1
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Liang Y, Schettini R, Kern N, Manciocchi L, Izzo I, Spichty M, Bodlenner A, Compain P. Deconstructing Best-in-Class Neoglycoclusters as a Tool for Dissecting Key Multivalent Processes in Glycosidase Inhibition. Chemistry 2024; 30:e202304126. [PMID: 38221894 DOI: 10.1002/chem.202304126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
Multivalency represents an appealing option to modulate selectivity in enzyme inhibition and transform moderate glycosidase inhibitors into highly potent ones. The rational design of multivalent inhibitors is however challenging because global affinity enhancement relies on several interconnected local mechanistic events, whose relative impact is unknown. So far, the largest multivalent effects ever reported for a non-polymeric glycosidase inhibitor have been obtained with cyclopeptoid-based inhibitors of Jack bean α-mannosidase (JBα-man). Here, we report a structure-activity relationship (SAR) study based on the top-down deconstruction of best-in-class multivalent inhibitors. This approach provides a valuable tool to understand the complex interdependent mechanisms underpinning the inhibitory multivalent effect. Combining SAR experiments, binding stoichiometry assessments, thermodynamic modelling and atomistic simulations allowed us to establish the significant contribution of statistical rebinding mechanisms and the importance of several key parameters, including inhitope accessibility, topological restrictions, and electrostatic interactions. Our findings indicate that strong chelate-binding, resulting from the formation of a cross-linked complex between a multivalent inhibitor and two dimeric JBα-man molecules, is not a sufficient condition to reach high levels of affinity enhancements. The deconstruction approach thus offers unique opportunities to better understand multivalent binding and provides important guidelines for the design of potent and selective multiheaded inhibitors.
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Affiliation(s)
- Yan Liang
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Rosaria Schettini
- Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di, Salerno, 84084, Fisciano (Salerno), Italy
| | - Nicolas Kern
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Luca Manciocchi
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042)-IRJBD, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
| | - Irene Izzo
- Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di, Salerno, 84084, Fisciano (Salerno), Italy
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042)-IRJBD, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
| | - Anne Bodlenner
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
| | - Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), University of Strasbourg|University of Haute-Alsace|CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67087, Strasbourg, France)
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2
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Archer C. Isothermal Titration Calorimetry for Fragment-Based Analysis of Ion Channel Interactions. Methods Mol Biol 2024; 2796:271-289. [PMID: 38856907 DOI: 10.1007/978-1-0716-3818-7_16] [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: 06/11/2024]
Abstract
Ion channels are membrane proteins that may also have intracellular and extracellular domains that interact with other ligands. In many cases, these interaction sites are highly mobile and may undergo changes in the configuration upon binding with regulatory signaling molecules. Isothermal titration calorimetry (ITC) is a powerful technique to quantify protein-ligand interactions of purified samples in solution. This chapter describes a fragment-based analysis method using ITC to quantify the interactions between a domain of the voltage-gated Kv7 channel and the calcium-regulated protein calmodulin. This example can be used to quantify the interactions between specific domains of other ion channels and their regulatory signaling proteins.
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Affiliation(s)
- Crystal Archer
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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3
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Omori A, Sasaki S, Kikukawa T, Shimono K, Miyauchi S. Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H +/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The Substrate Binding Driven by the Change in Entropy Implies the Release of Bound Water Molecules from the Binding Pocket. Biochemistry 2023. [PMID: 37163674 DOI: 10.1021/acs.biochem.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we have elucidated the substrate recognition mechanism by a prokaryotic H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic conditions (pH 6.0), the binding of a dipeptide, Val-Ala, to YdgR elicited endothermic enthalpy, which compensated for the increase in entropy due to dipeptide binding. A series of dipeptides were used in the binding titration. The dipeptides represent Val-X and X-Val, where X is Ala, Ser, Val, Tyr, or Phe. Most dipeptides revealed endothermic enthalpy, which was completely compensated by the increase in entropy due to dipeptide binding. The change in enthalpy due to binding correlated well with the change in entropy, whereas the Gibbs free energy involved in the binding of the dipeptide to YdgR remained unchanged irrespective of dipeptide sequences, implying that the binding reaction was driven by entropy, that is, the release of bound water molecules in the binding pocket. It is also important to clarify that, based on the prediction of water molecules in the ligand-binding pocket of YdgR, the release of three bound water molecules in the putative substrate binding pocket occurred through binding to YdgR. In the comparison of Val-X and X-Val dipeptides, the N-terminal region of the binding pocket might contain more bound water molecules than the C-terminal region. In light of these findings, we suggest that bound water molecules might play an important role in substrate recognition and binding by YdgR.
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Affiliation(s)
- Akiko Omori
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shotaro Sasaki
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda Nishi-ku, Kumamoto 860-0082, Japan
| | - Seiji Miyauchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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4
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Distinct roles of the Na + binding sites in the allosteric coupling mechanism of the glutamate transporter homolog, Glt Ph. Proc Natl Acad Sci U S A 2022; 119:e2121653119. [PMID: 35507872 DOI: 10.1073/pnas.2121653119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceGlutamate transporters harness ionic gradients present across the membrane for the rapid removal of glutamate from the synaptic space. Normal function of glutamate transporters is required for efficient synaptic transmission and preventing excitotoxicity. Central to the transport mechanism is the coupled binding of Na+ and the substrate. While structural studies have identified the Na+ and the substrate binding sites, the mechanism by which Na+ and substrate binding is coupled is not known. In this study, we developed assays to monitor Na+ binding and to track key conformational changes in GltPh, an archaeal homolog of glutamate transporters. We use these assays along with previously developed assays to describe the specific roles of the Na+ sites in the coupling mechanism.
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5
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Reddy KD, Ciftci D, Scopelliti AJ, Boudker O. The archaeal glutamate transporter homologue GltPh shows heterogeneous substrate binding. J Gen Physiol 2022; 154:e202213131. [PMID: 35452090 PMCID: PMC9044058 DOI: 10.1085/jgp.202213131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this protein family. Recent studies of an archaeal homologue, GltPh, revealed transport rate heterogeneity, which is inconsistent with simple kinetic models; however, its structural and mechanistic determinants remain undefined. Here, we demonstrate that in a mutant GltPh, which exclusively populates the outward-facing state, at least two substates coexist in slow equilibrium, binding the substrate with different apparent affinities. Wild type GltPh shows similar binding properties, and modulation of the substate equilibrium correlates with transport rates. The low-affinity substate of the mutant is transient following substrate binding. Consistently, cryo-EM on samples frozen within seconds after substrate addition reveals the presence of structural classes with perturbed helical packing of the extracellular half of the transport domain in regions adjacent to the binding site. By contrast, an equilibrated structure does not show such classes. The structure at 2.2-Å resolution details a pattern of waters in the intracellular half of the domain and resolves classes with subtle differences in the substrate-binding site. We hypothesize that the rigid cytoplasmic half of the domain mediates substrate and ion recognition and coupling, whereas the extracellular labile half sets the affinity and dynamic properties.
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Affiliation(s)
- Krishna D. Reddy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
| | - Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
- Tri-Institutional Training Program in Chemical Biology, New York, NY
| | | | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY
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6
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Neves AT, Stenner R, Race PR, Curnow P. Expression, purification and preliminary characterisation of the choline transporter LicB from opportunistic bacterial pathogens. Protein Expr Purif 2021; 190:106011. [PMID: 34737041 DOI: 10.1016/j.pep.2021.106011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022]
Abstract
Many opportunistic bacteria that infect the upper respiratory tract decorate their cell surface with phosphorylcholine to support colonisation and outgrowth. These surface modifications require the active import of choline from the host environment, a process thought to be mediated by a family of dedicated integral membrane proteins that act as choline permeases. Here, we present the expression and purification of the archetype of these choline transporters, LicB from Haemophilus influenzae. We show that LicB can be recombinantly produced in Escherichia coli and purified to homogeneity in a stable, folded state using the detergent n-dodecyl-β-d-maltopyranoside. Equilibrium binding studies with the fluorescent ligand dansylcholine suggest that LicB is selective towards choline, with reduced affinity for acetylcholine and no apparent activity towards other small molecules including glycine, carnitine and betaine. We also identify a conserved sequence motif within the LicB family and show that mutations within this motif compromise protein structure and function. Our results are consistent with previous observations that LicB is a specific high-affinity choline transporter, and provide an experimental platform for further studies of this permease family.
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Affiliation(s)
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, UK.
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7
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Ng LCT, Zhuang M, Van Petegem F, Li YX, Accili EA. Binding and structural asymmetry governs ligand sensitivity in a cyclic nucleotide-gated ion channel. J Gen Physiol 2019; 151:1190-1212. [PMID: 31481514 PMCID: PMC6785730 DOI: 10.1085/jgp.201812162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/26/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
HCN channel opening is facilitated by cyclic nucleotides, but what determines the sensitivity of these channels to cAMP or cGMP is unclear. Ng et al. propose that ligand sensitivity depends on negative cooperativity and the asymmetric effects of ligand binding on channel structure and pore opening. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels open more easily when cAMP or cGMP bind to a domain in the intracellular C-terminus in each of four identical subunits. How sensitivity of the channels to these ligands is determined is not well understood. Here, we apply a mathematical model, which incorporates negative cooperativity, to gating and mutagenesis data available in the literature and combine the results with binding data collected using isothermal titration calorimetry. This model recapitulates the concentration–response data for the effects of cAMP and cGMP on wild-type HCN2 channel opening and, remarkably, predicts the concentration–response data for a subset of mutants with single-point amino acid substitutions in the binding site. Our results suggest that ligand sensitivity is determined by negative cooperativity and asymmetric effects on structure and channel opening, which are tuned by ligand-specific interactions and residues within the binding site.
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Affiliation(s)
- Leo C T Ng
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Meiying Zhuang
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Yue Xian Li
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Eric A Accili
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
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8
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Thoppil AA, Chennuri BK, Gardas RL. Insights into the structural changes of bovine serum albumin in ethanolammonium laurate based surface active ionic liquids. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Thermodynamic Analysis of Protein-Lipid Interactions by Isothermal Titration Calorimetry. Methods Mol Biol 2019; 2003:71-89. [PMID: 31218614 DOI: 10.1007/978-1-4939-9512-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Isothermal titration calorimetry is a highly sensitive and powerful technique for the study of molecular interactions. This method can be applied universally for studying the interaction between moleculeAbstracts, molecular assembles and ions as it measures the heat changes resulting from such interactions and does not need any probe molecule/moiety to be incorporated into the system under investigation. This method has been applied quite extensively to investigate the interaction of proteins with other biomolecules such as small ligands, other proteins, nucleic acids, lipid membranes as well as to study the interaction of antibodies, drugs, metal ions and nanoparticles with target proteins or antigens, nucleic acids, and membranes. In this chapter, we describe the application of ITC for the investigation of thermodynamics of protein-lipid interaction. A number of important parameters such as enthalpy of binding (ΔH), entropy of binding (ΔS), association constant (Ka), binding stoichiometry (n) and free energy of binding (ΔG) can be obtained from a single calorimetric titration, providing a complete thermodynamic characterization of the interaction. The method is described in detail taking the major protein of the bovine seminal plasma, PDC-109, which exhibits a high preference for interaction with choline-containing lipids, as an example. The method can be applied to investigate thermodynamic parameters associated with the interaction of other soluble proteins with lipid membranes.
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10
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Sprakel LMJ, Schuur B. Thermal Activity in Affinity Separation Techniques Such as Liquid-Liquid Extraction Analyzed by Isothermal Titration Calorimetry and Accuracy Analysis of the Technique in the Molar Concentration Domain. Ind Eng Chem Res 2018; 57:12574-12582. [PMID: 30270979 PMCID: PMC6156095 DOI: 10.1021/acs.iecr.8b03066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 11/30/2022]
Abstract
![]()
The applicability and accuracy of
isothermal titration calorimetry
(ITC) to investigate intermolecular interactions in a high concentration
domain applicable to liquid–liquid extraction (LLX) was studied
for acid–base interactions. More accurate fits can be obtained
using a sequential binding mechanism compared to a single reaction
model, at the risk of finding a local minimum. Experiments with 0.24
M tri-n-octylamine (TOA) resulted in a residue of
fit of 4.3% for the single reaction model, with a standard deviation
σ of 1.6% in the stoichiometry parameter n,
12% in the complexation constant Kn,1, and 2.5% in the enthalpy ΔHn,1. For the sequential model, σ was
higher: 11% in K1,1, 26% in Kn+1,1, and 12% in ΔHn+1,1. This study clearly showed that,
at higher concentrations (order of moles per liter), accurate parameter
estimation is possible and parameter values are concentration dependent.
It is thus important to do ITC at the application concentration.
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Affiliation(s)
- Lisette M J Sprakel
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
| | - Boelo Schuur
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
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11
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Hariharan P, Andersson M, Jiang X, Pardon E, Steyaert J, Kaback HR, Guan L. Thermodynamics of Nanobody Binding to Lactose Permease. Biochemistry 2016; 55:5917-5926. [PMID: 27686537 DOI: 10.1021/acs.biochem.6b00826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Camelid nanobodies (Nbs) raised against the outward-facing conformer of a double-Trp mutant of the lactose permease of Escherichia coli (LacY) stabilize the permease in outward-facing conformations. Isothermal titration calorimetry is applied herein to dissect the binding thermodynamics of two Nbs, one that markedly improves access to the sugar-binding site and another that dramatically increases the affinity for galactoside. The findings presented here show that both enthalpy and entropy contribute favorably to binding of the Nbs to wild-type (WT) LacY and that binding of Nb to double-Trp mutant G46W/G262W is driven by a greater enthalpy at an entropic penalty. Thermodynamic analyses support the interpretation that WT LacY is stabilized in outward-facing conformations like the double-Trp mutant with closure of the water-filled cytoplasmic cavity through conformational selection. The LacY conformational transition required for ligand binding is reflected by a favorable entropy increase. Molecular dynamics simulations further suggest that the entropy increase likely stems from release of immobilized water molecules primarily from the cytoplasmic cavity upon closure.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
| | - Magnus Andersson
- Department of Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology , SE-171 21 Solna, Sweden
| | - Xiaoxu Jiang
- Department of Physiology, University of California , Los Angeles, California 90095, United States
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB , 1050 Brussel, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussel, Belgium
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB , 1050 Brussel, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology, University of California , Los Angeles, California 90095, United States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
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12
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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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13
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Bian X, Lockless SW. Preparation To Minimize Buffer Mismatch in Isothermal Titration Calorimetry Experiments. Anal Chem 2016; 88:5549-53. [PMID: 27092566 DOI: 10.1021/acs.analchem.6b01319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There is a growing need to study ligand binding to proteins in native or complex solution using isothermal titration calorimetry (ITC). For example, it is desirable to measure ligand binding to membrane proteins in more native lipid-like environments such as bicelles, where ligands can access both sides of the membrane in a homogeneous environment. A critical step to obtain high signal-to-noise is matching the reaction chamber solution to the ligand solution, typically through a final dialysis or gel filtration step. However, to obtain reproducible bicelles, the lipid concentrations must be carefully controlled which eliminates the use of dialysis that can disrupt these parameters. Here, we report and validate a rapid preparation ITC (RP-ITC) approach to measure ligand binding without the need for a dialysis step. This general approach is used to quantify ion binding to a K(+) channel embedded in bicelles and can be applied to complex, less defined systems.
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Affiliation(s)
- Xuelin Bian
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
| | - Steve W Lockless
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
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14
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Competitive binding of anticancer drugs 5-fluorouracil and cyclophosphamide with serum albumin: Calorimetric insights. Biochim Biophys Acta Gen Subj 2016; 1860:917-929. [DOI: 10.1016/j.bbagen.2016.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/27/2016] [Accepted: 01/30/2016] [Indexed: 11/22/2022]
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15
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LeVine MV, Cuendet MA, Khelashvili G, Weinstein H. Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters. Chem Rev 2016; 116:6552-87. [PMID: 26892914 DOI: 10.1021/acs.chemrev.5b00627] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Solute transport across cell membranes is ubiquitous in biology as an essential physiological process. Secondary active transporters couple the unfavorable process of solute transport against its concentration gradient to the energetically favorable transport of one or several ions. The study of such transporters over several decades indicates that their function involves complex allosteric mechanisms that are progressively being revealed in atomistic detail. We focus on two well-characterized sodium-coupled symporters: the bacterial amino acid transporter LeuT, which is the prototype for the "gated pore" mechanism in the mammalian synaptic monoamine transporters, and the archaeal GltPh, which is the prototype for the "elevator" mechanism in the mammalian excitatory amino acid transporters. We present the evidence for the role of allostery in the context of a quantitative formalism that can reconcile biochemical and biophysical data and thereby connects directly to recent insights into the molecular structure and dynamics of these proteins. We demonstrate that, while the structures and mechanisms of these transporters are very different, the available data suggest a common role of specific models of allostery in their functions. We argue that such allosteric mechanisms appear essential not only for sodium-coupled symport in general but also for the function of other types of molecular machines in the membrane.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Michel A Cuendet
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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16
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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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