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Schneider TD. Generalizing the isothermal efficiency by using Gaussian distributions. PLoS One 2023; 18:e0279758. [PMID: 36626367 PMCID: PMC9831307 DOI: 10.1371/journal.pone.0279758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023] Open
Abstract
Unlike the Carnot heat engine efficiency published in 1824, an isothermal efficiency derived from thermodynamics and information theory can be applied to biological systems. The original approach by Pierce and Cutler in 1959 to derive the isothermal efficiency equation came from Shannon's channel capacity of 1949 and from Felker's 1952 determination of the minimum energy dissipation needed to gain a bit. In 1991 and 2010 Schneider showed how the isothermal efficiency equation can be applied to molecular machines and that this can be used to explain why several molecular machines are 70% efficient. Surprisingly, some macroscopic biological systems, such as whole ecosystems, are also 70% efficient but it is hard to see how this could be explained by a thermodynamic and molecular theory. The thesis of this paper is that the isothermal efficiency can be derived without using thermodynamics by starting from a set of independent Gaussian distributions. This novel derivation generalizes the isothermal efficiency equation for use at all levels of biology, from molecules to ecosystems.
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Affiliation(s)
- Thomas D. Schneider
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, RNA Biology Laboratory, Frederick, MD, United States of America
- * E-mail:
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2
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Jouravleva K, Vega-Badillo J, Zamore PD. Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq. CELL REPORTS METHODS 2022; 2:100185. [PMID: 35475222 PMCID: PMC9017153 DOI: 10.1016/j.crmeth.2022.100185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/18/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022]
Abstract
RNA Bind-n-Seq (RBNS) is a cost-effective, high-throughput method capable of identifying the sequence preferences of RNA-binding proteins and of qualitatively defining relative dissociation constants. Although RBNS is often described as an unbiased method, several factors may influence the outcome of the analysis. Here, we discuss these biases and present an analytical strategy to estimate absolute binding affinities from RBNS data, extend RBNS to kinetic studies, and develop a framework to compute relative association and dissociation rate constants. As proof of principle, we measured the equilibrium binding properties of mammalian Argonaute2 (AGO2) guided by eight microRNAs (miRNAs) and kinetic parameters for let-7a. The miRNA-binding site repertoires, dissociation constants, and kinetic parameters calculated from RBNS data using our methods correlate well with values measured by traditional ensemble and single-molecule approaches. Our data provide additional quantitative measurements for Argonaute-bound miRNA binding that should facilitate development of quantitative targeting rules for individual miRNAs.
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Affiliation(s)
- Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Joel Vega-Badillo
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D. Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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3
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Villaluenga JP, Cao-García FJ. Cooperative kinetics of ligand binding to linear polymers. Comput Struct Biotechnol J 2022; 20:521-533. [PMID: 35495112 PMCID: PMC9019704 DOI: 10.1016/j.csbj.2021.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022] Open
Abstract
Cooperative kinetic equation for large ligands binding to long polymers. Cooperativity in general affects binding and release rates. Appropriate counting of the available binding sites for a ligand to a linear polymer. Positive cooperativity increases polymer coverage by the ligand. Large ligand size reduces cooperativity effects.
Ligands change the chemical and mechanical properties of polymers. In particular, single strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA), modifying the ssDNA stiffness and the DNA replication rate, as recently measured with single-molecule techniques. SSB is a large ligand presenting cooperativity in some of its binding modes. We aim to develop an accurate kinetic model for the cooperative binding kinetics of large ligands. Cooperativity accounts for the changes in the affinity of a ligand to the polymer due to the presence of another bound ligand. Large ligands, attaching to several binding sites, require a detailed counting of the available binding possibilities. This counting has been done by McGhee and von Hippel to obtain the equilibrium state of the ligands-polymer complex. The same procedure allows to obtain the kinetic equations for the cooperative binding of ligands to long polymers, for all ligand sizes. Here, we also derive approximate cooperative kinetic equations in the large ligand limit, at the leading and next-to-leading orders. We found cooperativity is negligible at the leading-order, and appears at the next-to-leading order. Positive cooperativity (increased affinity) can be originated by increased binding affinity or by decreased release affinity, implying different kinetics. Nevertheless, the equilibrium state is independent of the origin of cooperativity and only depends on the overall increase in affinity. Next-to-leading approximation is found to be accurate, particularly for small cooperativity. These results allow to understand and characterize relevant ligand binding processes, as the binding kinetics of SSB to ssDNA, which has been reported to affect the DNA replication rate for several SSB-polymerase pairs.
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Affiliation(s)
- Juan P.G. Villaluenga
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Plaza de Ciencias, 1, 28040 Madrid, Spain
- Corresponding author.
| | - Francisco Javier Cao-García
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Plaza de Ciencias, 1, 28040 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Calle Faraday, 9, 28049 Madrid, Spain
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4
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Villaluenga JPG, Vidal J, Cao-García FJ. Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model. Phys Rev E 2020; 102:012407. [PMID: 32795076 DOI: 10.1103/physreve.102.012407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages.
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Affiliation(s)
- Juan P G Villaluenga
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Jules Vidal
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Francisco Javier Cao-García
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/Faraday, 9, 28049 Madrid, Spain
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5
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Schneider TD, Jejjala V. Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences. PLoS One 2019; 14:e0222419. [PMID: 31671158 PMCID: PMC6822723 DOI: 10.1371/journal.pone.0222419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/29/2019] [Indexed: 11/19/2022] Open
Abstract
Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.
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Affiliation(s)
- Thomas D. Schneider
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, RNA Biology Laboratory, Frederick, Maryland, United States of America
| | - Vishnu Jejjala
- Mandelstam Institute for Theoretical Physics, School of Physics, NITheP, and CoE-MaSS, University of the Witwatersrand, Johannesburg, South Africa
- David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Bujalowski W, Jezewska MJ, Bujalowski PJ. Signal and binding. I. Physico-chemical response to macromolecule-ligand interactions. Biophys Chem 2017; 222:7-24. [PMID: 28092802 DOI: 10.1016/j.bpc.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/26/2016] [Accepted: 12/26/2016] [Indexed: 11/27/2022]
Abstract
Obtaining a detailed knowledge about energetics of ligand-macromolecule interactions is a prerequisite for elucidation of the nature, behavior, and activities of the formed complexes. The most commonly used methods in characterizing molecular interactions are physico-chemical techniques based mainly on spectroscopic, calorimetric, hydrodynamic, etc., measurements. The major advantage of the physico-chemical methods is that they do not require large quantities of material and, if performed carefully, do not perturb examined reactions. Applications of several different physico-chemical approaches, commonly encountered in analyses of biochemical interactions, are here reviewed and discussed, using examples of simple binding reactions. It is stressed that without determination of the relationship between the measured signal and the total average degree of binding, the performed analysis of a single physico-chemical titration curve may provide only fitting parameters, instead of meaningful interaction parameters, already for the binding systems with only two ligand molecules. Some possible pitfalls in the analyses of single titration curves are discussed.
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Affiliation(s)
- Wlodzimierz Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA; Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA; The Sealy Center for Structural Biology, Sealy Center for Cancer Cell Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA.
| | - Maria J Jezewska
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA; The Sealy Center for Structural Biology, Sealy Center for Cancer Cell Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA
| | - Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA; The Sealy Center for Structural Biology, Sealy Center for Cancer Cell Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1053, USA
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Signal and binding. II. Converting physico-chemical responses to macromolecule-ligand interactions into thermodynamic binding isotherms. Biophys Chem 2016; 222:25-40. [PMID: 28095332 DOI: 10.1016/j.bpc.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/26/2016] [Accepted: 12/26/2016] [Indexed: 11/23/2022]
Abstract
Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm. The quantitative methods reviewed and discussed here allow an experimenter to rigorously determine the degree of binding and the free ligand concentration, i.e., they lead to the construction of the thermodynamic binding isotherm in a model-independent fashion from physico-chemical titration curves.
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8
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Litwin TR, Solà M, Holt IJ, Neuman KC. A robust assay to measure DNA topology-dependent protein binding affinity. Nucleic Acids Res 2014; 43:e43. [PMID: 25552413 PMCID: PMC4402506 DOI: 10.1093/nar/gku1381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/18/2014] [Indexed: 02/04/2023] Open
Abstract
DNA structure and topology pervasively influence aspects of DNA metabolism including replication, transcription and segregation. However, the effects of DNA topology on DNA-protein interactions have not been systematically explored due to limitations of standard affinity assays. We developed a method to measure protein binding affinity dependence on the topology (topological linking number) of supercoiled DNA. A defined range of DNA topoisomers at equilibrium with a DNA binding protein is separated into free and protein-bound DNA populations using standard nitrocellulose filter binding techniques. Electrophoretic separation and quantification of bound and free topoisomers combined with a simple normalization procedure provide the relative affinity of the protein for the DNA as a function of linking number. Employing this assay we measured topology-dependent DNA binding of a helicase, a type IB topoisomerase, a type IIA topoisomerase, a non-specific mitochondrial DNA binding protein and a type II restriction endonuclease. Most of the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependent affinity differ among proteins in ways that expose differences in their interactions with DNA. The topology-dependent binding assay provides a robust and easily implemented method to probe topological influences on DNA-protein interactions for a wide range of DNA binding proteins.
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Affiliation(s)
- Tamara R Litwin
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA Mitochondrial Biology Unit, Medical Research Council, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Maria Solà
- Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), 08028 Barcelona, Spain
| | - Ian J Holt
- National Institute for Medical Research, Medical Research Council, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Keir C Neuman
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
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9
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Abstract
Elucidation of ligand - macromolecule interactions requires detailed knowledge of energetics of the formed complexes. Spectroscopic methods are most commonly used in characterizing molecular interactions in solution. The methods do not require large quantities of material and most importantly, do not perturb the studied reactions. However, spectroscopic methods absolutely require the determination of the relationship between the observed signal and the degree of binding in order to obtain meaningful interaction parameters. In other words, the meaningful, thermodynamic interaction parameters can be only determined if the relationship between the observed signal and the degree of binding is determined and not assumed, based on an ad hoc model of the relationship. The approaches discussed here allow an experimenter to quantitatively determine the degree of binding and the free ligand concentration, i.e., they enable to construct thermodynamic binding isotherms in a model-independent fashion.
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Affiliation(s)
- Wlodzimierz Bujalowski
- Department of Obstetrics and Gynecology, The Sealy Center for Structural Biology, Sealy Center for Cancer Cell Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555-1053
| | - Maria J Jezewska
- Department of Biochemistry and Molecular Biology, The Sealy Center for Structural Biology, Sealy Center for Cancer Cell Biology, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555-1053
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10
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Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods 2014; 76:99-115. [PMID: 25305413 DOI: 10.1016/j.ymeth.2014.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023] Open
Abstract
Isothermal titration calorimetry (ITC) has become the gold-standard technique for studying binding processes due to its high precision and sensitivity, as well as its capability for the simultaneous determination of the association equilibrium constant, the binding enthalpy and the binding stoichiometry. The current widespread use of ITC for biological systems has been facilitated by technical advances and the availability of commercial calorimeters. However, the complexity of data analysis for non-standard models is one of the most significant drawbacks in ITC. Many models for studying macromolecular interactions can be found in the literature, but it looks like each biological system requires specific modeling and data analysis approaches. The aim of this article is to solve this lack of unity and provide a unified methodological framework for studying binding interactions by ITC that can be applied to any experimental system. The apparent complexity of this methodology, based on the binding polynomial, is overcome by its easy generalization to complex systems.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; IIS Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Spain.
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11
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Abstract
The idea that we could build molecular communications systems can be advanced by investigating how actual molecules from living organisms function. Information theory provides tools for such an investigation. This review describes how we can compute the average information in the DNA binding sites of any genetic control protein and how this can be extended to analyze its individual sites. A formula equivalent to Claude Shannon's channel capacity can be applied to molecular systems and used to compute the efficiency of protein binding. This efficiency is often 70% and a brief explanation for that is given. The results imply that biological systems have evolved to function at channel capacity, which means that we should be able to build molecular communications that are just as robust as our macroscopic ones.
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Affiliation(s)
- Thomas D. Schneider
- National Institutes of Health, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201, United States
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12
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Schneider TD. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence. Nucleic Acids Res 2010; 38:5995-6006. [PMID: 20562221 PMCID: PMC2952855 DOI: 10.1093/nar/gkq389] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is Emin = Kb T ln 2 joules per bit (kB is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2=0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal.
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Affiliation(s)
- Thomas D Schneider
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702-1201, USA.
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13
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Gustchina E, Louis JM, Bewley CA, Clore GM. Synergistic inhibition of HIV-1 envelope-mediated membrane fusion by inhibitors targeting the N and C-terminal heptad repeats of gp41. J Mol Biol 2006; 364:283-9. [PMID: 17010381 PMCID: PMC1785329 DOI: 10.1016/j.jmb.2006.09.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/25/2006] [Accepted: 09/06/2006] [Indexed: 11/20/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) envelope (Env) proteins that mediate membrane fusion represent a major target for the development of new AIDS therapies. Three classes of Env-mediated membrane fusion inhibitors have been described that specifically target the pre-hairpin intermediate conformation of gp41. Class 2 inhibitors bind to the C-terminal heptad repeat (C-HR) of gp41. The single example of a class 3 inhibitor targets the trimeric N-terminal heptad repeat (N-HR) of gp41 and has been postulated to sequestrate the N-HR of the pre-hairpin intermediate through the formation of fusion incompetent heterotrimers. Here, we show that N(CCG)-gp41, a class 2 inhibitor, and N36(Mut(e,g)), a class 3 inhibitor, synergistically inhibit Env-mediated membrane fusion for several representative HIV-1 strains (X4 and R5) in both a cell fusion assay (with membrane-bound CD4) and an Env-pseudo-typed virus neutralization assay. The mechanistic, as well as potential therapeutic, implications of these observations for HIV-Env-mediated membrane fusion are discussed.
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Affiliation(s)
- Elena Gustchina
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - John M. Louis
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, Building 8, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0820
- *Authors to whom correspondence should be addressed. E-mails: G.M.C., ; C.A.B.,
| | - G. Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
- *Authors to whom correspondence should be addressed. E-mails: G.M.C., ; C.A.B.,
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Bujalowski W. Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems. Chem Rev 2006; 106:556-606. [PMID: 16464018 DOI: 10.1021/cr040462l] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wlodzimierz Bujalowski
- Department of Biochemistry and Molecular Biology, the Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, 77555-1053, USA.
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15
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Mary J, Révet B. Isolation and characterization of a protein with high affinity for DNA: the glutamine synthetase of Thermus thermophilus 111. J Mol Biol 1999; 286:121-34. [PMID: 9931254 DOI: 10.1006/jmbi.1998.2464] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a search of proteins from the thermophilic bacterium Thermus thermophilus 111 with a high affinity for DNA, the selected protein from this screening appears to be the glutamine synthetase (GS). The purified product gives one band in SDS-polyacrylamide gel electrophoresis (53,700 Da). The N-terminal 32 residues have been identified and present an homology of 80% with the glutamine synthetase of Bacillus subtilis and 76% with that of Thermotoga maritima. The protein displays the characteristic dodecameric structure of the eubacteria glutamine synthetase. From a detailed study of the interaction of this protein with DNA by dark-field electron microscopy and agarose gel electrophoresis, it is concluded that double-stranded DNA wraps the protein by a full turn of 150 bp length. An even number of GS molecules bound to a closed relaxed plasmid DNA does not alter its null topology. By using an inverted dimer DNA fragment, which contains twice a curved kinetoplast DNA insert in its central part, it is shown that DNA curvature rules the order in which GS binds to the DNA. DNA ends are also sites of high affinity for the GS. Supercoiling does not favor the binding of GS to the DNA with the exception of the apices that are by essence bent regions. By saturating a DNA molecule with GS one obtains a novel characteristic scalloped configuration in which the DNA undulates from one GS to the next. The DNA is condensed at least three times in these structures. By increasing the ratio of GS to DNA in solution the resulting material migrates as discrete bands relative to the free DNA in an agarose gel. By gel retardation and EM statistical distribution analysis of GS within the complexes, an average affinity constant of 10(7) M-1 was obtained. The potential implications of this novel interaction of the glutamine synthetase with DNA for the regulation of its own gene are briefly discussed.
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Affiliation(s)
- J Mary
- Laboratoire de Microscopie Cellulaire et Moléculaire, CNRS, UMR 1772, Institut Gustave-Roussy, Villejuif Cedex, F-94805, France
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Pray TR, Burz DS, Ackers GK. Cooperative non-specific DNA binding by octamerizing lambda cI repressors: a site-specific thermodynamic analysis. J Mol Biol 1998; 282:947-58. [PMID: 9753546 DOI: 10.1006/jmbi.1998.2056] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Relationships between dimerization and site-specific binding have been characterized previously for wild-type and mutant cI repressors at the right operator (OR) of bacteriophage lambda DNA. However, the roles of higher-order oligomers (tetramers and octamers) that are also formed from these cI molecules have remained elusive. In this study, a clear correlation has been established between repressor oligomerization and non-specific DNA-binding activity. A modification of the quantitative DNase I footprint titration technique has been used to evaluate the degree of saturation of non-specific, OR-flanking lambda DNA by cI repressor oligomers. With the exception of one mutant, only those repressors capable of octamerizing were found to exhibit non-specific DNA-binding activity. The non-specific interaction was accurately modeled using either a one-dimensional, univalent, site-specific Ising lattice approximation, or a more traditional, multivalent lattice approach. It was found that non-specific DNA-binding by repressor oligomers is highly cooperative and energetically independent from site-specific binding at OR. Furthermore, the coupling free energy resolved for non-specific binding was similar to that of site-specific binding for each repressor, suggesting that similar structural elements may mediate the cooperative component of both binding processes. It is proposed that the state of assembly of the repressor molecule modulates its relative affinity for specific and non-specific DNA sequences. These specificities are allosterically regulated by the transmission of assembly-state information from the C-terminal domain, which mediates self-association and cooperativity, to the N-terminal domain, which primarily mediates DNA-binding. While dimers have a high affinity for their cognate sites within OR, tetramers and octamers may preferentially recognize non-specific DNA sequences. The concepts and findings developed in this study may facilitate quantitative characterization of the relationships between specific, and non-specific binding in other systems that utilize multiple modes of DNA-binding cooperativity.
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Affiliation(s)
- T R Pray
- School of Medicine, Washington University, St Louis, MO, 63110, USA
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17
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Hendrix M, Priestley ES, Joyce GF, Wong CH. Direct observation of aminoglycoside-RNA interactions by surface plasmon resonance. J Am Chem Soc 1997; 119:3641-8. [PMID: 11540136 DOI: 10.1021/ja964290o] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The specificity of neomycin B and related aminoglycoside antibiotics in their interaction with the Rev responsive element (RRE) of HIV-1 mRNA has been studied by directly observing the aminoglycoside-RNA complexes using surface plasmon resonance. Several different RNA sequences, each with a biotin tag, have been prepared using T7 RNA polymerase-catalyzed transcription of synthetic DNA templates and have been immobilized on a streptavidin-coated surface for the binding study. The results indicate that neomycin B is not specific for the G-rich bubble region in RRE. Rather, it appears to interact with three different sites, each with a submicromolar dissociation constant, within the 67-nucleotide domain II of RRE. Further analysis of neomycin B binding with three short synthetic RNA hairpins showed binding with submicromolar affinity and 1:1 stoichiometry in each case. This suggests that neomycin B may generally bind with this affinity to regular A-form RNA or hairpin loops. The approach described here is generally useful for understanding the fundamental interactions involved in the specific recognition of nucleic acids by small molecules which is the basis of rational drug design.
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MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/metabolism
- Antibody Affinity
- Base Sequence
- Binding Sites
- Biotinylation
- Chemistry, Pharmaceutical
- Framycetin/chemistry
- Framycetin/metabolism
- Gene Products, rev/chemistry
- Gene Products, rev/genetics
- Gene Products, rev/metabolism
- Genes, env
- HIV-1/chemistry
- HIV-1/genetics
- Paromomycin/chemistry
- Paromomycin/metabolism
- Protein Binding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Structure-Activity Relationship
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- M Hendrix
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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18
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Künne AG, Meierhans D, Allemann RK. Basic helix-loop-helix protein MyoD displays modest DNA binding specificity. FEBS Lett 1996; 391:79-83. [PMID: 8706935 DOI: 10.1016/0014-5793(96)00707-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The expression of MyoD can activate muscle specific genes and myogenic differentiation in many cell types. The hypothesis that the DNA binding specificity of MyoD is responsible for its biological specificity was tested. Homodimers of MyoD bind to E-box containing DNA with high affinity, but do not form stable and well defined complexes with heterologous DNA sequences. The physiologically active heterodimer of MyoD and E12 binds an oligonucleotide containing an E-box sequence with an affinity only two orders of magnitude higher than a completely unrelated DNA sequence, stressing the importance of cooperative interactions with other proteins of the transcriptional machinery for specific gene activation.
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Affiliation(s)
- A G Künne
- Department of Chemistry, ETH-Zurich, Switzerland
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19
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Affiliation(s)
- A J Dombroski
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston 77030, USA
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20
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Meierhan D, el-Ariss C, Neuenschwander M, Sieber M, Stackhouse JF, Allemann RK. DNA binding specificity of the basic-helix-loop-helix protein MASH-1. Biochemistry 1995; 34:11026-36. [PMID: 7669760 DOI: 10.1021/bi00035a008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.
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Affiliation(s)
- D Meierhan
- Department of Chemistry, ETH-Zurich, Switzerland
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21
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Jen-Jacobson L. Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. Methods Enzymol 1995; 259:305-44. [PMID: 8538460 DOI: 10.1016/0076-6879(95)59050-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- L Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260, USA
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22
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Teyssier C, Laine B, Gervais A, Maurizot JC, Culard F. Archaebacterial histone-like protein MC1 can exhibit a sequence-specific binding to DNA. Biochem J 1994; 303 ( Pt 2):567-73. [PMID: 7980419 PMCID: PMC1137365 DOI: 10.1042/bj3030567] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The binding of MC1 protein, the major chromosomal protein of the archaebacterium Methanosarcina sp. CHTI 55, to the region preceding the strongly expressed genes encoding methyl coenzyme reductase in a closely related micro-organism has been investigated. By gel retardation and DNAase I footprinting assays, we identified a preferential binding sequence in an open reading frame of unknown function. The large area of DNA protected against DNAase I is interrupted by a strong cleavage enhancement site on each strand. By circular permutation assays, we showed that the DNA bends upon MC1 binding. Furthermore we observed that the presence of a sequence outside the binding site can induce an unusual electrophoretic behaviour in some complexes.
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Affiliation(s)
- C Teyssier
- Centre de biophysique moléculaire, Orléans, France
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23
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Wong I, Lohman TM. A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions. Proc Natl Acad Sci U S A 1993; 90:5428-32. [PMID: 8516284 PMCID: PMC46733 DOI: 10.1073/pnas.90.12.5428] [Citation(s) in RCA: 326] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Nitrocellulose-filter binding is a powerful technique commonly used to study protein-nucleic acid interactions; however, its utility in quantitative studies is often compromised by its lack of precision. To improve precision and accuracy, we have introduced two modifications to the traditional technique: the use of a 96-well dot-blot apparatus and the addition of a DEAE membrane beneath the nitrocellulose membrane. Using the dot-blot apparatus, an entire triplicate set of data spanning 20-24 titrant concentrations can be collected on a single 4.5 x 5 inch sheet of nitrocellulose, obviating the need to manipulate separate filters for each titration point. The entire titration can then be quantitated simultaneously with direct two-dimensional beta-emission imaging technology. The DEAE second membrane traps all DNA that does not bind to the nitrocellulose, enabling a direct determination of the total amount of DNA filtered. This measurement improves precision by allowing the amount of DNA retained by the nitrocellulose to be normalized against the total amount of DNA filtered. The DEAE membrane also permits a more accurate quantitation of filter-retention efficiency and nonspecific background retention based on free DNA rather than total DNA filtered. The general approach and methods of analysis to obtain equilibrium binding isotherms are discussed, using as examples our studies of the Escherichia coli Rep protein, a helicase, and its interactions with short oligodeoxynucleotides.
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Affiliation(s)
- I Wong
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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24
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Pozidis C, Vlatakis G, Bouriotis V. Sequence-specific DNA affinity chromatography: application of a group-specific adsorbent for the isolation of restriction endonucleases. J Chromatogr A 1993; 630:151-7. [PMID: 8383139 DOI: 10.1016/0021-9673(93)80451-d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The use of sequence-specific DNA affinity adsorbents for the isolation of restriction endonucleases EcoRI and SphI to near homogeneity has been reported. However, the high cost of these adsorbents is a limiting factor for their wider application. This paper reports the application of sequence-specific DNA affinity ligands containing recognition sequences for 34 restriction endonucleases as group-specific ligands in the isolation of restriction endonucleases. Crude samples of six restriction endonucleases, namely BshFI, BamHI, SmaI, SacII, PvuII and SalI, were shown to bind to these adsorbents and could be eluted at different KCl concentrations. High purification factors and recoveries were obtained. Restriction endonuclease BshFI, an isoschizomer of HaeIII, from the microorganism Bacillus sphaericus was purified to near homogeneity employing a two-step procedure which involves DNA-cellulose chromatography and oligonucleotide-ligand affinity chromatography. The enzyme exists as a monomer with an apparent relative molecular mass of 34,000 as determined by both sodium dodecyl sulphate-polyacrylamide gel electrophoresis and size-exclusion chromatography.
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Affiliation(s)
- C Pozidis
- Institute of Molecular Biology and Biotechnology, Enzyme Technology Division, Crete, Greece
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25
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Wong I, Chao K, Bujalowski W, Lohman T. DNA-induced dimerization of the Escherichia coli rep helicase. Allosteric effects of single-stranded and duplex DNA. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42558-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Koblan KS, Bain DL, Beckett D, Shea MA, Ackers GK. Analysis of site-specific interaction parameters in protein-DNA complexes. Methods Enzymol 1992; 210:405-25. [PMID: 1584044 DOI: 10.1016/0076-6879(92)10021-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- K S Koblan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
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27
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Takahashi M, Kubista M, Nordén B. Binding of RecA Protein to Z-form DNA Studied with Circular and Linear Dichroism Spectroscopy. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81829-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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28
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Bennett SP, Halford SE. Recognition of DNA by type II restriction enzymes. CURRENT TOPICS IN CELLULAR REGULATION 1989; 30:57-104. [PMID: 2695290 DOI: 10.1016/b978-0-12-152830-0.50005-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- S P Bennett
- Department of Biochemistry, School of Medical Sciences, University of Bristol, England
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29
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The binding in vitro of the intermediate filament protein vimentin to synthetic oligonucleotides containing telomere sequences. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37346-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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30
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Maurizot JC, Grebert P. Thermodynamic parameters of the binding of the tight-binding I12X86 lac repressor to operator and non-operator DNA. FEBS Lett 1988; 239:105-8. [PMID: 3053243 DOI: 10.1016/0014-5793(88)80554-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The thermodynamic parameters delta H and delta S corresponding to the binding of the tight-binding double mutant lac repressor I12X86 with operator and non-operator DNA fragments were determined using the nitrocellulose filter binding assay. In both cases the binding processes are entropically driven and accompanied by an unfavorable enthalpy variation. The differences between these parameters and those previously reported for the wild type lac repressor show that the strategy adopted by the mutant to interact with DNA is highly different from that of the wild type repressor and suggest more hydrophobic contacts between the mutant and DNA.
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Affiliation(s)
- J C Maurizot
- Centre de Biophysique Moleculaire, Orleans, France
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31
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Gent ME, Gronenborn AM, Davies RW, Clore GM. Probing the sequence-specific interaction of the cyclic AMP receptor protein with DNA by site-directed mutagenesis. Biochem J 1987; 242:645-53. [PMID: 3109398 PMCID: PMC1147760 DOI: 10.1042/bj2420645] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mutants in the DNA-binding helix of the cyclic AMP receptor protein (CRP), as well as mutants in a synthetic DNA-binding site derived from the sequence in the lac regulatory region, have been constructed by oligonucleotide-directed mutagenesis, and used to study the effect of selected amino acid substitutions on CRP-mediated transcriptional activity and on sequence-specific DNA binding. It has been shown that mutation of Arg-180 to Lys or Leu abolishes both CRP-mediated expression of beta-galactosidase in vivo and CRP binding of DNA as measured by immunoprecipitation. In contrast, the mutation of Arg-185 to Leu or Lys and the mutation of Lys-188 to Leu does not appear to influence these two parameters significantly. On the DNA side, both substitutions studied, namely the exchange of the G . C base pair in position 2 of the consensus T1G2T3G4A5 motif into an A . T base pair and the exchange of the A . T base pair in position 5 for a G . C base pair, abolish specific binding. Implications of these findings with respect to the present models for specific CRP-DNA recognition are discussed.
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32
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Minter SJ, Clore GM, Gronenborn AM, Davies RW. Cooperative DNA binding by lambda integration protein--a key component of specificity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 161:727-31. [PMID: 3024982 DOI: 10.1111/j.1432-1033.1986.tb10500.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Quantitative analysis of nitrocellulose filter binding data by the method of Clore, Gronenborn and Davies [(1982) J. Mol. Biol. 155, 447-466] has been used to show that lambda integration protein (Int) exhibits cooperativity in binding to specific recognition sites within the attachment site region (lambda attP) of bacteriophage lambda DNA. Optimal values of the equilibrium constant obtained were 3.0(+/- 1.0) X 10(10) M-1 for the P' site using a model of three sites with equal affinity and 1.9(+/- 0.4) X 10(10) M-1 for the P1 site on a two-site model. The value of the cooperativity parameter alpha is 172(+106)(-66) in all cases. The occurrence of a consensus recognition sequence is necessary but not sufficient for strong binding; cooperative interaction between Int molecules binding to adjacent members of an array of binding sites is also essential. The occurrence of binding site arrays distinguishes lambda attP very clearly from other DNA sequences containing single recognition sites by chance.
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33
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Brenowitz M, Senear DF, Shea MA, Ackers GK. "Footprint" titrations yield valid thermodynamic isotherms. Proc Natl Acad Sci U S A 1986; 83:8462-6. [PMID: 3464963 PMCID: PMC386950 DOI: 10.1073/pnas.83.22.8462] [Citation(s) in RCA: 124] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A central issue in gene regulation is the mechanism, and biological function, of the cooperative binding of regulatory protein ligands to specific sites on DNA. To elucidate the physical-chemical basis of these interactions we have developed a thermodynamically rigorous method for conducting DNase I "footprint" (protection) titration experiments. The intrinsic binding constants and also those for cooperative interactions between various sites can be resolved from the individual-site binding curves determined by this technique. Experimental studies of cI-repressor-operator binding have demonstrated that the method provides an accurate representation of the fractional saturation of a binding site. We present individual-site binding curves for a lambda operator with two competent sites that demonstrate the presence of cooperative interactions between the sites. These curves set a lower limit to the magnitude of the cooperative free energy without comparison to single-site mutant operators.
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34
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Grebert P, Maurizot JC. Interaction of the tight-binding I12-X86 lac repressor with non operator DNA: salt dependence of complex formation. Nucleic Acids Res 1986; 14:6613-20. [PMID: 3529038 PMCID: PMC311668 DOI: 10.1093/nar/14.16.6613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The interaction of the wild-type lac repressor and its tight binding double mutant I12-X86 with a non operator-210 base pair-DNA fragment has been investigated using the nitrocellulose filter binding assay. While the affinity of the double mutant for this non specific DNA is increased as compared to that of the wild-type repressor, the number of ions released from the vicinity of the DNA upon complex formation is less important for the mutant than for the wild-type. These results demonstrate that the adaptation in the recognition surface of the repressor recently proposed by Mossing et al (J. Mol. Biol., 1985, 186, 295-305) in the case of an Oc mutant may be a more general phenomenon.
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35
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Brenowitz M, Senear DF, Shea MA, Ackers GK. Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol 1986; 130:132-81. [PMID: 3773731 DOI: 10.1016/0076-6879(86)30011-9] [Citation(s) in RCA: 276] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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36
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Eker AP. Evidence for the presence of an essential arginine residue in photoreactivating enzyme from Streptomyces griseus. Biochem J 1985; 229:469-76. [PMID: 3929771 PMCID: PMC1145079 DOI: 10.1042/bj2290469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Butane-2,3-dione inhibits the enzymic activity of Streptomyces griseus photoreactivating enzyme (PRE). Some characteristics of the inhibition, notably the enhancement by borate buffer and the reversibility, indicate that arginine residues are modified. From the kinetics of inhibition it can be concluded that a single essential arginine residue is involved. U.v.-irradiated DNA, the substrate for PRE, protects the enzyme against inactivation by butane-2,3-dione. This suggests that the essential arginine residue is situated in or near the u.v.-irradiated-DNA-binding site. Non-irradiated DNA at higher concentrations also protects against inactivation, indicating that PRE can form non-specific complexes. From the ratio of complex constants obtained from protection experiments with non-irradiated and u.v.-irradiated DNA it appears that PRE preferably binds to dimer sites.
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37
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Andrews J, Clore GM, Davies RW, Gronenborn AM, Gronenborn B, Kalderon D, Papadopoulos PC, Schäfer S, Sims PF, Stancombe R. Nucleotide sequence of the dihydrofolate reductase gene of methotrexate-resistant Lactobacillus casei. Gene 1985; 35:217-22. [PMID: 3928445 DOI: 10.1016/0378-1119(85)90174-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nucleotide sequence of the dihydrofolate reductase (DHFR) gene of a methotrexate-resistant strain of Lactobacillus casei, which is the source of DHFR for nuclear magnetic resonance (NMR) studies, has been determined. The derived amino acid sequence differs from that obtained by protein sequencing by the presence of aspartic acid instead of asparagine at position 8 and proline instead of leucine at position 90. The nucleotide sequences of 320-bp 5' and 335-bp 3' flanking regions of this gene have also been determined.
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38
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39
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Clore GM, Gronenborn AM, Davies RW. Cooperative non-specific DNA binding of the N-terminal core of the cyclic AMP receptor protein of Escherichia coli and its modulation by cyclic AMP. FEBS Lett 1983; 164:57-62. [PMID: 6317444 DOI: 10.1016/0014-5793(83)80018-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The non-specific DNA binding of CRP and its N-terminal core, alpha CRP, to a 298 base pair DNA fragment, in the presence and absence of cAMP, has been studied using the nitrocellulose filter binding technique and analysed quantitatively using the theory of Clore et al. [J. Mol. Biol. (1982) 155, 447-466]. It is shown that both CRP and alpha CRP bind cooperatively to DNA. At an ionic strength of 100 mM and pH 7.5, the intrinsic equilibrium association constant for the binding of alpha CRP to DNA is approximately 10-times smaller than that for CRP, but the cooperativity parameter is approximately 17-times larger for alpha CRP than CRP. cAMP exerts its effect solely on the intrinsic equilibrium constant and does not alter the cooperativity. In the case of alpha CRP, cAMP reduces the intrinsic equilibrium association constant by a factor of 3, in contrast to the case of CRP where cAMP increases it by a factor of 3. The possible location of the DNA binding site present in the N-terminal core of CRP is discussed in the light of crystallographic data on the cAMP . CRP complex [McKay et al. (1982) J. Biol. Chem. 257, 9518-9524].
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40
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Gronenborn AM, Clore GM. Characterization of the DNA binding region recognized by dihydrofolate reductase from lactobacillus casei. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44411-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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41
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Abstract
Single turnovers of the EcoRI restriction endonuclease, cleaving its recognition site on the covalently closed form of plasmid pMB9, were examined. Two methods were used to monitor the progress of the reactions: one involved quenching the reaction at various times followed by the electrophoretic separation of the products cleaved in one and in both strands of the duplex; the other employed a stopped-flow fluorimeter to measure the amount of ethidium bromide bound to the DNA as it changes when the DNA, cleaved in at least one strand, dissociates from the enzyme. Two procedures were used to initiate the reactions. For some, one solution containing the enzyme was mixed with a second containing both DNA and MgCl2: in these reactions, the fluorescence changed at the same rate as the cleavage of the first strand of the duplex. Other reactions were started by the addition of MgCl2 to a pre-equilibrium of enzyme and DNA: here, both strands of the DNA were cleaved faster than before, with the fluorescence signal now occurring at the same time as the cleavage of the second strand. The different kinetics from the two assays and the two mixing procedures are consistent with the rates of these reactions being controlled by protein conformational changes. These may affect either one subunit alone within the dimeric EcoRI enzyme, allowing the enzyme to cleave only one strand of the DNA in each turnover. Alternatively, both subunits of the dimer may change, so that the enzyme then cleaves both strands during the life-time of one enzyme-DNA complex.
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