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Upadhyay V, Lucas A, Patrick C, Mallela KMG. Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions. Methods 2024; 225:52-61. [PMID: 38492901 DOI: 10.1016/j.ymeth.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024] Open
Abstract
Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Casey Patrick
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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2
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Groslambert L, Cornaton Y, Ditte M, Aubert E, Pale P, Tkatchenko A, Djukic JP, Mamane V. Affinity of Telluronium Chalcogen Bond Donors for Lewis Bases in Solution: A Critical Experimental-Theoretical Joint Study. Chemistry 2024; 30:e202302933. [PMID: 37970753 DOI: 10.1002/chem.202302933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/17/2023]
Abstract
Telluronium salts [Ar2 MeTe]X were synthesized, and their Lewis acidic properties towards a number of Lewis bases were addressed in solution by physical and theoretical means. Structural X-ray diffraction analysis of 21 different salts revealed the electrophilicity of the Te centers in their interactions with anions. Telluroniums' propensity to form Lewis pairs was investigated with OPPh3 . Diffusion-ordered NMR spectroscopy suggested that telluroniums can bind up to three OPPh3 molecules. Isotherm titration calorimetry showed that the related heats of association in 1,2-dichloroethane depend on the electronic properties of the substituents of the aryl moiety and on the nature of the counterion. The enthalpies of first association of OPPh3 span -0.5 to -5 kcal mol-1 . Study of the affinity of telluroniums for OPPh3 by state-of-the-art DFT and ab-initio methods revealed the dominant Coulombic and dispersion interactions as well as an entropic effect favoring association in solution. Intermolecular orbital interactions between [Ar2 MeTe]+ cations and OPPh3 are deemed insufficient on their own to ensure the cohesion of [Ar2 MeTe ⋅ Bn ]+ complexes in solution (B=Lewis base). Comparison of Grimme's and Tkatchenko's DFT-D4/MBD-vdW thermodynamics of formation of higher [Ar2 MeTe ⋅ Bn ]+ complexes revealed significant molecular size-dependent divergence of the two methodologies, with MBD yielding better agreement with experiment.
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Affiliation(s)
- Loïc Groslambert
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Yann Cornaton
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | | | - Patrick Pale
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Jean-Pierre Djukic
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Victor Mamane
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
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3
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Estelle AB, George A, Barbar EJ, Zuckerman DM. Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS Comput Biol 2023; 19:e1011059. [PMID: 37083599 PMCID: PMC10155966 DOI: 10.1371/journal.pcbi.1011059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/03/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Multistep protein-protein interactions underlie most biological processes, but their characterization through methods such as isothermal titration calorimetry (ITC) is largely confined to simple models that provide little information on the intermediate, individual steps. In this study, we primarily examine the essential hub protein LC8, a small dimer that binds disordered regions of 100+ client proteins in two symmetrical grooves at the dimer interface. Mechanistic details of LC8 binding have remained elusive, hampered in part by ITC data analyses employing simple models that treat bivalent binding as a single event with a single binding affinity. We build on existing Bayesian ITC approaches to quantify thermodynamic parameters for multi-site binding interactions impacted by significant uncertainty in protein concentration. Using a two-site binding model, we identify positive cooperativity with high confidence for LC8 binding to multiple client peptides. In contrast, application of an identical model to the two-site binding between the coiled-coil NudE dimer and the intermediate chain of dynein reveals little evidence of cooperativity. We propose that cooperativity in the LC8 system drives the formation of saturated induced-dimer structures, the functional units of most LC8 complexes. In addition to these system-specific findings, our work advances general ITC analysis in two ways. First, we describe a previously unrecognized mathematical ambiguity in concentrations in standard binding models and clarify how it impacts the precision with which binding parameters are determinable in cases of high uncertainty in analyte concentrations. Second, building on observations in the LC8 system, we develop a system-agnostic heat map of practical parameter identifiability calculated from synthetic data which demonstrates that the ability to determine microscopic binding parameters is strongly dependent on both the parameters themselves and experimental conditions. The work serves as a foundation for determination of multi-step binding interactions, and we outline best practices for Bayesian analysis of ITC experiments.
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Affiliation(s)
- Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - August George
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
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Ionic Strength Dependence of the Complex Coacervation between Lactoferrin and β-Lactoglobulin. Foods 2023; 12:foods12051040. [PMID: 36900563 PMCID: PMC10001252 DOI: 10.3390/foods12051040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Heteroprotein complex coacervation is an assembly formed by oppositely charged proteins in aqueous solution that leads to liquid-liquid phase separation. The ability of lactoferrin and β-lactoglobulin to form complex coacervates at pH 5.5 under optimal protein stoichiometry has been studied in a previous work. The goal of the current study is to determine the influence of ionic strength on the complex coacervation between these two proteins using direct mixing and desalting protocols. The initial interaction between lactoferrin and β-lactoglobulin and subsequent coacervation process were highly sensitive to the ionic strength. No microscopic phase separation was observed beyond a salt concentration of 20 mM. The coacervate yield decreased drastically with increasing added NaCl from 0 to 60 mM. The charge-screening effect induced by increasing the ionic strength is attributed to a decrease of interaction between the two oppositely charged proteins throughout a decrease in Debye length. Interestingly, as shown by isothermal titration calorimetry, a small concentration of NaCl around 2.5 mM promoted the binding energy between the two proteins. These results shed new light on the electrostatically driven mechanism governing the complex coacervation in heteroprotein systems.
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Cavender CE, Schroeder GM, Mathews DH, Wedekind JE. Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model. Methods Mol Biol 2023; 2568:53-73. [PMID: 36227562 DOI: 10.1007/978-1-0716-2687-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Isothermal titration calorimetry (ITC) is a powerful biophysical tool to characterize energetic profiles of biomacromolecular interactions without any alteration of the underlying chemical structures. In this protocol, we describe procedures for performing, analyzing, and interpreting ITC data obtained from a cooperative riboswitch-ligand interaction.
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Affiliation(s)
- Chapin E Cavender
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - Griffin M Schroeder
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA.
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA.
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Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O. Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility. Nat Commun 2022; 13:6208. [PMID: 36266333 PMCID: PMC9584906 DOI: 10.1038/s41467-022-34017-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (PresTS), complexed with chloride, sulfate, or salicylate at 3.52-3.63 Å resolutions. The central positively-charged cavity allows flexible binding of various anion species, which likely accounts for the known distinct modulations of nonlinear capacitance (NLC) by different anions. Comparisons of these PresTS structures with recent prestin structures suggest rigid-body movement between the core and gate domains, and provide mechanistic insights into prestin inhibition by salicylate. Mutations at the dimeric interface severely diminished NLC, suggesting that stabilization of the gate domain facilitates core domain movement, thereby contributing to the expression of NLC. These findings advance our understanding of the molecular mechanism underlying mammalian cochlear amplification.
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Affiliation(s)
- Haon Futamata
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiro Fukuda
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.26999.3d0000 0001 2151 536XPresent Address: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo; Meguro-ku, Tokyo, 153-8503 Japan
| | - Rie Umeda
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Keitaro Yamashita
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.42475.300000 0004 0605 769XPresent Address: MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Atsuhiro Tomita
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Satoe Takahashi
- grid.16753.360000 0001 2299 3507Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Takafumi Shikakura
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Shigehiko Hayashi
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tsukasa Kusakizako
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tomohiro Nishizawa
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.268441.d0000 0001 1033 6139Present Address: Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kazuaki Homma
- grid.16753.360000 0001 2299 3507Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL 60608 USA
| | - Osamu Nureki
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
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Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2. Cell Rep 2022; 40:111254. [PMID: 36001965 PMCID: PMC9440770 DOI: 10.1016/j.celrep.2022.111254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 05/23/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Allosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain-the αX I-domain-corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg2+-binding site establish long-range couplings, leading to both pH- and Mg2+-occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH- and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.
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A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nat Commun 2022; 13:199. [PMID: 35017488 PMCID: PMC8752633 DOI: 10.1038/s41467-021-27790-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development. Riboswitches contain an aptamer domain that recognizes a metabolite and an expression platform that regulates gene expression. Here the authors report the crystal structure of a preQ1-sensing riboswitch from Carnobacterium antarcticus that shows two metabolites in a single binding pocket.
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9
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Björklund E, du Rietz A, Lundström P. Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions. Protein Sci 2021; 31:301-307. [PMID: 34791737 PMCID: PMC8740844 DOI: 10.1002/pro.4240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022]
Abstract
We present PLIS, a publicly available, open‐source software for the determination of protein–ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.
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Affiliation(s)
- Emil Björklund
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Anna du Rietz
- Division of Molecular Surface Physics and Nanoscience, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Patrik Lundström
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
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11
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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12
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Shi S, Quarta N, Zhang H, Lu Z, Hof M, Šachl R, Liu R, Hoernke M. Hidden complexity in membrane permeabilization behavior of antimicrobial polycations. Phys Chem Chem Phys 2021; 23:1475-1488. [DOI: 10.1039/d0cp05651k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There are diverse membrane permeabilization behaviors of antimicrobial polycations in zwitterionic or charged vesicles; different mechanisms may occur over time.
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Affiliation(s)
- Shuai Shi
- Chemistry and Pharmacy
- Albert-Ludwigs-Universität
- 79104 Freiburg i.Br
- Germany
| | - Ndjali Quarta
- Chemistry and Pharmacy
- Albert-Ludwigs-Universität
- 79104 Freiburg i.Br
- Germany
- Department of Chemistry, Biochemistry
| | - Haodong Zhang
- State Key Laboratory of Bioreactor Engineering
- Frontiers Science Center for Materiobiology and Dynamic Chemistry
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Ziyi Lu
- State Key Laboratory of Bioreactor Engineering
- Frontiers Science Center for Materiobiology and Dynamic Chemistry
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences
- 182 23 Prague
- Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences
- 182 23 Prague
- Czech Republic
| | - Runhui Liu
- State Key Laboratory of Bioreactor Engineering
- Frontiers Science Center for Materiobiology and Dynamic Chemistry
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Maria Hoernke
- Chemistry and Pharmacy
- Albert-Ludwigs-Universität
- 79104 Freiburg i.Br
- Germany
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13
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Wheeler LC, Perkins A, Wong CE, Harms MJ. Learning peptide recognition rules for a low-specificity protein. Protein Sci 2020; 29:2259-2273. [PMID: 32979254 PMCID: PMC7586891 DOI: 10.1002/pro.3958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022]
Abstract
Many proteins interact with short linear regions of target proteins. For some proteins, however, it is difficult to identify a well-defined sequence motif that defines its target peptides. To overcome this difficulty, we used supervised machine learning to train a model that treats each peptide as a collection of easily-calculated biochemical features rather than as an amino acid sequence. As a test case, we dissected the peptide-recognition rules for human S100A5 (hA5), a low-specificity calcium binding protein. We trained a Random Forest model against a recently released, high-throughput phage display dataset collected for hA5. The model identifies hydrophobicity and shape complementarity, rather than polar contacts, as the primary determinants of peptide binding specificity in hA5. We tested this hypothesis by solving a crystal structure of hA5 and through computational docking studies of diverse peptides onto hA5. These structural studies revealed that peptides exhibit multiple binding modes at the hA5 peptide interface-all of which have few polar contacts with hA5. Finally, we used our trained model to predict new, plausible binding targets in the human proteome. This revealed a fragment of the protein α-1-syntrophin that binds to hA5. Our work helps better understand the biochemistry and biology of hA5, as well as demonstrating how high-throughput experiments coupled with machine learning of biochemical features can reveal the determinants of binding specificity in low-specificity proteins.
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Affiliation(s)
- Lucas C. Wheeler
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Arden Perkins
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Caitlyn E. Wong
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Michael J. Harms
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
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14
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Saunders SH, Tse ECM, Yates MD, Otero FJ, Trammell SA, Stemp EDA, Barton JK, Tender LM, Newman DK. Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms. Cell 2020; 182:919-932.e19. [PMID: 32763156 DOI: 10.1016/j.cell.2020.07.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/19/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022]
Abstract
Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.
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Affiliation(s)
- Scott H Saunders
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA
| | - Edmund C M Tse
- Division of Chemistry and Chemical Engineering, Caltech, Pasadena, CA, USA; Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | | | - Scott A Trammell
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Eric D A Stemp
- Department of Physical Sciences, Mt. Saint Mary's University, Los Angeles, CA, USA
| | | | - Leonard M Tender
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA.
| | - Dianne K Newman
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA; Division of Geological and Planetary Sciences, Caltech, Pasadena, CA, USA.
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15
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Gorman SD, Winston DS, Sahu D, Boehr DD. Different Solvent and Conformational Entropy Contributions to the Allosteric Activation and Inhibition Mechanisms of Yeast Chorismate Mutase. Biochemistry 2020; 59:2528-2540. [DOI: 10.1021/acs.biochem.0c00277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Scott D. Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dennis S. Winston
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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16
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Rennie ML, Crowley PB. A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold. Chemphyschem 2019; 20:1011-1017. [DOI: 10.1002/cphc.201900153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
- Present address: Institute of Molecular Cell and System BiologyUniversity of Glasgow University Avenue Glasgow UK
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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17
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Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, Crowley PB. Calixarene-mediated assembly of a small antifungal protein. IUCRJ 2019; 6:238-247. [PMID: 30867921 PMCID: PMC6400181 DOI: 10.1107/s2052252519000411] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/08/2019] [Indexed: 05/24/2023]
Abstract
Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Gábor Lehoczki
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Hajdu Dorottya
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Ádám Fizil
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Gyula Batta
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
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