC data of metal ions binding to ligands and proteins. Biochim Biophys Acta Gen Subj 2015; 1860:892-901. [PMID: 26327285 DOI: 10.1016/j.bbagen.2015.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND ITC is a powerful technique that can reliably assess the thermodynamic underpinnings of a wide range of binding events. When metal ions are involved, complications arise in evaluating the data due to unavoidable solution chemistry that includes metal speciation and a variety of linked equilibria. SCOPE OF REVIEW This paper identifies these concerns, provides recommendations to avoid common mistakes, and guides the reader through the mathematical treatment of ITC data to arrive at a set of thermodynamic state functions that describe identical chemical events and, ideally, are independent of solution conditions. Further, common metal chromophores used in biological metal sensing studies are proposed as a robust system to determine unknown solution competition. MAJOR CONCLUSIONS Metal ions present several complications in ITC experiments. This review presents strategies to avoid these pitfalls and proposes and experimentally validates mathematical approaches to deconvolute complex equilibria that exist in these systems. GENERAL SIGNIFICANCE This review discusses the wide range of complications that exists in metal-based ITC experiments. It provides a starting point for scientists new to this field and articulates concerns that will help experienced researchers troubleshoot experiments.
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Affiliation(s)
- Rachel A Johnson
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Olivia M Manley
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States
| | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States.
| | - Nicholas E Grossoehme
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States.
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Zhuo Y, Cano KE, Wang L, Ilangovan U, Hinck AP, Sousa R, Lafer EM. Nuclear Magnetic Resonance Structural Mapping Reveals Promiscuous Interactions between Clathrin-Box Motif Sequences and the N-Terminal Domain of the Clathrin Heavy Chain. Biochemistry 2015; 54:2571-80. [PMID: 25844500 PMCID: PMC4429812 DOI: 10.1021/acs.biochem.5b00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The recruitment and organization
of clathrin at endocytic sites
first to form coated pits and then clathrin-coated vesicles depend
on interactions between the clathrin N-terminal domain (TD) and multiple
clathrin binding sequences on the cargo adaptor and accessory proteins
that are concentrated at such sites. Up to four distinct protein binding
sites have been proposed to be present on the clathrin TD, with each
site proposed to interact with a distinct clathrin binding motif.
However, an understanding of how such interactions contribute to clathrin
coat assembly must take into account observations that any three of
these four sites on clathrin TD can be mutationally ablated without
causing loss of clathrin-mediated endocytosis. To take an unbiased
approach to mapping binding sites for clathrin-box motifs on clathrin
TD, we used isothermal titration calorimetry (ITC) and nuclear magnetic
resonance spectroscopy. Our ITC experiments revealed that a canonical
clathrin-box motif peptide from the AP-2 adaptor binds to clathrin
TD with a stoichiometry of 3:1. Assignment of 90% of the total visible
amide resonances in the TROSY-HSQC spectrum of 13C-, 2H-, and 15N-labeled TD40 allowed us to map these
three binding sites by analyzing the chemical shift changes as clathrin-box
motif peptides were titrated into clathrin TD. We found that three
different clathrin-box motif peptides can each simultaneously bind
not only to the previously characterized clathrin-box site but also
to the W-box site and the β-arrestin splice loop site on a single
TD. The promiscuity of these binding sites can help explain why their
mutation does not lead to larger effects on clathrin function and
suggests a mechanism by which clathrin may be transferred between
different proteins during the course of an endocytic event.
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Affiliation(s)
- Yue Zhuo
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Kristin E Cano
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Liping Wang
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Udayar Ilangovan
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Andrew P Hinck
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Rui Sousa
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Eileen M Lafer
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
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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: 233] [Impact Index Per Article: 25.9] [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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59
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Scheuermann TH, Brautigam CA. High-precision, automated integration of multiple isothermal titration calorimetric thermograms: new features of NITPIC. Methods 2014; 76:87-98. [PMID: 25524420 DOI: 10.1016/j.ymeth.2014.11.024] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 11/25/2022] Open
Abstract
Isothermal titration calorimetry (ITC) has become a standard and widely available tool to measure the thermodynamic parameters of macromolecular associations. Modern applications of the method, including global analysis and drug screening, require the acquisition of multiple sets of data; sometimes these data sets number in the hundreds. Therefore, there is a need for quick, precise, and automated means to process the data, particularly at the first step of data analysis, which is commonly the integration of the raw data to yield an interpretable isotherm. Herein, we describe enhancements to an algorithm that previously has been shown to provide an automated, unbiased, and high-precision means to integrate ITC data. These improvements allow for the speedy and precise serial integration of an unlimited number of ITC data sets, and they have been implemented in the freeware program NITPIC, version 1.1.0. We present a comprehensive comparison of the performance of this software against an older version of NITPIC and a current version of Origin, which is commonly used for integration. The new methods recapitulate the excellent performance of the previous versions of NITPIC while speeding it up substantially, and their precision is significantly better than that of Origin. This new version of NITPIC is therefore well suited to the serial integration of many ITC data sets.
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Affiliation(s)
- Thomas H Scheuermann
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA.
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