1
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Huppertz MC, Wilhelm J, Grenier V, Schneider MW, Falt T, Porzberg N, Hausmann D, Hoffmann DC, Hai L, Tarnawski M, Pino G, Slanchev K, Kolb I, Acuna C, Fenk LM, Baier H, Hiblot J, Johnsson K. Recording physiological history of cells with chemical labeling. Science 2024; 383:890-897. [PMID: 38386755 DOI: 10.1126/science.adg0812] [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: 12/01/2022] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.
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Affiliation(s)
- Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Wilhelm
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Vincent Grenier
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin W Schneider
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tjalda Falt
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nicola Porzberg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - David Hausmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ling Hai
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Pino
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Krasimir Slanchev
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ilya Kolb
- GENIE Project Team, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Claudio Acuna
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Lisa M Fenk
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Herwig Baier
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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2
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Zhou X, Luo Z, Wang H, Luo Y, Yu R, Zhou S, Wang Z, Hu G, Xing B. Machine learning application in forecasting tire wear particles emission in China under different potential socioeconomic and climate scenarios with tire microplastics context. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129878. [PMID: 36084463 DOI: 10.1016/j.jhazmat.2022.129878] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Little information is available on different contribution of TMPs from tire wear particles (TWPs), recycled tire crumbs (RTCs) and tire repair-polished Debris (TRDs) in the environment at national scale and their potential tendency. In this study, the TWPs were predicted using machine learning method of CNN (Convolutional Neural Networks) algorithms under different potential socioeconomic and climate scenarios based on the estimation of TMPs in China. Results showed that TWPs emission exhibited the most important part of TMPs, followed by RTCs and TRDs in China. The three mentioned tire microplastics largely distributed in Chinese coastal provinces. After machine learning applied in CNN using the dataset of estimated emission of TWPs from 2008 to 2018, the express delivery volume and education funding at the current increased rate would not have significant impacts on TWPs emissions; Additionally, TWPs emissions were also sensitive to changes of economic and transportation development; Low temperature conditions would further promote TWPs emissions. Accordingly, the rational development of logistics and green economy, the equilibrium improvement of education quality, and the increase of public traffic with new energy would be helpful to mitigate TWPs emissions. The obtained findings can enhance the understanding TMPs emission at particular scale and their corresponding precise management.
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Affiliation(s)
- Xinyi Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Zhuanxi Luo
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China.
| | - Haiming Wang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Yinchai Luo
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Ruilian Yu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Shufeng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Zhenhong Wang
- College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Key Laboratory of Modern Separation and Analysis Science and Technology, Key Laboratory of Pollution Monitoring and Control, Zhangzhou 363000, China
| | - Gongren Hu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
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3
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Bakman AS, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Pre-steady-state kinetic and mutational insights into mechanisms of endo- and exonuclease DNA processing by mutant forms of human AP endonuclease. Biochim Biophys Acta Gen Subj 2022; 1866:130198. [PMID: 35809816 DOI: 10.1016/j.bbagen.2022.130198] [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] [Received: 03/21/2022] [Revised: 06/09/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
Abstract
Human apurinic/apyrimidinic endonuclease APE1 catalyzes endonucleolytic hydrolysis of phosphodiester bonds on the 5' side of structurally unrelated damaged nucleotides in DNA or native nucleotides in RNA. APE1 additionally possesses 3'-5'-exonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities. According to structural data, endo- and exonucleolytic cleavage of DNA is executed in different complexes when the excised residue is everted from the duplex or placed within the intrahelical DNA cavity without nucleotide flipping. In this study, we investigated the functions of residues Arg177, Arg181, Tyr171 and His309 in the APE1 endo- and exonucleolytic reactions. The interaction between residues Arg177 and Met270, which was hypothesized recently to be a switch for endo- and exonucleolytic catalytic mode regulation, was verified by pre-steady-state kinetic analysis of the R177A APE1 mutant. The function of another DNA-binding-site residue, Arg181, was analyzed too; it changed its conformation when enzyme-substrate and enzyme-product complexes were compared. Mutation R181A significantly facilitated the product dissociation stage and only weakly affected DNA-binding affinity. Moreover, R181A reduced the catalytic rate constant severalfold due to a loss of contact with a phosphate group. Finally, the protonation/deprotonation state of residues Tyr171 and His309 in the catalytic reaction was verified by their substitution. Mutations Y171F and H309A inhibited the chemical step of the AP endonucleolytic reaction by several orders of magnitude with retention of capacity for (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran-containing-DNA binding and without changes in the pH dependence profile of AP endonuclease activity, indicating that deprotonation of these residues is likely not important for the catalytic reaction.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Murat Saparbaev
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
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4
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Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Engineered HaloTag variants for fluorescence lifetime multiplexing. Nat Methods 2022; 19:65-70. [PMID: 34916672 PMCID: PMC8748199 DOI: 10.1038/s41592-021-01341-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.
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Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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5
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Ingram ZM, Scull NW, Schneider DS, Lucius AL. Multi-start Evolutionary Nonlinear OpTimizeR (MENOTR): A hybrid parameter optimization toolbox. Biophys Chem 2021; 279:106682. [PMID: 34634538 DOI: 10.1016/j.bpc.2021.106682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 10/20/2022]
Abstract
Parameter optimization or "data fitting" is a computational process that identifies a set of parameter values that best describe an experimental data set. Parameter optimization is commonly carried out using a computer program utilizing a non-linear least squares (NLLS) algorithm. These algorithms work by continuously refining a user supplied initial guess resulting in a systematic increase in the goodness of fit. A well-understood problem with this class of algorithms is that in the case of models with correlated parameters the optimized output parameters are initial guess dependent. This dependency can potentially introduce user bias into the resultant analysis. While many optimization programs exist, few address this dilemma. Here we present a data analysis tool, MENOTR, that is capable of overcoming the initial guess dependence in parameter optimization. Several case studies with published experimental data are presented to demonstrate the capabilities of this tool. The results presented here demonstrate how to effectively overcome the initial guess dependence of NLLS leading to greater confidence that the resultant optimized parameters are the best possible set of parameters to describe an experimental data set. While the optimization strategies implemented within MENOTR are not entirely novel, the application of these strategies to optimize parameters in kinetic and thermodynamic biochemical models is uncommon. MENOTR was designed to require minimal modification to accommodate a new model making it immediately accessible to researchers with a limited programming background. We anticipate that this toolbox can be used in a wide variety of data analysis applications. Prototype versions of this toolbox have been used in a number of published investigations already, as well as ongoing work with chemical-quenched flow, stopped-flow, and molecular tweezers data sets. STATEMENT OF SIGNIFICANCE: Non-linear least squares (NLLS) is a common form of parameter optimization in biochemistry kinetic and thermodynamic investigations These algorithms are used to fit experimental data sets and report corresponding parameter values. The algorithms are fast and able to provide good quality solutions for models involving few parameters. However, initial guess dependence is a well-known drawback of this optimization strategy that can introduce user bias. An alternative method of parameter optimization are genetic algorithms (GA). Genetic algorithms do not have an initial guess dependence but are slow at arriving at the best set of fit parameters. Here, we present MENOTR, a parameter optimization toolbox utilizing a hybrid GA/NLLS algorithm. The toolbox maximizes the strength of each strategy while minimizing the inherent drawbacks.
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Affiliation(s)
- Zachariah M Ingram
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathaniel W Scull
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David S Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA.
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6
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Denisov IG, Grinkova YV, Camp T, McLean MA, Sligar SG. Midazolam as a Probe for Drug-Drug Interactions Mediated by CYP3A4: Homotropic Allosteric Mechanism of Site-Specific Hydroxylation. Biochemistry 2021; 60:1670-1681. [PMID: 34015213 DOI: 10.1021/acs.biochem.1c00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We developed an efficient and sensitive probe for drug-drug interactions mediated by human CYP3A4 by using midazolam (MDZ) as a probe substrate. Using global analysis of four parameters over several experimental data sets, we demonstrate that the first MDZ molecule (MDZ1) binds with high affinity at the productive site near the heme iron and gives only hydroxylation at the 1 position (1OH). The second midazolam molecule (MDZ2) binds at an allosteric site at the membrane surface and perturbs the position and mobility of MDZ1 such that the minor hydroxylation product at the 4 position (4OH) is formed in a 1:2 ratio (35%). No increase in catalytic rate is observed after the second MDZ binding. Hence, the site of the 1OH:4OH metabolism ratio is a sensitive probe for drugs, such as progesterone, that bind with high affinity to the allosteric site and serve as effectors. We observe similar changes in the MDZ 1OH:4OH ratio in the presence of progesterone (PGS), suggesting a direct communication between the active and allosteric sites. Mutations introduced into the F-F' loop indicate that residues F213 and D214 are directly involved in allosteric interactions leading to MDZ homotropic cooperativity, and these same residues, together with L211, are involved in heterotropic allosteric interactions in which PGS is the effector and MDZ the substrate. Molecular dynamics simulations provide a mechanistic picture of the origin of this cooperativity. These results show that the midazolam can be used as a sensitive probe for drug-drug interactions in human P450 CYP3A4.
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8
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Penix J, DeFazio RA, Dulka EA, Schnell S, Moenter SM. Firing patterns of gonadotropin-releasing hormone neurons are sculpted by their biologic state. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201040. [PMID: 32968535 PMCID: PMC7481724 DOI: 10.1098/rsos.201040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Gonadotropin-releasing hormone (GnRH) neurons form the final pathway for the central neuronal control of fertility. GnRH is released in pulses that vary in frequency in females, helping drive hormonal changes of the reproductive cycle. In the common fertility disorder polycystic ovary syndrome (PCOS), persistent high-frequency hormone release is associated with disrupted cycles. We investigated long- and short-term action potential patterns of GnRH neurons in brain slices before and after puberty in female control and prenatally androgenized (PNA) mice, which mimic aspects of PCOS. A Monte Carlo (MC) approach was used to randomize action potential interval order. Dataset distributions were analysed to assess (i) if organization persists in GnRH neuron activity in vitro, and (ii) to determine if any organization changes with development and/or PNA treatment. GnRH neurons in adult control, but not PNA, mice produce long-term patterns different from MC distributions. Short-term patterns differ from MC distributions before puberty but become absorbed into the distributions with maturation, and the distributions narrow. These maturational changes are blunted by PNA treatment. Firing patterns of GnRH neurons in brain slices thus maintain organization dictated at least in part by the biologic status of the source and are disrupted in models of disease.
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Affiliation(s)
- Jonathon Penix
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - R. Anthony DeFazio
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eden A. Dulka
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Santiago Schnell
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Suzanne M. Moenter
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
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9
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Denisov IG, Grinkova YV, Nandigrami P, Shekhar M, Tajkhorshid E, Sligar SG. Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213. Biochemistry 2019; 58:1411-1422. [PMID: 30785734 DOI: 10.1021/acs.biochem.8b01268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of Phe213 in the allosteric mechanism of human cytochrome P450 CYP3A4 was studied using a combination of progesterone (PGS) and carbamazepine (CBZ) as probe substrates. We expressed, purified, and incorporated into POPC Nanodiscs three mutants, F213A, F213S, and F213Y, and compared them with wild-type (WT) CYP3A4 by monitoring spectral titration, the rate of NADPH oxidation, and steady-state product turnover rates with pure substrates and substrate mixtures. All mutants demonstrated higher activity with CBZ, lower activity with PGS, and a reduced level of activation of CBZ epoxidation by PGS, which was most pronounced in the F213A mutant. Using all-atom molecular dynamics simulations, we compared the dynamics of WT CYP3A4 and the F213A mutant incorporated into the lipid bilayer and the effect of the presence of the PGS molecule at the allosteric peripheral site and evaluated the critical role of Phe213 in mediating the heterotropic allosteric interactions in CYP3A4.
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10
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Khoroshyy P, Bína D, Gardian Z, Litvín R, Alster J, Pšenčík J. Quenching of chlorophyll triplet states by carotenoids in algal light-harvesting complexes related to fucoxanthin-chlorophyll protein. PHOTOSYNTHESIS RESEARCH 2018; 135:213-225. [PMID: 28669083 DOI: 10.1007/s11120-017-0416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
We have used time-resolved absorption and fluorescence spectroscopy with nanosecond resolution to study triplet energy transfer from chlorophylls to carotenoids in a protective process that prevents the formation of reactive singlet oxygen. The light-harvesting complexes studied were isolated from Chromera velia, belonging to a group Alveolata, and Xanthonema debile and Nannochloropsis oceanica, both from Stramenopiles. All three light-harvesting complexes are related to fucoxanthin-chlorophyll protein, but contain only chlorophyll a and no chlorophyll c. In addition, they differ in the carotenoid content. This composition of the complexes allowed us to study the quenching of chlorophyll a triplet states by different carotenoids in a comparable environment. The triplet states of chlorophylls bound to the light-harvesting complexes were quenched by carotenoids with an efficiency close to 100%. Carotenoid triplet states were observed to rise with a ~5 ns lifetime and were spectrally and kinetically homogeneous. The triplet states were formed predominantly on the red-most chlorophylls and were quenched by carotenoids which were further identified or at least spectrally characterized.
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Affiliation(s)
- Petro Khoroshyy
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, 121 16, Prague 2, Czech Republic
| | - David Bína
- Biological Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Zdenko Gardian
- Biological Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Radek Litvín
- Biological Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Jan Alster
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, 121 16, Prague 2, Czech Republic
| | - Jakub Pšenčík
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, 121 16, Prague 2, Czech Republic.
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11
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Fleming JK, Glass TR, Lackie SJ, Wojciak JM. A novel approach for measuring sphingosine-1-phosphate and lysophosphatidic acid binding to carrier proteins using monoclonal antibodies and the Kinetic Exclusion Assay. J Lipid Res 2016; 57:1737-47. [PMID: 27444045 DOI: 10.1194/jlr.d068866] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 01/01/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA) are bioactive signaling lysophospholipids that activate specific G protein-coupled receptors on the cell surface triggering numerous biological events. In circulation, S1P and LPA associate with specific carrier proteins or chaperones; serum albumin binds both S1P and LPA while HDL shuttles S1P via interactions with apoM. We used a series of kinetic exclusion assays in which monoclonal anti-S1P and anti-LPA antibodies competed with carrier protein for the lysophospholipid to measure the equilibrium dissociation constants (Kd) for these carrier proteins binding S1P and the major LPA species. Fatty acid-free (FAF)-BSA binds these lysophospholipids with the following Kd values: LPA(16:0), 68 nM; LPA(18:1), 130 nM; LPA(18:2), 350 nM; LPA(20:4), 2.2 μM; and S1P, 41 μM. FAF human serum albumin binds each lysophospholipid with comparable affinities. By measuring the apoM concentration and expanding the model to include endogenous ligand, we were able to resolve the Kd values for S1P binding apoM in the context of human HDL and LDL particles (21 nM and 2.4 nM, respectively). The novel competitive assay and analysis described herein enables measurement of Kd values of completely unmodified lysophospholipids binding unmodified carrier proteins in solution, and thus provide insights into S1P and LPA storage in the circulation system and may be useful in understanding chaperone-dependent receptor activation and signaling.
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12
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Hines KE, Middendorf TR, Aldrich RW. Determination of parameter identifiability in nonlinear biophysical models: A Bayesian approach. ACTA ACUST UNITED AC 2014; 143:401-16. [PMID: 24516188 PMCID: PMC3933937 DOI: 10.1085/jgp.201311116] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A major goal of biophysics is to understand the physical mechanisms of biological molecules and systems. Mechanistic models are evaluated based on their ability to explain carefully controlled experiments. By fitting models to data, biophysical parameters that cannot be measured directly can be estimated from experimentation. However, it might be the case that many different combinations of model parameters can explain the observations equally well. In these cases, the model parameters are not identifiable: the experimentation has not provided sufficient constraining power to enable unique estimation of their true values. We demonstrate that this pitfall is present even in simple biophysical models. We investigate the underlying causes of parameter non-identifiability and discuss straightforward methods for determining when parameters of simple models can be inferred accurately. However, for models of even modest complexity, more general tools are required to diagnose parameter non-identifiability. We present a method based in Bayesian inference that can be used to establish the reliability of parameter estimates, as well as yield accurate quantification of parameter confidence.
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Affiliation(s)
- Keegan E Hines
- Center for Learning and Memory and Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
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13
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Ramos I, Fernández-Rivero N, Arranz R, Aloria K, Finn R, Arizmendi JM, Ausió J, Valpuesta JM, Muga A, Prado A. The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. Nucleic Acids Res 2013; 42:1311-25. [PMID: 24121686 PMCID: PMC3902905 DOI: 10.1093/nar/gkt899] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics.
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Affiliation(s)
- Isbaal Ramos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del PaísVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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14
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Pryse KM, Rong X, Whisler JA, McConnaughey WB, Jiang YF, Melnykov AV, Elson EL, Genin GM. Confidence intervals for concentration and brightness from fluorescence fluctuation measurements. Biophys J 2013; 103:898-906. [PMID: 23009839 DOI: 10.1016/j.bpj.2012.07.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 11/19/2022] Open
Abstract
The theory of photon count histogram (PCH) analysis describes the distribution of fluorescence fluctuation amplitudes due to populations of fluorophores diffusing through a focused laser beam and provides a rigorous framework through which the brightnesses and concentrations of the fluorophores can be determined. In practice, however, the brightnesses and concentrations of only a few components can be identified. Brightnesses and concentrations are determined by a nonlinear least-squares fit of a theoretical model to the experimental PCH derived from a record of fluorescence intensity fluctuations. The χ(2) hypersurface in the neighborhood of the optimum parameter set can have varying degrees of curvature, due to the intrinsic curvature of the model, the specific parameter values of the system under study, and the relative noise in the data. Because of this varying curvature, parameters estimated from the least-squares analysis have varying degrees of uncertainty associated with them. There are several methods for assigning confidence intervals to the parameters, but these methods have different efficacies for PCH data. Here, we evaluate several approaches to confidence interval estimation for PCH data, including asymptotic standard error, likelihood joint-confidence region, likelihood confidence intervals, skew-corrected and accelerated bootstrap (BCa), and Monte Carlo residual resampling methods. We study these with a model two-dimensional membrane system for simplicity, but the principles are applicable as well to fluorophores diffusing in three-dimensional solution. Using simulated fluorescence fluctuation data, we find the BCa method to be particularly well-suited for estimating confidence intervals in PCH analysis, and several other methods to be less so. Using the BCa method and additional simulated fluctuation data, we find that confidence intervals can be reduced dramatically for a specific non-Gaussian beam profile.
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Affiliation(s)
- Kenneth M Pryse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri, USA.
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15
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Le VH, Buscaglia R, Chaires JB, Lewis EA. Modeling complex equilibria in isothermal titration calorimetry experiments: thermodynamic parameters estimation for a three-binding-site model. Anal Biochem 2012; 434:233-41. [PMID: 23262283 DOI: 10.1016/j.ab.2012.11.030] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 11/13/2012] [Accepted: 11/28/2012] [Indexed: 12/21/2022]
Abstract
Isothermal titration calorimetry (ITC) is a powerful technique that can be used to estimate a complete set of thermodynamic parameters (e.g., K(eq) (or ΔG), ΔH, ΔS, and n) for a ligand-binding interaction described by a thermodynamic model. Thermodynamic models are constructed by combining equilibrium constant, mass balance, and charge balance equations for the system under study. Commercial ITC instruments are supplied with software that includes a number of simple interaction models, for example, one binding site, two binding sites, sequential sites, and n-independent binding sites. More complex models, for example, three or more binding sites, one site with multiple binding mechanisms, linked equilibria, or equilibria involving macromolecular conformational selection through ligand binding, need to be developed on a case-by-case basis by the ITC user. In this paper we provide an algorithm (and a link to our MATLAB program) for the nonlinear regression analysis of a multiple-binding-site model with up to four overlapping binding equilibria. Error analysis demonstrates that fitting ITC data for multiple parameters (e.g., up to nine parameters in the three-binding-site model) yields thermodynamic parameters with acceptable accuracy.
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Affiliation(s)
- Vu H Le
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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16
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Ruckebusch C, Sliwa M, Pernot P, de Juan A, Tauler R. Comprehensive data analysis of femtosecond transient absorption spectra: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2011.10.002] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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17
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Moody AD, Miura MT, Connaghan KD, Bain DL. Thermodynamic dissection of estrogen receptor-promoter interactions reveals that steroid receptors differentially partition their self-association and promoter binding energetics. Biochemistry 2012; 51:739-49. [PMID: 22201220 DOI: 10.1021/bi2017156] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steroid receptors define a family of ligand-activated transcription factors. Recent work has demonstrated that the receptors regulate distinct but overlapping gene networks, yet the mechanisms by which they do so remain unclear. We previously determined the microscopic binding energetics for progesterone receptor (PR) isoform assembly at promoters containing multiple response elements. We found that the two isoforms (PR-A and PR-B) share nearly identical dimerization and intrinsic DNA binding free energies but maintain large differences in cooperative free energy. Moreover, cooperativity can be modulated by monovalent ion binding and promoter layout, suggesting that differences in cooperativity might control isoform-specific promoter occupancy and thus receptor function. To determine whether cooperative binding energetics are common to other members of the steroid receptor family, we dissected the thermodynamics of estrogen receptor-α (ER-α):promoter interactions. We find that the ER-α intrinsic DNA binding free energy is identical to that of the PR isoforms. This was expected, noting that receptor DNA binding domains are highly conserved. Unexpectedly, ER-α generates negligible cooperativity-orders of magnitude less than predicted based on our studies of the PR isoforms. However, analysis of the cooperativity term suggests that it reflects a balance between highly favorable cooperative stabilization and unfavorable promoter bending. Moreover, ER-α cooperative free energy is compensated for by a large increase in dimerization free energy. Collectively, the results demonstrate that steroid receptors differentially partition not only cooperative energetics but also dimerization energetics. We speculate that this ability serves as a framework for regulating receptor-specific promoter occupancy and thus receptor-specific gene regulation.
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Affiliation(s)
- Amie D Moody
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
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18
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Abstract
In this chapter, we demonstrate the advantage of the simultaneous multicurve nonlinear least-squares analysis over that of the conventional single-curve analysis. Fitting results are subjected to thorough Monte Carlo analysis for rigorous assessment of confidence intervals and parameter correlations. The comparison is performed on a practical example of simulated steady-state reaction kinetics complemented with isothermal calorimetry (ITC) data resembling allosteric behavior of rabbit muscle pyruvate kinase (RMPK). Global analysis improves accuracy and confidence limits of model parameters. Cross-correlation between parameters is also reduced with accompanying enhancement of the model-testing power. This becomes especially important for validation of models with "difficult" highly cross-correlated parameters. We show how proper experimental design and critical evaluation of data can improve the chance of differentiating models.
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Affiliation(s)
- Petr Herman
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Prague, Czech Republic
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19
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Quinn JG. Modeling Taylor dispersion injections: determination of kinetic/affinity interaction constants and diffusion coefficients in label-free biosensing. Anal Biochem 2011; 421:391-400. [PMID: 22197421 DOI: 10.1016/j.ab.2011.11.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/14/2011] [Accepted: 11/21/2011] [Indexed: 11/17/2022]
Abstract
A new method based on Taylor dispersion has been developed that enables an analyte gradient to be titrated over a ligand-coated surface for kinetic/affinity analysis of interactions from a minimal number of injections. Taylor dispersion injections generate concentration ranges in excess of four orders of magnitude and enable the analyte diffusion coefficient to be reliably estimated as a fitted parameter when fitting binding interaction models. A numerical model based on finite element analysis, Monte Carlo simulations, and statistical profiling were used to compare the Taylor dispersion method with standard fixed concentration injections in terms of parameter correlation, linearity of parameter error space, and global versus local model fitting. A dramatic decrease in parameter correlations was observed for TDi curves relative to curves from standard fixed concentration injections when surface saturation was achieved. In FCI the binding progress is recorded with respect to injection time, whereas in TDi the second time dependency encoded in the analyte gradient increases resolving power. This greatly lowers the dependence of all parameters on each other and on experimental interferences. When model parameters were fitted locally, the performance of TDis remained comparable to global model fitting, whereas fixed concentration binding response curves yielded unreliable parameter estimates.
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Affiliation(s)
- John G Quinn
- FLIR/ICx Nomadics, Oklahoma City, OK 73104, USA.
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20
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Kuzmič P. Optimal design for the dose–response screening of tight-binding enzyme inhibitors. Anal Biochem 2011; 419:117-22. [DOI: 10.1016/j.ab.2011.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 05/26/2011] [Accepted: 06/07/2011] [Indexed: 10/17/2022]
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21
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Malik SS, Rich E, Viswanathan R, Cairns BR, Fischer CJ. Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC. Biochemistry 2011; 50:7881-90. [PMID: 21834590 DOI: 10.1021/bi200837b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RSC (remodel the structure of chromatin) is an essential chromatin remodeler of Saccharomyces cerevisiae that has been shown to have DNA translocase properties. We studied the DNA binding properties of a "trimeric minimal RSC" (RSCt) of the RSC chromatin remodeling complex and the effect of nucleotides on this interaction using fluorescence anisotropy. RSCt binds to 20 bp fluorescein-labeled double-stranded DNA with a K(d) of ∼100 nM. The affinity of RSCt for DNA is reduced in the presence of AMP-PNP and ADP in a concentration-dependent manner with the addition of AMP-PNP having more pronounced effect. These differences in the magnitude at which the binding of ADP and AMP-PNP affects the affinity of DNA binding by RSCt suggest that the physical movement of the enzyme along DNA begins between the binding of ATP and its subsequent hydrolysis. Furthermore, the fact that the highest affinity for DNA binding by RSCt occurs in the absence of bound nucleotide offers a mechanistic explanation for the apparent low processivity of DNA translocation by the enzyme.
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Affiliation(s)
- Shuja Shafi Malik
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, Kansas 66045, USA
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22
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Frank DJ, Denisov IG, Sligar SG. Analysis of heterotropic cooperativity in cytochrome P450 3A4 using alpha-naphthoflavone and testosterone. J Biol Chem 2010; 286:5540-5. [PMID: 21177853 DOI: 10.1074/jbc.m110.182055] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) displays non-Michaelis-Menten kinetics for many of the substrates it metabolizes, including testosterone (TST) and α-naphthoflavone (ANF). Heterotropic effects between these two substrates can further complicate the metabolic profile of the enzyme. In this work, monomeric CYP3A4 solubilized in Nanodiscs has been studied for its ability to interact with varying molar ratios of ANF and TST. Comparison of the observed heme spin state, NADPH consumption, and product formation rates with a non-cooperative model calculated from a linear combination of the global analysis of each substrate reveals a detailed landscape of the heterotropic interactions and indicates negligible binding cooperativity between ANF and TST. The observed effect of ANF on the kinetics of TST metabolism is due to the additive action of the second substrate with no specific allosteric effects.
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Affiliation(s)
- Daniel J Frank
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801, USA
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23
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Rajendar B, Lucius AL. Molecular mechanism of polypeptide translocation catalyzed by the Escherichia coli ClpA protein translocase. J Mol Biol 2010; 399:665-79. [PMID: 20380838 DOI: 10.1016/j.jmb.2010.03.061] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/25/2010] [Accepted: 03/29/2010] [Indexed: 11/26/2022]
Abstract
The removal of damaged or unneeded proteins by ATP-dependent proteases is crucial for cell survival in all organisms. Integral components of ATP-dependent proteases are motor proteins that unfold stably folded proteins that have been targeted for removal. These protein unfoldases/polypeptide translocases use ATP to unfold the target proteins and translocate them into a proteolytic component. Despite the central role of these motor proteins in cell homeostasis, a number of important questions regarding the molecular mechanisms of enzyme catalyzed protein unfolding and translocation remain unanswered. Here, we demonstrate that Escherichia coli ClpA, in the absence of the proteolytic component ClpP, processively and directionally steps along the polypeptide backbone with a kinetic step size of approximately 14 amino acids, independent of the concentration of ATP with a rate of approximately 19 amino acids s(-1) at saturating concentrations of ATP. In contrast to earlier studies by others, we have developed single-turnover fluorescence stopped-flow methods that allow us to quantitatively examine the molecular mechanism of the motor component ClpA decoupled from the proteolytic component ClpP. For the first time, we reveal that in the absence of ClpP ClpA translocates polypeptides directionally, processively and in discrete steps similar to other motor proteins that translocate vectorially on a linear lattice, such as nucleic acid helicases and kinesin. We believe that the methods employed here will be generally applicable to the examination of other AAA+ protein translocases involved in a variety of important biological functions where the substrate is not covalently modified; for example, membrane fusion, membrane transport, protein disaggregation, and protein refolding.
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Affiliation(s)
- Burki Rajendar
- The University of Alabama at Birmingham, Department of Chemistry, 1530 3rd Avenue South, Birmingham, AL 35294-1240, USA
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24
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Gahl RF, Scheraga HA. Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues. Biochemistry 2009; 48:2740-51. [PMID: 19309163 DOI: 10.1021/bi802327j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxidative folding pathways of two four-disulfide proteins of the ribonuclease family, ONC and RNase A, which have similar three-dimensional folds but only 30% sequence homology, are compared. In this study, a mechanism for the oxidative folding pathway of ONC is proposed. In particular, the kinetic roles and thermodynamic characteristics of key intermediates along the oxidative folding pathway, specifically, the structured intermediates, I(1), I(2), and I(3), previously identified as des-[19-68,30-75], des-[30-75], and des-[19-68], respectively, are discussed. In addition, the effects of temperature on the oxidative folding pathway have been examined. Differences in the folding mechanism between ONC and RNase A are attributed to the differences in their amino acid sequences and related inter-residue interactions, including differences in hydrophobic interactions. Compared to RNase A, ONC utilizes more efficient interactions along the oxidative folding pathway to adopt its native fold more rapidly.
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Affiliation(s)
- Robert F Gahl
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853, USA
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25
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26
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Nikolova N, Tenekedjiev K, Kolev K. Uses and misuses of progress curve analysis in enzyme kinetics. CENTRAL EUROPEAN JOURNAL OF BIOLOGY 2008; 3:345-350. [PMID: 19562082 PMCID: PMC2701647 DOI: 10.2478/s11535-008-0035-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Progress curve analysis is a convenient tool for the characterization of enzyme action: a single reaction mixture provides multiple experimental measured points for continuously varying amounts of substrates and products with exactly the same enzyme and modulator concentrations. The determination of kinetic parameters from the progress curves, however, requires complex mathematical evaluation of the time-course data. Some freely available programs (e.g. FITSIM, DYNAFIT) are widely applied to fit kinetic parameters to user-defined enzymatic mechanisms, but users often overlook the stringent requirements of the analytic procedures for appropriate design of the input experiments. Flaws in the experimental setup result in unreliable parameters with consequent misinterpretation of the biological phenomenon under study. The present commentary suggests some helpful mathematical tools to improve the analytic procedure in order to diagnose major errors in concept and design of kinetic experiments.
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Affiliation(s)
- Natalia Nikolova
- Department of Economics and Management, Technical University - Varna, 9010 Varna, Bulgaria
| | - Kiril Tenekedjiev
- Department of Economics and Management, Technical University - Varna, 9010 Varna, Bulgaria
| | - Krasimir Kolev
- Department of Medical Biochemistry, Semmelweis University, 1088 Budapest, Hungary
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27
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Townsend HL, Jha BK, Han JQ, Maluf NK, Silverman RH, Barton DJ. A viral RNA competitively inhibits the antiviral endoribonuclease domain of RNase L. RNA (NEW YORK, N.Y.) 2008; 14:1026-1036. [PMID: 18426919 PMCID: PMC2390801 DOI: 10.1261/rna.958908] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 02/18/2008] [Indexed: 05/26/2023]
Abstract
Ribonuclease L (RNase L) is a latent endoribonuclease in an evolutionarily ancient interferon-regulated dsRNA-activated antiviral pathway. 2'-5' oligoadenylate (2-5A), the product of dsRNA-activated oligoadenylate synthetases (OASes), binds to ankyrin repeats near the amino terminus of RNase L, initiating a series of conformational changes that result in the activation of the endoribonuclease. A phylogenetically conserved RNA structure within group C enteroviruses inhibits the endoribonuclease activity of RNase L. In this study we report the mechanism by which group C enterovirus RNA inhibits RNase L. Viral RNA did not affect 2-5A binding to RNase L. Rather, the viral RNA inhibited the endoribonuclease domain. We used purified RNase L, purified 2-5A, and an RNA substrate with a 5' fluorophore and 3' quencher in FRET assays to measure inhibition of RNase L activity by the viral RNA. The group C enterovirus RNA was a competitive inhibitor of the endoribonuclease with a K(i) of 34 nM. Consistent with the kinetic profile of a competitive inhibitor, the viral RNA inhibited the constitutively active endoribonuclease domain of RNase L. We call this viral RNA the RNase L competitive inhibitor RNA (RNase L ciRNA).
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Affiliation(s)
- Hannah L Townsend
- Department of Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado 80045, USA
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28
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Donmez I, Patel SS. Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase. EMBO J 2008; 27:1718-26. [PMID: 18497749 DOI: 10.1038/emboj.2008.100] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/25/2008] [Indexed: 01/06/2023] Open
Abstract
The ring-shaped T7 helicase uses the energy of dTTP hydrolysis to perform the mechanical work of translocation and base pair (bp) separation. We have shown that the unwinding rate of T7 helicase decreases with increasing DNA stability. Here, we show that the dTTPase rate also decreases with increasing DNA stability, which indicates close linkage between chemical transition steps and translocation steps of unwinding. We find that the force-producing step during unwinding is not associated with dTTP binding, but dTTP hydrolysis or P(i) release. We determine that T7 helicase extracts approximately 3.7 kcal/mol energy from dTTPase to carry out the work of strand separation. Using this energy, T7 helicase unwinds approximately 4 bp of AT-rich DNA or 1-2 bp of GC-rich DNA. T7 helicase therefore adjusts both its speed and coupling ratio (bp/dTTP) to match the work of DNA unwinding. We discuss the mechanistic implications of the variable bp/dTTP that indicates T7 helicase either undergoes backward movements/futile hydrolysis or unwinds DNA with a variable bp-step size; 'long and fast' steps on AT-rich and 'short and slow' steps on GC-rich DNA.
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Affiliation(s)
- Ilker Donmez
- Department of Biochemistry, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ, USA
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29
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Connaghan-Jones KD, Heneghan AF, Miura MT, Bain DL. Thermodynamic dissection of progesterone receptor interactions at the mouse mammary tumor virus promoter: monomer binding and strong cooperativity dominate the assembly reaction. J Mol Biol 2008; 377:1144-60. [PMID: 18313072 DOI: 10.1016/j.jmb.2008.01.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 10/22/2022]
Abstract
Progesterone receptors (PRs) play critical roles in eukaryotic gene regulation, yet the mechanisms by which they assemble at their promoters are poorly understood. One of the few promoters amenable to analysis is the mouse mammary tumor virus gene regulatory sequence. Embedded within this sequence are four progesterone response elements (PREs) corresponding to a palindromic PRE and three half-site PREs. Early mutational studies indicated that the presence of all four sites generated a synergistic and strong transcriptional response. However, DNA binding analyses suggested that receptor assembly at the promoter occurred in the absence of significant cooperativity. Taken together, the results indicated that cooperative interactions among PREs could not account for the observed functional synergy. More broadly, the studies raised the question of whether cooperativity was a common feature of PR-mediated gene regulation. As a step toward obtaining a quantitative and, thus, predictive understanding of receptor function, we have carried out a thermodynamic dissection of PR A-isoform interactions at the mouse mammary tumor virus promoter. Utilizing analytical ultracentrifugation and quantitative footprinting, we have resolved the microscopic energetics of PR A-isoform binding, including cooperativity terms. Our results reveal a model contrary to that inferred from previous biochemical investigations. Specifically, the binding unit at a half-site is not a receptor dimer but is instead a monomer; monomers bound at half-sites are capable of significant pairwise cooperative interactions; occupancy of all three half-sites is required to cooperatively engage the palindromic-bound dimer; and finally, large unfavorable forces accompany assembly. Overall, monomer binding accounts for the majority of the intrinsic binding energetics and cooperativity contributes an approximately 1000-fold increase in receptor-promoter stability. Finally, the partitioning of cooperativity suggests a framework for interpreting in vivo transcriptional synergy. These results highlight the insight available from rigorous analysis and demonstrate that receptor-promoter interactions are considerably more complex than typically envisioned.
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Affiliation(s)
- Keith D Connaghan-Jones
- Department of Pharmaceutical Sciences, C-238, University of Colorado Denver, 4200 East 9th Avenue, Denver, CO 80262, USA
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Niedziela-Majka A, Chesnik MA, Tomko EJ, Lohman TM. Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro. J Biol Chem 2007; 282:27076-27085. [PMID: 17631491 DOI: 10.1074/jbc.m704399200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural studies of the Bacillus stearothermophilus PcrA protein along with biochemical studies of the single-stranded (ss) DNA translocation activity of PcrA monomers have led to the suggestion that a PcrA monomer possesses processive helicase activity in vitro. Yet definitive studies testing whether the PcrA monomer possesses processive helicase activity have not been performed. Here we show, using single turnover kinetic methods, that monomers of PcrA are able to translocate along ssDNA, in the 3' to 5' direction, rapidly and processively, whereas these same monomers display no detectable helicase activity under the same solution conditions in vitro. The PcrA monomer ssDNA translocation activity, although necessary, is not sufficient for processive helicase activity, and thus the translocase and helicase activities of PcrA are separable. These results also suggest that the helicase activity of PcrA needs to be activated either by self-assembly or through interactions with accessory proteins. This same behavior is displayed by both the Escherichia coli Rep and UvrD monomers. Hence, all three of these SF1 enzymes are ssDNA translocases as monomers but do not display processive helicase activity in vitro unless activated. The fact that the translocase and helicase activities are separable suggests that each activity may be used for different functions in vivo.
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Affiliation(s)
- Anita Niedziela-Majka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110-1093
| | - Marla A Chesnik
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110-1093
| | - Eric J Tomko
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110-1093
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110-1093.
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31
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Armstrong KM, Baker BM. A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction. Biophys J 2007; 93:597-609. [PMID: 17449678 PMCID: PMC1896243 DOI: 10.1529/biophysj.107.104570] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The alphabeta T cell receptor (TCR) is responsible for recognizing peptides bound and "presented" by major histocompatibility complex (MHC) molecules. We recently reported that at 25 degrees C the A6 TCR, which recognizes the Tax peptide presented by the class I MHC human leukocyte antigen-A*0201 (HLA-A2), binds with a weak DeltaH degrees , a favorable DeltaS degrees , and a moderately negative DeltaC(p). These observations were of interest given the unfavorable binding entropies and large heat capacity changes measured for many other TCR-ligand interactions, suggested to result from TCR conformational changes occurring upon binding. Here, we further investigated the A6-Tax/HLA-A2 interaction using titration calorimetry. We found that binding results in a pK(a) shift, complicating interpretation of measured binding thermodynamics. To better characterize the interaction, we measured binding as a function of pH, temperature, and buffer ionization enthalpy. A global analysis of the resulting data allowed determination of both the intrinsic binding thermodynamics separated from the influence of protonation as well as the thermodynamics associated with the pK(a) shift. Our results indicate that intrinsically, A6 binds Tax/HLA-A2 with a very weak DeltaH degrees , an even more favorable DeltaS degrees than previously thought, and a relatively large negative DeltaC(p). Comparison of these energetics with the makeup of the protein-protein interface suggests that conformational adjustments are required for binding, but these are more likely to be structural shifts, rather than disorder-to-order transitions. The thermodynamics of the pK(a) shift suggest protonation may be linked to an additional process such as ion binding.
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Affiliation(s)
- Kathryn M Armstrong
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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32
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Territo PR, Heil J, Bose S, Evans FJ, Balaban RS. Fluorescence absorbance inner-filter decomposition: the role of emission shape on estimates of free Ca(2+) using Rhod-2. APPLIED SPECTROSCOPY 2007; 61:138-47. [PMID: 17331304 DOI: 10.1366/000370207779947530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A method for decomposing complex emission spectra by correcting for known inner-filter effects is described. This approach builds on previous work using a linear combination of model emission spectra and combines the known absorption characteristics of the system to fit the composite emission spectrum. Rhod-2, which has a small Stokes shift and significant self-absorption, was used as the model system. By adding the absorption characteristics of Rhod-2 to the model, the degree of fit was significantly improved, thus minimizing residuals, and accurately predicted the spectral shape changes with increasing concentration, [Rhod-2]. More complex studies were conducted with Rhod-2 in isolated cardiac mitochondria with multiple emission and absorption elements. By including known absorbances to the spectral decomposition, the overall precision increased almost four fold. Moreover, this approach eliminated the significant [Rhod-2] dependence on the apparent K(50) and therefore improved the accuracy of free [Ca(2+)] calculations. These data demonstrate that secondary inner-filter correction can significantly improve spectral decomposition of complex emission spectra, which are used in a variety of biological applications.
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Affiliation(s)
- Paul R Territo
- Lilly Center for Molecular and Anatomical Imaging, Lilly Research Laboratories, Eli Lilly and Company, 2001 West Main Street, B220/GL54, Greenfield, Indiana 46140, USA.
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33
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Gutierrez OA, Danielson UH. Sensitivity analysis and error structure of progress curves. Anal Biochem 2006; 358:1-10. [PMID: 16979133 DOI: 10.1016/j.ab.2006.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2005] [Revised: 07/10/2006] [Accepted: 07/10/2006] [Indexed: 11/15/2022]
Abstract
Both the sensitivity of the monitored signal in progress curves to variations in enzyme concentration and the standard deviation of this signal were analyzed as a function of the proportion of transformed substrate. Three enzymes catalyzing essentially irreversible reactions were used as model systems: HIV-1 protease, glutathione reductase, and glutathione transferase. For all enzymes analyzed, the sensitivity was maximal when 60-80% of the substrate had been transformed. The standard deviation of reaction progress curve data replicates was also maximal at these substrate conversion levels, a result that was attributed to the influence of the sensitivity to random dispersion of the enzyme concentration. On this basis, we developed a model for the standard deviation of reaction progress curves that gave a good description of the experimental data and efficiently reduced the heteroscedasticity of residuals in a weighted fit of progress curves. This standard deviation model can be used for obtaining more efficient parameter estimates, to simulate noise in Monte Carlo procedures, and to delineate detection limits of enzyme inhibition. The transient increases in the sensitivity and in the standard deviation in progress curves are proposed to be features common to most enzymatic assays.
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Affiliation(s)
- Omar A Gutierrez
- Department of Biochemistry and Organic Chemistry, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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34
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Xue WF, Carey J, Linse S. Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin. Proteins 2005; 57:586-95. [PMID: 15382228 DOI: 10.1002/prot.20241] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Accurate and precise determinations of thermodynamic parameters of binding are important steps toward understanding many biological mechanisms. Here, a multi-method approach to binding analysis is applied and a detailed error analysis is introduced. Using this approach, the binding thermodynamics and kinetics of the reconstitution of the protein monellin have been quantitatively determined in detail by simultaneous analysis of data collected with fluorescence spectroscopy, surface plasmon resonance and isothermal titration calorimetry at 25 degrees C, pH 7.0 and 150 mM NaCl. Monellin is an intensely sweet protein composed of two peptide chains that form a single globular domain. The kinetics of the reconstitution reaction are slow, with an association rate constant, k(on) of 8.8 x 10(3) M(-1) s(-1) and a dissociation rate constant, k(off) of 3.1 x 10(-4) s(-1). The equilibrium constant K(A) is 2.8 x 10(7) M(-1) corresponding to a standard free energy of association, DeltaG degrees , of -42.5 kJ/mol. The enthalpic component, DeltaH degrees , is -18.7 kJ/mol and the entropic contribution, DeltaS degrees , is 79.8 J mol(-1) K(-1) (-TDeltaS degrees = -23.8 kJ/mol). The association of monellin is therefore a bimolecular intra-protein association whose energetics are slightly dominated by entropic factors.
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Affiliation(s)
- Wei-Feng Xue
- Department of Biophysical Chemistry, Lund University, Lund, Sweden
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35
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Giustini M, Castelli F, Husu I, Giomini M, Mallardi A, Palazzo G. Influence of Cardiolipin on the Functionality of the QA Site of the Photosynthetic Bacterial Reaction Center. J Phys Chem B 2005; 109:21187-96. [PMID: 16853745 DOI: 10.1021/jp054104d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The effect of cardiolipin on the functionality of the Q(A) site of a photosynthetic reaction center (RC) was studied in RCs from the purple non-sulfur bacterium Rhodobacter sphaeroides by means of time-resolved absorbance measurements. The binding of the ubiquinone-10 to the Q(A) site of the RC embedded in cardiolipin or lecithin liposomes has been followed at different temperatures and phospholipid loading. A global fit of the experimental data allowed us to get quite reliable values of the thermodynamic parameters joined to the binding process. The presence of cardiolipin does not affect the affinity of the Q(A) site for ubiquinone but has a marked influence on the rate of P+QA(-) --> PQA electron transfer. The P+QA(-) charge recombination kinetics has been examined in liposomes made of cardiolipin/lecithin mixtures and in detergent (DDAO) micelles doped with cardiolipin. The electron-transfer rate constant increases upon cardiolipin loading. It appears that the main effect of cardiolipin on the electron transfer can be ascribed to a destabilization of the charge-separated state. Results obtained in micelles and vesicles follow the same titration curve when cardiolipin concentration evaluated with respect to the apolar phase is used as a relevant variable. The dependence of the P+QA(-) recombination rate on cardiolipin loading suggests two classes of binding sites. In addition to a high-affinity site (compatible with previous crystallographic studies), a cooperative binding, involving about four cardiolipin molecules, takes place at high cardiolipin loading.
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Affiliation(s)
- Mauro Giustini
- Dipartimento di Chimica, Università La Sapienza, via Orabona 4, I-00185 Rome, Italy
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36
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Fischer CJ, Maluf NK, Lohman TM. Mechanism of ATP-dependent translocation of E.coli UvrD monomers along single-stranded DNA. J Mol Biol 2005; 344:1287-309. [PMID: 15561144 DOI: 10.1016/j.jmb.2004.10.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 10/04/2004] [Accepted: 10/04/2004] [Indexed: 11/28/2022]
Abstract
Escherichia coli UvrD protein is a 3' to 5' SF1 DNA helicase involved in methyl-directed mismatch repair and nucleotide excision repair of DNA. Using stopped-flow methods we have examined the kinetic mechanism of translocation of UvrD monomers along single-stranded DNA (ssDNA) in vitro by monitoring the transient kinetics of arrival of protein at the 5'-end of the ssDNA. Arrival at the 5'-end was monitored by the effect of protein on the fluorescence intensity of fluorophores (Cy3 or fluorescein) attached to the 5'-end of a series of oligodeoxythymidylates varying in length from 16 to 124 nt. We find that UvrD monomers are capable of ATP-dependent translocation along ssDNA with a biased 3' to 5' directionality. Global non-linear least-squares analysis of the full kinetic time-courses in the presence of a protein trap to prevent rebinding of free protein to the DNA using the methods described in the accompanying paper enabled us to obtain quantitative estimates of the kinetic parameters for translocation. We find that UvrD monomers translocate in discrete steps with an average kinetic step-size, m=3.68(+/-0.03) nt step(-1), a translocation rate constant, kt=51.3(+/-0.6) steps s(-1), (macroscopic translocation rate, mkt=189.0(+/-0.7) nt s(-1)), with a processivity corresponding to an average translocation distance of 2400(+/-600) nt before dissociation (10 mM Tris-HCl (pH 8.3), 20 mM NaCl, 20% (v/v) glycerol, 25 degrees C). However, in spite of its ability to translocate rapidly and efficiently along ssDNA, a UvrD monomer is unable to unwind even an 18 bp duplex in vitro. DNA helicase activity in vitro requires a UvrD dimer that unwinds DNA with a similar kinetic step-size of 4-5 bp step(-1), but an approximately threefold slower unwinding rate of 68(+/-9) bp s(-1) under the same solution conditions, indicating that DNA unwinding activity requires more than the ability to simply translocate directionally along ss-DNA.
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Affiliation(s)
- Christopher J Fischer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110-1093, USA
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37
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Bacchiocchi C, Graceffa P, Lehrer SS. Myosin-induced movement of alphaalpha, alphabeta, and betabeta smooth muscle tropomyosin on actin observed by multisite FRET. Biophys J 2004; 86:2295-307. [PMID: 15041668 PMCID: PMC1304079 DOI: 10.1016/s0006-3495(04)74287-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The interaction of the alphaalpha, betabeta, and alphabeta smooth muscle tropomyosin (Tm) isoforms with F-actin was systematically studied in the absence and in the presence of myosin subfragment 1 (S1) using multifrequency phase/modulation Förster resonance energy transfer (FRET). A Gaussian double distance distribution model was adopted to fit FRET data between a 5-(2-iodoacetyl-amino-ethyl-amino)naphthalene-1-sulfonic acid donor at either Cys-36 of the beta-chain or Cys-190 of the alpha-chain and a 4-dimethylaminophenylazophenyl 4'-maleimide acceptor at Cys-374 of F-actin. Experimental data were obtained for singly and doubly labeled alphabeta Tm (donor only at alpha, only at beta, or both) and for doubly labeled alphaalpha or betabeta Tm. Data for singly labeled alphabetaTm were combined in a global analysis with doubly labeled alphabetaTm. In all doubly labeled isoforms, upon S1 binding, one donor-acceptor "apparent" distance increased slightly by 0.5-2 A, whereas the other decreased by 6-9 A. These changes are consistent with a uniform "rolling" motion of Tm over the F-actin surface. The analysis indicates that Tm occupies relatively well-defined positions, with some flexibility, in both the predominantly closed (-S1) and open (+S1) thin-filament states. The results for the alphabetaTm heterodimer indicate that the local twofold symmetry of alphaalpha or betabeta Tm is effectively broken in alphabetaTm bound to F-actin, which implies a difference between the alpha- and beta-chains in terms of their interaction with F-actin.
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Affiliation(s)
- Corrado Bacchiocchi
- Muscle and Motility Group, Boston Biomedical Research Institute, Watertown, Massachusetts 02472, USA.
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38
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Lucius AL, Lohman TM. Effects of temperature and ATP on the kinetic mechanism and kinetic step-size for E.coli RecBCD helicase-catalyzed DNA unwinding. J Mol Biol 2004; 339:751-71. [PMID: 15165848 DOI: 10.1016/j.jmb.2004.04.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 04/01/2004] [Accepted: 04/01/2004] [Indexed: 11/24/2022]
Abstract
The kinetic mechanism by which Escherichia coli RecBCD helicase unwinds duplex DNA was studied using a fluorescence stopped-flow method. Single turnover DNA unwinding experiments were performed using a series of fluorescently labeled DNA substrates containing duplex DNA regions ranging from 24 bp to 60 bp. All or no DNA unwinding time courses were obtained by monitoring the changes in fluorescence resonance energy transfer between a Cy3 donor and Cy5 acceptor fluorescent pair placed on opposite sides of a nick in the duplex DNA. From these experiments one can determine the average rates of DNA unwinding as well as a kinetic step-size, defined as the average number of base-pairs unwound between two successive rate-limiting steps repeated during DNA unwinding. In order to probe how the kinetic step-size might relate to a mechanical step-size, we performed single turnover experiments as a function of [ATP] and temperature. The apparent unwinding rate constant, kUapp, decreases with decreasing [ATP], exhibiting a hyperbolic dependence on [ATP] (K1/2=176(+/-30) microM) and a maximum rate of kUapp=204(+/-4) steps s(-1) (mkUapp=709(+/-14) bp s(-1)) (10 mM MgCl2, 30 mM NaCl (pH 7.0), 5% (v/v) glycerol, 25.0 degrees C). kUapp also increases with increasing temperature (10-25 degrees C), with Ea=19(+/-1) kcal mol(-1). However, the average kinetic step-size, m=3.9(+/-0.5) bp step(-1), remains independent of [ATP] and temperature. This indicates that even though the values of the rate constants change, the same elementary kinetic step in the unwinding cycle remains rate-limiting over this range of conditions and this kinetic step remains coupled to ATP binding. The implications of the constancy of the measured kinetic step-size for the mechanism of RecBCD-catalyzed DNA unwinding are discussed.
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Affiliation(s)
- Aaron L Lucius
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110-1093, USA
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39
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Lopez F, Cinelli G, Ambrosone L, Colafemmina G, Ceglie A, Palazzo G. Role of the cosurfactant in water-in-oil microemulsion: interfacial properties tune the enzymatic activity of lipase. Colloids Surf A Physicochem Eng Asp 2004. [DOI: 10.1016/j.colsurfa.2004.01.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Kolev K, Tenekedjiev K, Ajtai K, Kovalszky I, Gombas J, Váradi B, Machovich R. Myosin: a noncovalent stabilizer of fibrin in the process of clot dissolution. Blood 2003; 101:4380-6. [PMID: 12543859 DOI: 10.1182/blood-2002-10-3227] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myosin modulates the fibrinolytic process as a cofactor of the tissue plasminogen activator and as a substrate of plasmin. We report now that myosin is present in arterial thrombi and it forms reversible noncovalent complexes with fibrinogen and fibrin with equilibrium dissociation constants in the micromolar range (1.70 and 0.94 microM, respectively). Competition studies using a peptide inhibitor of fibrin polymerization (glycl-prolyl-arginyl-proline [GPRP]) indicate that myosin interacts with domains common in fibrinogen and fibrin and this interaction is independent of the GPRP-binding polymerization site in the fibrinogen molecule. An association rate constant of 1.81 x 10(2) M(-1) x s(-1) and a dissociation rate constant of 3.07 x 10(-4) s(-1) are determined for the fibrinogen-myosin interaction. Surface plasmon resonance studies indicate that fibrin serves as a matrix core for myosin aggregation. The fibrin clots equilibrated with myosin are stabilized against dissolution initiated by plasminogen and tissue-type plasminogen activator (tPA) or urokinase (at fibrin monomer-myosin molar ratio as high as 30) and by plasmin under static and flow conditions (at fibrin monomer-myosin molar ratio lower than 15). Myosin exerts similar effects on the tPA-induced dissolution of blood plasma clots. Covalent modification involving factor XIIIa does not contribute to this stabilizing effect; myosin is not covalently attached to the clot by the time of complete cross-linking of fibrin. Thus, our in vitro data suggest that myosin detected in arterial thrombi binds to the polymerized fibrin, in the bound form its tPA-cofactor properties are masked, and the myosin fibrin clot is relatively resistant to plasmin.
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Affiliation(s)
- Krasimir Kolev
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary
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41
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Maluf NK, Lohman TM. Self-association equilibria of Escherichia coli UvrD helicase studied by analytical ultracentrifugation. J Mol Biol 2003; 325:889-912. [PMID: 12527298 DOI: 10.1016/s0022-2836(02)01276-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Escherichia coli UvrD protein (helicase II) is an SF1 superfamily helicase required for methyl-directed mismatch repair and nucleotide excision repair of DNA. We have characterized quantitatively the self-assembly equilibria of the UvrD protein as a function of [NaCl], [glycerol], and temperature (5-35 degrees C; pH 8.3) using analytical sedimentation velocity and equilibrium techniques, and find that UvrD self-associates into dimeric and tetrameric species over a range of solution conditions (t</=25 degrees C). Increasing [NaCl] from 20mM to 200 mM decreases the dimerization equilibrium constant (L(20)) from 2.33(+/-0.30) microM(-1) to 0.297(+/-0.006) microM(-1) (pH 8.3, 20% (v/v) glycerol, 25 degrees C). The overall tetramerization equilibrium constant (L(40)) is 5.11(+/-0.80) microM(-3) at 20mM NaCl, but decreases so that it is not measurable at 200 mM NaCl. At 500 mM NaCl, only UvrD monomers are detectable. Increasing [glycerol] over the range from 20% to 40% (v/v) decreases both L(20) and L(40). We find no evidence for hexamer formation, although a species consistent in size with an octamer is detected at 35 degrees C. Inclusion of either ADP or ATPgammaS does not affect either L(20) or L(40) significantly, and does not induce the formation of additional assembly states. We also investigated the stoichiometry of UvrD binding to a 3'-(dT)(20)-18 bp DNA substrate by sedimentation equilibrium. At saturating concentrations of UvrD, three UvrD monomers can bind to the DNA substrate, although only two UvrD monomers are required to form a processive helicase complex. When the total DNA substrate concentration is about twofold greater than the total UvrD concentration, the vast majority of the DNA is bound by a single UvrD monomer.
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Affiliation(s)
- Nasib K Maluf
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, St. Louis, MO 63110-1093, USA
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42
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Lucius AL, Vindigni A, Gregorian R, Ali JA, Taylor AF, Smith GR, Lohman TM. DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies. J Mol Biol 2002; 324:409-28. [PMID: 12445778 DOI: 10.1016/s0022-2836(02)01067-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism by which Escherichia coli RecBCD DNA helicase unwinds duplex DNA was examined in vitro using pre-steady-state chemical quenched-flow kinetic methods. Single turnover DNA unwinding experiments were performed by addition of ATP to RecBCD that was pre-bound to a series of DNA substrates containing duplex DNA regions ranging from 24 bp to 60 bp. In each case, the time-course for formation of completely unwound DNA displayed a distinct lag phase that increased with duplex length, reflecting the transient formation of partially unwound DNA intermediates during unwinding catalyzed by RecBCD. Quantitative analysis of five independent sets of DNA unwinding time courses indicates that RecBCD unwinds duplex DNA in discrete steps, with an average unwinding "step-size", m=3.9(+/-1.3)bp step(-1), with an average unwinding rate of k(U)=196(+/-77)steps s(-1) (mk(U)=790(+/-23)bps(-1)) at 25.0 degrees C (10mM MgCl(2), 30 mM NaCl (pH 7.0), 5% (v/v) glycerol). However, additional steps, not linked directly to DNA unwinding are also detected. This kinetic DNA unwinding step-size is similar to that determined for the E.coli UvrD helicase, suggesting that these two SF1 superfamily helicases may share similar mechanisms of DNA unwinding.
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Affiliation(s)
- Aaron L Lucius
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, MO 63110, USA
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43
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Stano NM, Levin MK, Patel SS. The +2 NTP binding drives open complex formation in T7 RNA polymerase. J Biol Chem 2002; 277:37292-300. [PMID: 12151383 DOI: 10.1074/jbc.m201600200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription initiation as catalyzed by T7 RNA polymerase consists primarily of promoter binding, strand separation, nucleotide binding, and synthesis of the first phosphodiester bond. The promoter strand separation process occurs at a very fast rate, but promoter opening is incomplete in the absence of the initiating NTPs. In this paper, we investigate how initiating NTPs affect the kinetics and thermodynamics of open complex formation. Transient state kinetic studies show that the open complex, ED(o), is formed via an intermediate ED(c), and the conversion of ED(c) to ED(o) occurs with an unfavorable equilibrium constant. In the presence of the initiating NTP that base-pairs with the template at position +2, the process of open complex formation is nearly complete. Our studies reveal that the nucleotide that drives open complex formation needs to be a triphosphate and to be correctly base-paired with the template. These results indicate that the melted template DNA in the open complex is positioned to bind the +2 NTP. The addition of +1 NTP alone does not stabilize the open complex; nor is it required for +2 NTP binding. However, there appears to be cooperativity in initiating NTP binding in that the binding of +2 NTP facilitates +1 NTP binding. The dissection of the initiation pathway provides insights into how open complex formation steps that are sensitive to the promoter sequence upstream from the initiation start site modulate the affinity of initiating NTPs and allow transcription initiation to be regulated by initiating NTP concentration.
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Affiliation(s)
- Natalie M Stano
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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44
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Bacchiocchi C, Lehrer SS. Ca(2+)-induced movement of tropomyosin in skeletal muscle thin filaments observed by multi-site FRET. Biophys J 2002; 82:1524-36. [PMID: 11867466 PMCID: PMC1301952 DOI: 10.1016/s0006-3495(02)75505-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
To obtain information on Ca(2+)-induced tropomyosin (Tm) movement in Ca(2+)-regulated muscle thin filaments, frequency-domain fluorescence energy transfer data were collected between 5-(2-iodoacetyl-amino-ethyl-amino)naphthalene-1-sulfonic acid at Cys-190 of Tm and phalloidin-tetramethylrhodamine B isothiocyanate bound to F-actin. Two models were used to fit the experimental data: an atomic coordinate (AC) model coupled with a search algorithm that varies the position and orientation of Tm on F-actin, and a double Gaussian distance distribution (DD) model. The AC model showed that little or no change in transfer efficiency is to be expected between different sites on F-actin and Tm if Ca(2+) causes azimuthal movement of Tm of the magnitude suggested by structural data (C. Xu, R. Craig, L. Tobacman, R. Horowitz, and W. Lehman. 1999. Biophys. J. 77:985-992). However, Ca(2+) produced a small but significant change in our phase/modulation versus frequency data, showing that changes in lifetime decay can be detected even when a change of the steady-state transfer efficiency is very small. A change in Tm azimuthal position of 17 on the actin filament obtained with the AC model indicates that solution data are in reasonable agreement with EM image reconstruction data. In addition, the data indicate that Tm also appears to rotate about its axis, resulting in a rolling motion over the F-actin surface. The DD model showed that the distance from one of the two chains of Tm to F-actin was mainly affected, further verifying that Ca(2+) causes Tm to roll over the F-actin surface. The width of the distance distributions indicated that the position of Tm in absence and in presence of Ca(2+) is well defined with appreciable local flexibility.
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Affiliation(s)
- Corrado Bacchiocchi
- Muscle and Motility Group, Boston Biomedical Research Institute, Watertown, Massachusetts 02472, USA.
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45
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de Wijn R, van Gorkom HJ. Kinetics of electron transfer from Q(a) to Q(b) in photosystem II. Biochemistry 2001; 40:11912-22. [PMID: 11570892 DOI: 10.1021/bi010852r] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation kinetics of the reduced photosystem II electron acceptor Q(A)(-) was investigated by measurement of the chlorophyll fluorescence yield transients on illumination of dark-adapted spinach chloroplasts by a series of saturating flashes. Q(A)(-) oxidation depends on the occupancy of the "Q(B) binding site", where this reaction reduces plastoquinone to plastoquinol in two successive photoreactions. The intermediate, one-electron-reduced plastosemiquinone anion Q(B)(-) remains tightly bound, and its reduction by Q(A)(-) may proceed with simple first-order kinetics. The next photoreaction, in contrast, may find the Q(B) binding site occupied by a plastoquinone, a plastoquinol, or neither of the two, resulting in heterogeneous Q(A)(-) oxidation kinetics. The assumption of monophasic Q(B)(-) reduction kinetics is shown to allow unambiguous decomposition of the observed multiphasic Q(A)(-) oxidation. At pH 6.5 the time constant for Q(A)(-) oxidation was found to be 0.2-0.4 ms with Q(B) in the site, 0.6-0.8 ms with Q(B)(-) in the site, 2-3 ms when the site is empty and Q(B) has to bind first, and of the order of 0.1 s if the site is temporarily blocked by the presence of Q(B)H(2) or other low-affinity inhibitors such as carbonyl cyanide m-chlorophenylhydrazone (CCCP). Effects of pH and H(2)O/D(2)O exchange were found to be remarkably nonspecific. No influence of the S-states could be demonstrated.
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Affiliation(s)
- R de Wijn
- Department of Biophysics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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Abstract
Binding studies provide information of fundamental and central importance for the complete understanding of ligand-DNA interactions. Studies of ligand binding to long natural DNA samples, to synthetic deoxypolynucleotides of simple repeating sequence, and to oligonucleotides of defined sequence are all needed to begin to understand the interaction in detail. Binding studies provide entry into the thermodynamics of the DNA interactions, which in turn provides great insight into the molecular forces that drive the binding process. This chapter summarizes both model-dependent and -independent approaches for the analysis and interpretation of binding isotherms, and should serve as a concise guide for handling experimental data.
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Affiliation(s)
- J B Chaires
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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47
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Affiliation(s)
- S P Edmondson
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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48
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de Wijn R, Schrama T, van Gorkom HJ. Secondary stabilization reactions and proton-coupled electron transport in photosystem II investigated by electroluminescence and fluorescence spectroscopy. Biochemistry 2001; 40:5821-34. [PMID: 11341848 DOI: 10.1021/bi002824z] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidized primary electron donor in photosystem II, P(680)(+), is reduced in several phases, extending over 4 orders of magnitude in time. Especially the slower phases may reflect the back-pressure exerted by water oxidation and provide information on the reactions involved. The kinetics of secondary electron-transfer reactions in the microseconds time range after charge separation were investigated in oxygen-evolving thylakoids suspended in H2O or D2O. Flash-induced changes of chlorophyll fluorescence yield and electric field-induced recombination luminescence were decomposed into contributions from oxidation states S(0), S(1), S(2), and S(3) of the oxygen-evolving complex and interpreted in terms of stabilization kinetics of the initial charge-separated state S(j)Y(Z)P(680)(+)Q(A)(-)Q(B). In approximately 10% of the centers, only charge recombination took place. Otherwise, no static heterogeneity was involved in the microsecond reduction of P(680)(+) by Y(Z) (stabilization) or Q(A)(-) (recombination). The recombination component in active centers occurs mainly upon charge separation in S(3), and, in the presence of D2O, in S(2) as well and is tentatively attributed to the presence of Y(Z)(ox)S(j-1) in equilibrium with Y(Z)S(j). A 20-30 micros stabilization occurs in all S-states, but to different extents. Possible mechanisms for this component are discussed. D2O was found to decrease: (i) the rate of the reaction Y(Z)(ox)S(1) to Y(Z)S(2), (ii) the equilibrium constant between P680(+)Y(Z)S(2) and P(680)Y(Z)(ox)S(2), (iii) the rate of the slow phase of P(680)(+) reduction for the S(3) --> S(0) transition, and (iv) the rate of electron transfer from Q(A)(-) to Q(B) /Q(B)(-). The increased 'miss probability' in D2O is due to (iii).
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Affiliation(s)
- R de Wijn
- Department of Biophysics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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Williams DJ, Hall KB. Monte Carlo applications to thermal and chemical denaturation experiments of nucleic acids and proteins. Methods Enzymol 2001; 321:330-52. [PMID: 10909065 DOI: 10.1016/s0076-6879(00)21201-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D J Williams
- Department of Biochemistry, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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50
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Affiliation(s)
- X Qu
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505, USA
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