1
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Ben-Tal Y, Boaler PJ, Dale HJA, Dooley RE, Fohn NA, Gao Y, García-Domínguez A, Grant KM, Hall AMR, Hayes HLD, Kucharski MM, Wei R, Lloyd-Jones GC. Mechanistic analysis by NMR spectroscopy: A users guide. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 129:28-106. [PMID: 35292133 DOI: 10.1016/j.pnmrs.2022.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (1/2H, 10/11B, 13C, 15N, 19F, 29Si, 31P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, 1H/19F DOSY NMR, and in situ illumination NMR.
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Affiliation(s)
- Yael Ben-Tal
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Patrick J Boaler
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Harvey J A Dale
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ruth E Dooley
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom; Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Nicole A Fohn
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Yuan Gao
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrés García-Domínguez
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Katie M Grant
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrew M R Hall
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Hannah L D Hayes
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Maciej M Kucharski
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ran Wei
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Guy C Lloyd-Jones
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom.
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2
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Wei R, Hall AMR, Behrens R, Pritchard MS, King EJ, Lloyd‐Jones GC. Stopped‐Flow
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F NMR Spectroscopic Analysis of a Protodeboronation Proceeding at the Sub‐Second Time‐Scale. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100290] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ran Wei
- School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Andrew M. R. Hall
- School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Richard Behrens
- Laboratory of Engineering Thermodynamics (LTD) Technische Universität Kaiserslautern Erwin-Schrödinger-Straße 44 Kaiserslautern 67663 Germany
| | | | - Edward J. King
- TgK Scientific Ltd. Bradford on Avon Wiltshire BA15 1DH UK
| | - Guy C. Lloyd‐Jones
- School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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3
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Martin SR, Schilstra MJ. Interactions of a Signal Transduction Protein Investigated by Fluorescence Stopped-Flow Kinetics. Methods Mol Biol 2021; 2263:83-104. [PMID: 33877594 DOI: 10.1007/978-1-0716-1197-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To understand cellular processes such as biochemical pathways and signaling networks, we need to understand binding and reaction rates of often competing reactions, their dependence on cellular concentrations of participating molecules, and the regulation of these rates through allostery, posttranslational modifications, or other mechanisms. To do so, we break these systems down into their elementary steps, which are almost invariably either unimolecular or bimolecular reactions that frequently occur on sub-second, often sub-millisecond, time scales. Rapid mixing techniques, which generally achieve mixing in less than 2 ms, are generally suitable for the study of such reactions. The application of these techniques to the study of enzyme mechanisms is described in several excellent texts (Cornish-Bowden, Fundamentals of enzyme kinetics, 1995; Gutfreund, Kinetics for the life sciences. Receptors, transmitters and catalysis, 1995); flow techniques are used to study individual steps by monitoring the approach to equilibrium (the pre-steady state) under single turnover conditions.The individual steps in complex biochemical reaction schemes determine how fast systems can respond to incoming signals and adapt to changed conditions [1, 2]. This chapter is concerned with in vitro techniques that have been developed to study fast reactions in solution, and we present the study of various interactions of calmodulin as an example. The kinetic information obtained with these techniques is indispensable for understanding the dynamics of biochemical processes and complements the static structural and thermodynamic information available from X-ray crystallography, NMR, and equilibrium binding studies.
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Affiliation(s)
- Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.
| | - Maria J Schilstra
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
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4
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Abstract
RNA-binding proteins often contain multiple RNA-binding domains connected by short flexible linkers. This domain arrangement allows the protein to bind the RNA with greater affinity and specificity than would be possible with individual domains and sometimes to remodel its structure. It is therefore important to understand how multiple modules interact with RNA because it is the modular nature of these proteins which specifies their biological function. This chapter is concerned with the use of biolayer interferometry to study protein-RNA interactions.
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Affiliation(s)
- Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Andres Ramos
- Department of Structural & Molecular Biology, University College London, London, UK
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.
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5
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Thiophenethieno[2,3-b]pyridine-chitosan nanorods; synthesis, characterization, BSA-Binding and kinetic interactions with BSA, antibacterial and in-vitro release studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Kostrz D, Wayment-Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR, Gosse C. A modular DNA scaffold to study protein-protein interactions at single-molecule resolution. NATURE NANOTECHNOLOGY 2019; 14:988-993. [PMID: 31548690 DOI: 10.1038/s41565-019-0542-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The residence time of a drug on its target has been suggested as a more pertinent metric of therapeutic efficacy than the traditionally used affinity constant. Here, we introduce junctured-DNA tweezers as a generic platform that enables real-time observation, at the single-molecule level, of biomolecular interactions. This tool corresponds to a double-strand DNA scaffold that can be nanomanipulated and on which proteins of interest can be engrafted thanks to widely used genetic tagging strategies. Thus, junctured-DNA tweezers allow a straightforward and robust access to single-molecule force spectroscopy in drug discovery, and more generally in biophysics. Proof-of-principle experiments are provided for the rapamycin-mediated association between FKBP12 and FRB, a system relevant in both medicine and chemical biology. Individual interactions were monitored under a range of applied forces and temperatures, yielding after analysis the characteristic features of the energy profile along the dissociation landscape.
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Affiliation(s)
- Dorota Kostrz
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France
| | | | - Jing L Wang
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France
| | - Maryne Follenfant
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Institut Jacques Monod, CNRS, Université Paris Diderot, Université de Paris, Paris, France.
- Programme Equipe Labellisée, Ligue Nationale Contre le Cancer, Paris, France.
| | - Charlie Gosse
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS) CNRS, INSERM, PSL Research University, Paris, France.
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Marcoussis, France.
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7
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Pellissier-Tanon A, Chouket R, Le Saux T, Jullien L, Lemarchand A. Light-assisted dynamic titration: from theory to an experimental protocol. Phys Chem Chem Phys 2018; 20:23998-24010. [DOI: 10.1039/c8cp03953d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Forced light oscillations are used to titrate any targeted species using its specific kinetics and choosing adapted control parameter values.
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Affiliation(s)
| | - Raja Chouket
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Thomas Le Saux
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Ludovic Jullien
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Annie Lemarchand
- Sorbonne Université
- Centre National de la Recherche Scientifique (CNRS) Laboratoire de Physique Théorique de la Matière Condensée (LPTMC)
- 75252 Paris Cedex 05
- France
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8
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Quérard J, Le Saux T, Gautier A, Alcor D, Croquette V, Lemarchand A, Gosse C, Jullien L. Kinetics of Reactive Modules Adds Discriminative Dimensions for Selective Cell Imaging. Chemphyschem 2016; 17:1396-413. [PMID: 26833808 DOI: 10.1002/cphc.201500987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 11/07/2022]
Abstract
Living cells are chemical mixtures of exceptional interest and significance, whose investigation requires the development of powerful analytical tools fulfilling the demanding constraints resulting from their singular features. In particular, multiplexed observation of a large number of molecular targets with high spatiotemporal resolution appears highly desirable. One attractive road to address this analytical challenge relies on engaging the targets in reactions and exploiting the rich kinetic signature of the resulting reactive module, which originates from its topology and its rate constants. This review explores the various facets of this promising strategy. We first emphasize the singularity of the content of a living cell as a chemical mixture and suggest that its multiplexed observation is significant and timely. Then, we show that exploiting the kinetics of analytical processes is relevant to selectively detect a given analyte: upon perturbing the system, the kinetic window associated to response read-out has to be matched with that of the targeted reactive module. Eventually, we introduce the state-of-the-art of cell imaging exploiting protocols based on reaction kinetics and draw some promising perspectives.
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Affiliation(s)
- Jérôme Quérard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Thomas Le Saux
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Arnaud Gautier
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Damien Alcor
- INSERM U1065, C3M; 151 route Saint Antoine de Ginestière, BP 2 3194 F-06204 Nice Cedex 3 France
| | - Vincent Croquette
- Ecole Normale Supérieure; Département de Physique and Département de Biologie, Laboratoire de Physique Statistique UMR CNRS-ENS 8550; 24 rue Lhomond F-75005 Paris France
| | - Annie Lemarchand
- Sorbonne Universités; UPMC Univ Paris 06, Laboratoire de Physique Théorique de la Matière Condensée; 4 place Jussieu, case courrier 121 75252 Paris cedex 05 France
- CNRS, UMR 7600 LPTMC; 75005 Paris France
| | - Charlie Gosse
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS; route de Nozay 91460 Marcoussis France
| | - Ludovic Jullien
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
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9
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García-Márquez A, Gijsbers A, de la Mora E, Sánchez-Puig N. Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein. J Biol Chem 2015; 290:17669-17678. [PMID: 25991726 DOI: 10.1074/jbc.m114.626275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Indexed: 11/06/2022] Open
Abstract
Ribosome biogenesis is orchestrated by the action of several accessory factors that provide time and directionality to the process. One such accessory factor is the GTPase EFL1 involved in the cytoplasmic maturation of the ribosomal 60S subunit. EFL1 and SBDS, the protein mutated in the Shwachman-Diamond syndrome (SBDS), release the anti-association factor eIF6 from the surface of the ribosomal subunit 60S. Here we report a kinetic analysis of fluorescent guanine nucleotides binding to EFL1 alone and in the presence of SBDS using fluorescence stopped-flow spectroscopy. Binding kinetics of EFL1 to both GDP and GTP suggests a two-step mechanism with an initial binding event followed by a conformational change of the complex. Furthermore, the same behavior was observed in the presence of the SBDS protein irrespective of the guanine nucleotide evaluated. The affinity of EFL1 for GTP is 10-fold lower than that calculated for GDP. Association of EFL1 to SBDS did not modify the affinity for GTP but dramatically decreased that for GDP by increasing the dissociation rate of the nucleotide. Thus, SBDS acts as a guanine nucleotide exchange factor (GEF) for EFL1 promoting its activation by the release of GDP. Finally, fluorescence anisotropy measurements showed that the S143L mutation present in the Shwachman-Diamond syndrome altered a surface epitope for EFL1 and largely decreased the affinity for it. These results suggest that loss of interaction between these proteins due to mutations in the disease consequently prevents the nucleotide exchange regulation the SBDS exerts on EFL1.
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Affiliation(s)
- Adrián García-Márquez
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, c.p 04510, México D.F., México
| | - Abril Gijsbers
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, c.p 04510, México D.F., México
| | - Eugenio de la Mora
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, c.p 04510, México D.F., México
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, c.p 04510, México D.F., México.
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10
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Closa F, Gosse C, Jullien L, Lemarchand A. Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species. J Chem Phys 2015; 142:174108. [PMID: 25956091 DOI: 10.1063/1.4919632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored.
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Affiliation(s)
- F Closa
- Sorbonne Universités, UPMC Univ. Paris 06, Laboratoire de Physique Théorique de la Matière Condensée, 4 place Jussieu, case courrier 121, 75252 Paris Cedex 05, France
| | - C Gosse
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS, route de Nozay, 91460 Marcoussis, France
| | - L Jullien
- Department of Chemistry, Ecole Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005 Paris, France
| | - A Lemarchand
- Sorbonne Universités, UPMC Univ. Paris 06, Laboratoire de Physique Théorique de la Matière Condensée, 4 place Jussieu, case courrier 121, 75252 Paris Cedex 05, France
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11
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Abstract
Most biochemical processes occur on sub-second time scales. Relaxation and rapid mixing methods allow reactions from microsecond time scales onwards to be monitored in real time. This chapter describes the instrumentation for these techniques and it discusses general topics of sample excitation and signal detection.
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12
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Toseland CP. Fluorescence to study the ATPase mechanism of motor proteins. ACTA ACUST UNITED AC 2014; 105:67-86. [PMID: 25095991 DOI: 10.1007/978-3-0348-0856-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This chapter provides an overview of different methodologies to dissect the ATPase mechanism of motor proteins. The use of ATP is fundamental to how these molecular engines work and how they can use the energy to perform various cellular roles. Rapid reaction and single-molecule techniques will be discussed to monitor reactions in real time through the application of fluorescence intensity, anisotropy and FRET. These approaches utilise fluorescent nucleotides and biosensors. While not every technique may be suitable for your motor protein, the different ways to determine the ATPase mechanism should allow a good evaluation of the kinetic parameters.
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Affiliation(s)
- Christopher P Toseland
- Chromosome Organisation and Dynamics, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany,
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13
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Challier L, Miranda-Castro R, Marchal D, Noël V, Mavré F, Limoges B. Kinetic Rotating Droplet Electrochemistry: A Simple and Versatile Method for Reaction Progress Kinetic Analysis in Microliter Volumes. J Am Chem Soc 2013; 135:14215-28. [DOI: 10.1021/ja405415q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Damien Marchal
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - François Mavré
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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14
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Abstract
Almost all of the elementary steps in a biochemical reaction scheme are either unimolecular or bimolecular processes that frequently occur on sub-second, often sub-millisecond, time scales. The traditional approach in kinetic studies is to mix two or more reagents and monitor the changes in concentrations with time. Conventional spectrophotometers cannot generally be used to study reactions that are complete within less than about 20 s, as it takes that amount of time to manually mix the reagents and activate the instrument. Rapid mixing techniques, which generally achieve mixing in less than 2 ms, overcome this limitation. This chapter is concerned with the use of these techniques in the study of reactions which reach equilibrium; the application of these methods to the study of enzyme kinetics is described in several excellent texts (Cornish-Bowden, Fundamentals of enzyme kinetics. Portland Press, 1995; Gutfreund, Kinetics for the life sciences. Receptors, transmitters and catalysis. Cambridge University Press, 1995).There are various ways to monitor changes in concentration of reactants, intermediates and products after mixing, but the most common way is to use changes in optical signals (absorbance or fluorescence) which often accompany reactions. Although absorbance can sometimes be used, fluorescence is often preferred because of its greater sensitivity, particularly in monitoring conformational changes. Such methods are continuous with good time resolution but they seldom permit the direct determination of the concentrations of individual species. Alternatively, samples may be taken from the reaction volume, mixed with a chemical quenching agent to stop the reaction, and their contents assessed by techniques such as HPLC. These methods can directly determine the concentrations of different species, but are discontinuous and have a limited time resolution.
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Affiliation(s)
- Stephen R Martin
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, UK
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15
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Lemarchand A, Berthoumieux H, Jullien L, Gosse C. Chemical mechanism identification from frequency response to small temperature modulation. J Phys Chem A 2012; 116:8455-63. [PMID: 22835083 DOI: 10.1021/jp305737e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The description of interactions between biochemical species and the elucidation of the corresponding chemical mechanisms encounter an increasing interest both for the comprehension of biological pathways at the molecular scale and for the rationalization of drug design. Relying on powerful experimental tools such as thermal microfluidics and fluorescence detection, we propose a methodology to determine the chemical mechanism of a reaction without fitting parameters. A mechanism consistent with the accessible knowledge is assumed, and the assumption is checked through an iterative protocol. The test is based on the frequency analysis of the response of a targeted reactive species to temperature modulation. We build specific functions of the frequency that are constant for the assumed mechanism and show that the graph of these functions can be drawn from appropriate data analysis. The method is general and can be applied to any complex mechanism. It is here illustrated in detail in the case of single relaxation time mechanisms.
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Affiliation(s)
- A Lemarchand
- Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie - Paris 6, UMR 7600 LPTMC, 4, place Jussieu, case courrier 121, 75252 Paris cedex 05, France
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16
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Adedeji AO, Marchand B, te Velthuis AJW, Snijder EJ, Weiss S, Eoff RL, Singh K, Sarafianos SG. Mechanism of nucleic acid unwinding by SARS-CoV helicase. PLoS One 2012; 7:e36521. [PMID: 22615777 PMCID: PMC3352918 DOI: 10.1371/journal.pone.0036521] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/03/2012] [Indexed: 02/04/2023] Open
Abstract
The non-structural protein 13 (nsp13) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) is a helicase that separates double-stranded RNA (dsRNA) or DNA (dsDNA) with a 5′→3′ polarity, using the energy of nucleotide hydrolysis. We determined the minimal mechanism of helicase function by nsp13. We showed a clear unwinding lag with increasing length of the double-stranded region of the nucleic acid, suggesting the presence of intermediates in the unwinding process. To elucidate the nature of the intermediates we carried out transient kinetic analysis of the nsp13 helicase activity. We demonstrated that the enzyme unwinds nucleic acid in discrete steps of 9.3 base-pairs (bp) each, with a catalytic rate of 30 steps per second. Therefore the net unwinding rate is ∼280 base-pairs per second. We also showed that nsp12, the SARS-CoV RNA-dependent RNA polymerase (RdRp), enhances (2-fold) the catalytic efficiency of nsp13 by increasing the step size of nucleic acid (RNA/RNA or DNA/DNA) unwinding. This effect is specific for SARS-CoV nsp12, as no change in nsp13 activity was observed when foot-and-mouth-disease virus RdRp was used in place of nsp12. Our data provide experimental evidence that nsp13 and nsp12 can function in a concerted manner to improve the efficiency of viral replication and enhance our understanding of nsp13 function during SARS-CoV RNA synthesis.
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Affiliation(s)
- Adeyemi O. Adedeji
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Bruno Marchand
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Aartjan J. W. te Velthuis
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J. Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan Weiss
- Department of Microbiology, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Kamalendra Singh
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
| | - Stefan G. Sarafianos
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri, United States of America
- * E-mail:
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Bizzarri AR, Cannistraro S. Atomic Force Spectroscopy in Biological Complex Formation: Strategies and Perspectives. J Phys Chem B 2009; 113:16449-64. [DOI: 10.1021/jp902421r] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
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Correia JJ, Stafford WF. Extracting equilibrium constants from kinetically limited reacting systems. Methods Enzymol 2009; 455:419-46. [PMID: 19289215 DOI: 10.1016/s0076-6879(08)04215-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It has been known for some time that slow kinetics will distort the shape of a reversible reaction boundary. Here we present a tutorial on direct boundary fitting of sedimentation velocity data for a monomer-dimer system that exhibits kinetic effects. Previous analysis of a monomer-dimer system suggested that rapid reaction behavior will persist until the relaxation time of the system exceeds 100 s (reviewed in Kegeles and Cann, 1978). Utilizing a kinetic integrator feature in Sedanal (Stafford and Sherwood, 2004), we can now fit for the k(off) values and measure the uncertainty at the 95% confidence interval. For the monomer-dimer system the range of well determined k(off) values is limited to 0.005 to 10(-5) s(-1) corresponding to relaxation times (at a loading concentration of the Kd) of approximately 70 to approximately 33,000 s. For shorter relaxation times the system is fast and only the equilibrium constant K but not k(off) can be uniquely determined. For longer relaxation times the system is irreversibly slow, and assuming the system was at initial equilibrium before the start of the run, only the equilibrium constant K but not k(off) can be uniquely determined.
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Affiliation(s)
- John J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi, USA
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