1
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Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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2
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Madhurima K, Nandi B, Munshi S, Naganathan AN, Sekhar A. Functional regulation of an intrinsically disordered protein via a conformationally excited state. SCIENCE ADVANCES 2023; 9:eadh4591. [PMID: 37379390 PMCID: PMC10306299 DOI: 10.1126/sciadv.adh4591] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
A longstanding goal in the field of intrinsically disordered proteins (IDPs) is to characterize their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function. Here, we use multinuclear chemical exchange saturation (CEST) nuclear magnetic resonance to determine the structure of a thermally accessible globally folded excited state in equilibrium with the intrinsically disordered native ensemble of a bacterial transcriptional regulator CytR. We further provide evidence from double resonance CEST experiments that the excited state, which structurally resembles the DNA-bound form of cytidine repressor (CytR), recognizes DNA by means of a "folding-before-binding" conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR therefore operates through a dynamical variant of the lock-and-key mechanism where the structurally complementary conformation is transiently accessed via thermal fluctuations.
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Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
| | - Sneha Munshi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
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3
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Baxter‐Koenigs AR, El Nesr G, Barrick D. Singular value decomposition of protein sequences as a method to visualize sequence and residue space. Protein Sci 2022; 31:e4422. [PMID: 36173173 PMCID: PMC9514065 DOI: 10.1002/pro.4422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/05/2022] [Accepted: 08/06/2022] [Indexed: 11/08/2022]
Abstract
Singular value decomposition (SVD) of multiple sequence alignments (MSAs) is an important and rigorous method to identify subgroups of sequences within the MSA, and to extract consensus and covariance sequence features that define the alignment and distinguish the subgroups. This information can be correlated to structure, function, stability, and taxonomy. However, the mathematics of SVD is unfamiliar to many in the field of protein science. Here, we attempt to present an intuitive yet comprehensive description of SVD analysis of MSAs. We begin by describing the underlying mathematics of SVD in a way that is both rigorous and accessible. Next, we use SVD to analyze sequences generated with a simplified model in which the extent of sequence conservation and covariance between different positions is controlled, to show how conservation and covariance produce features in the decomposed coordinate system. We then use SVD to analyze alignments of two protein families, the homeodomain and the Ras superfamilies. Both families show clear evidence of sequence clustering when projected into singular value space. We use k-means clustering to group MSA sequences into specific clusters, show how the residues that distinguish these clusters can be identified, and show how these clusters can be related to taxonomy and function. We end by providing a description a set of Python scripts that can be used for SVD analysis of MSAs, displaying results, and identifying and analyzing sequence clusters. These scripts are freely available on GitHub.
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Affiliation(s)
- Autum R. Baxter‐Koenigs
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of GeneticsHarvard Medical School, New Research Building 0356, 77 Avenue Louis PasteurBostonMassachusetts02115USA
| | - Gina El Nesr
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Program in BiophysicsStanford UniversityStanfordCalifornia94305USA
| | - Doug Barrick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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4
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Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. Int J Mol Sci 2022; 23:ijms23052412. [PMID: 35269555 PMCID: PMC8910618 DOI: 10.3390/ijms23052412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
Transcription factors must scan genomic DNA, recognize the cognate sequence of their control element(s), and bind tightly to them. The DNA recognition process is primarily carried out by their DNA binding domains (DBD), which interact with the cognate site with high affinity and more weakly with any other DNA sequence. DBDs are generally thought to bind to their cognate DNA without changing conformation (lock-and-key). Here, we used nuclear magnetic resonance and circular dichroism to investigate the interplay between DNA recognition and DBD conformation in the engrailed homeodomain (enHD), as a model case for the homeodomain family of eukaryotic DBDs. We found that the conformational ensemble of enHD is rather flexible and becomes gradually more disordered as ionic strength decreases following a Debye–Hückel’s dependence. Our analysis indicates that enHD’s response to ionic strength is mediated by a built-in electrostatic spring-loaded latch that operates as a conformational transducer. We also found that, at moderate ionic strengths, enHD changes conformation upon binding to cognate DNA. This change is of larger amplitude and somewhat orthogonal to the response to ionic strength. As a consequence, very high ionic strengths (e.g., 700 mM) block the electrostatic-spring-loaded latch and binding to cognate DNA becomes lock-and-key. However, the interplay between enHD conformation and cognate DNA binding is robust across a range of ionic strengths (i.e., 45 to 300 mM) that covers the physiologically-relevant conditions. Therefore, our results demonstrate the presence of a mechanism for the conformational control of cognate DNA recognition on a eukaryotic DBD. This mechanism can function as a signal transducer that locks the DBD in place upon encountering the cognate site during active DNA scanning. The electrostatic-spring-loaded latch of enHD can also enable the fine control of DNA recognition in response to transient changes in local ionic strength induced by variate physiological processes.
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5
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Yu B, Bien KG, Pletka CC, Iwahara J. Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy. Anal Chem 2022; 94:2444-2452. [PMID: 35080384 PMCID: PMC8829827 DOI: 10.1021/acs.analchem.1c04197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by 23Na diffusion nuclear magnetic resonance (NMR) spectroscopy. NMR probe hardware capable of generating strong magnetic field gradients enables 23Na NMR-based diffusion measurements for Na+ ions in solutions of biological macromolecules and their complexes. The dynamic properties of Na+ ions interacting with the macromolecules can be investigated using apparent 23Na diffusion coefficients measured under various conditions. Our diffusion data clearly show that Na+ ions retain high mobility within the ion atmosphere around DNA. The 23Na diffusion NMR method also permits direct observation of the release of Na+ ions from nucleic acids upon protein-nucleic acid association. The entropy change due to the ion release can be estimated from the diffusion data.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Karina G Bien
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
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6
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Hadži S, Lah J. Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures. Methods Mol Biol 2022; 2516:239-257. [PMID: 35922630 DOI: 10.1007/978-1-0716-2413-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.
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Affiliation(s)
- San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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7
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Abstract
The molecular properties of proteins are influenced by various ions present in the same solution. While site-specific strong interactions between multivalent metal ions and proteins are well characterized, the behavior of other ions that are only weakly interacting with proteins remains elusive. In the current study, using NMR spectroscopy, we have investigated anion-protein interactions for three proteins that are similar in size but differ in overall charge. Using a unique NMR-based approach, we quantified anions accumulated around the proteins. The determined numbers of anions that are electrostatically attracted to the charged proteins were notably smaller than the overall charge valences and were consistent with predictions from the Poisson-Boltzmann theory. This NMR-based approach also allowed us to measure ionic diffusion and characterize the anions interacting with the positively charged proteins. Our data show that these anions rapidly diffuse while bound to the proteins. Using the same experimental approach, we observed the release of the anions from the protein surface upon the formation of the Antp homeodomain-DNA complex. Using paramagnetic relaxation enhancement (PRE), we visualized the spatial distribution of anions around the free proteins and the Antp homeodomain-DNA complex. The obtained PRE data revealed the localization of anions in the vicinity of the highly positively charged regions of the free Antp homeodomain and provided further evidence of the release of anions from the protein surface upon the protein-DNA association. This study sheds light on the dynamic behavior of anions that electrostatically interact with proteins.
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8
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Smith NC, Wilkinson-White LE, Kwan AHY, Trewhella J, Matthews JM. Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100043. [PMID: 33458649 PMCID: PMC7797366 DOI: 10.1016/j.yjsbx.2020.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown. EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours. SAXS shows ISL1/LHX3:DNA complexes are flexible in nature. ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.
The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.
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Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | - Ann H Y Kwan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, University of Sydney, NSW 2006, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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9
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Jakubec D, Vondrášek J. Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations. J Chem Theory Comput 2020; 16:2034-2041. [PMID: 32208691 DOI: 10.1021/acs.jctc.0c00006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Estimation of binding free energies is one of the central aims of simulations of biomolecular complexes. We explore the accuracy and efficiency of setups based on nonequilibrium pulling simulations applied to the estimation of binding affinities of DNA-binding proteins. Absolute binding free energies are calculated over a range of temperatures and compared to results obtained previously using an equilibrium method. We show that realistic binding affinities can be obtained with the presented nonequilibrium approach, which also entails lower computational requirements. Errors of the binding free energy estimates are investigated and are shown to be comparable to those observed previously. Bounds are provided on the convergence of the errors with respect to the number of pulling simulations performed and with respect to the applied pull rate.
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Affiliation(s)
- David Jakubec
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry of the CAS, 166 10 Praha 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 128 43 Praha 2, Czech Republic
| | - Jiří Vondrášek
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry of the CAS, 166 10 Praha 6, Czech Republic
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10
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Castellanos M, Mothi N, Muñoz V. Eukaryotic transcription factors can track and control their target genes using DNA antennas. Nat Commun 2020; 11:540. [PMID: 31992709 PMCID: PMC6987225 DOI: 10.1038/s41467-019-14217-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/12/2019] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic transcription factors (TF) function by binding to short 6-10 bp DNA recognition sites located near their target genes, which are scattered through vast genomes. Such process surmounts enormous specificity, efficiency and celerity challenges using a molecular mechanism that remains poorly understood. Combining biophysical experiments, theory and bioinformatics, we dissect the interplay between the DNA-binding domain of Engrailed, a Drosophila TF, and the regulatory regions of its target genes. We find that Engrailed binding affinity is strongly amplified by the DNA regions flanking the recognition site, which contain long tracts of degenerate recognition-site repeats. Such DNA organization operates as an antenna that attracts TF molecules in a promiscuous exchange among myriads of intermediate affinity binding sites. The antenna ensures a local TF supply, enables gene tracking and fine control of the target site's basal occupancy. This mechanism illuminates puzzling gene expression data and suggests novel engineering strategies to control gene expression.
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Affiliation(s)
- Milagros Castellanos
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain.,Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Nivin Mothi
- Department of Bioengineering, School of Engineering, University of California, 95343, Merced, CA, USA
| | - Victor Muñoz
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain. .,Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain. .,Department of Bioengineering, School of Engineering, University of California, 95343, Merced, CA, USA.
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11
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Pletka CC, Nepravishta R, Iwahara J. Detecting Counterion Dynamics in DNA–Protein Association. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201910960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Channing C. Pletka
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
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12
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Pletka CC, Nepravishta R, Iwahara J. Detecting Counterion Dynamics in DNA-Protein Association. Angew Chem Int Ed Engl 2020; 59:1465-1468. [PMID: 31743557 PMCID: PMC6980997 DOI: 10.1002/anie.201910960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/14/2019] [Indexed: 01/10/2023]
Abstract
Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called "ion atmosphere". Although the release of counterions upon DNA-protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA-protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA-protein association.
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Affiliation(s)
- Channing C Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
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13
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Munshi S, Gopi S, Asampille G, Subramanian S, Campos LA, Atreya HS, Naganathan AN. Tunable order-disorder continuum in protein-DNA interactions. Nucleic Acids Res 2019; 46:8700-8709. [PMID: 30107436 PMCID: PMC6158747 DOI: 10.1093/nar/gky732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/31/2018] [Indexed: 11/23/2022] Open
Abstract
DNA-binding protein domains (DBDs) sample diverse conformations in equilibrium facilitating the search and recognition of specific sites on DNA over millions of energetically degenerate competing sites. We hypothesize that DBDs have co-evolved to sense and exploit the strong electric potential from the array of negatively charged phosphate groups on DNA. We test our hypothesis by employing the intrinsically disordered DBD of cytidine repressor (CytR) as a model system. CytR displays a graded increase in structure, stability and folding rate on increasing the osmolarity of the solution that mimics the non-specific screening by DNA phosphates. Electrostatic calculations and an Ising-like statistical mechanical model predict that CytR exhibits features of an electric potential sensor modulating its dimensions and landscape in a unique distance-dependent manner, while DNA plays the role of a non-specific macromolecular chaperone. Accordingly, CytR binds its natural half-site faster than the diffusion-controlled limit and even random DNA conforming to an electrostatic-steering binding mechanism. Our work unravels for the first time the synergistic features of a natural electrostatic potential sensor, a novel binding mechanism driven by electrostatic frustration and disorder, and the role of DNA in promoting distance-dependent protein structural transitions critical for switching between specific and non-specific DNA-binding modes.
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Affiliation(s)
- Sneha Munshi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sandhyaa Subramanian
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Luis A Campos
- National Biotechnology Center, Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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14
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Winzor DJ, Wills PR. Quantitative interpretation of isopiestic measurements on aqueous solutions: Urea revisited. Biophys Chem 2019; 251:106175. [PMID: 31128561 DOI: 10.1016/j.bpc.2019.106175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 10/27/2022]
Abstract
This investigation amends the analysis of isopiestic measurements of solvent thermodynamic activity by taking into account the fact that the solvent activity, traditionally expressed in mole-fraction terms, is a molal parameter because of the constraints (constant temperature and pressure) under which the measurements are made. Application of the revised procedure to published isopiestic measurements on aqueous urea solutions at 25 °C yields a dimerization constant of 0.066 molal-1, which is two-fold larger than an earlier published estimate based on an incorrect definition of the solute activity coefficient. Despite amendments to the quantitative detail, the present study confirms the existence of a large negative entropic contribution that largely counters its enthalpic counterpart arising from the hydrogen bonding responsible for dimer formation. This evidence of enthalpy-entropy compensation is entirely consistent with quantum-mechanical predictions of the adverse effect of water on urea dimerization. Changes in water structure thus contribute significantly to the energetics of urea dimerization in aqueous solution.
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Affiliation(s)
- Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter R Wills
- Department of Physics, University of Auckland, PB 92019, Auckland 1142, New Zealand.
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15
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Jakubec D, Vondrášek J. Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria? J Chem Theory Comput 2019; 15:2635-2648. [PMID: 30807142 DOI: 10.1021/acs.jctc.8b01144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We systematically investigate the applicability of a molecular dynamics-based setup for the calculations of standard binding free energies of biologically relevant protein-DNA complexes. The free energies are extracted from a potential of mean force calculated using umbrella sampling simulations. Two protein-DNA systems derived from a homeodomain transcription factor complex are studied in order to investigate the binding of both disordered and globular proteins. Free energies and trajectories obtained using two modern molecular mechanical force fields are compared to each other and to experimental data. The temperature dependence of the calculated standard binding free energies is investigated by performing all simulations over a range of temperatures. We show that the values of standard binding free energies obtained from these simulations are overestimated compared to experimental results. Significant differences are observed between the two protein-DNA systems and between the two force fields, which are explained by different propensities to form inter- and intramolecular contacts. The number of protein-DNA contacts increases with increasing temperature, in agreement with the experimentally known temperature dependence of enthalpies of binding. However, conclusions about the temperature dependence of the standard binding free energies cannot be made with confidence, as the differences among the values are on the order of statistical uncertainty.
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Affiliation(s)
- David Jakubec
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , 166 10 Praha 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science , Charles University , 128 43 Praha 2, Czech Republic
| | - Jiří Vondrášek
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , 166 10 Praha 6, Czech Republic
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16
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Hydration differences between the major and minor grooves of DNA revealed from heat capacity measurements. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 48:131-138. [PMID: 30552448 PMCID: PMC6411667 DOI: 10.1007/s00249-018-1340-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/22/2018] [Accepted: 12/01/2018] [Indexed: 11/04/2022]
Abstract
The nature of water on the surface of a macromolecule is reflected in the temperature dependence of the heat effect, i.e., the heat capacity change, ΔCp, that accompanies its removal on forming a complex. The relationship between ΔCp and the nature of the surface dehydrated cannot be modeled for DNA by the use of small molecules, as previously done for proteins, since the contiguous surfaces of the grooves cannot be treated as the sum of small component molecules such as nucleotides. An alternative approach is used here in which ΔCp is measured for the formation of several protein/DNA complexes and the calculated contribution from protein dehydration subtracted to yield the heat capacity change attributable to dehydration of the DNA. The polar and apolar surface areas of the DNA dehydrated on complex formation were calculated from the known structures of the complexes, allowing heat capacity coefficients to be derived representing dehydration of unit surface area of polar and apolar surface in both grooves. Dehydration of apolar surfaces in both grooves is essentially identical and accompanied by a reduction in ΔCp by about 3 J K−1 mol−1 (Å2)−1, a value of somewhat greater magnitude than observed for proteins {ΔCp = − 1.79 J K−1 mol−1 (Å2)−1}. In contrast, dehydration of polar surfaces is very different in the two grooves: in the minor groove ΔCp increases by 2.7 J K−1 mol−1 (Å2)−1, but in the major groove, although ΔCp is also positive, it is low in value: + 0.4 J K−1 mol−1 (Å2)−1. Physical explanations for the magnitudes of ΔCp are discussed.
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17
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Privalov PL, Crane-Robinson C. Forces maintaining the DNA double helix and its complexes with transcription factors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 135:30-48. [DOI: 10.1016/j.pbiomolbio.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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18
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Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 2018; 356:356/6337/eaaj2239. [PMID: 28473536 DOI: 10.1126/science.aaj2239] [Citation(s) in RCA: 703] [Impact Index Per Article: 117.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Abstract
The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.
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Affiliation(s)
- Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Ekaterina Morgunova
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Arttu Jolma
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Eevi Kaasinen
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Biswajyoti Sahu
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Syed Khund-Sayeed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Pratyush K Das
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Teemu Kivioja
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Kashyap Dave
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Fan Zhong
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Kazuhiro R Nitta
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Minna Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Paul A Ginno
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Silvia Domcke
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Jian Yan
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Dirk Schübeler
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden. .,Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
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19
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Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem 2017; 38:1974-1979. [PMID: 28602026 PMCID: PMC5495612 DOI: 10.1002/jcc.24831] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/21/2017] [Accepted: 04/22/2017] [Indexed: 11/06/2022]
Abstract
The standard treatment of ions in the framework of the Poisson-Boltzmann equation relies on molecular surfaces, which are commonly constructed along with the Stern layer. The molecular surface determines where ions can be present. In the Gaussian-based smooth dielectric function in DelPhi, smooth boundaries between the solute and solvent take the place of molecular surface. Therefore, this invokes the question of how to model mobile ions in the water phase without a definite solute-solvent boundary. This article reports a natural extension of the Gaussian-based smooth dielectric function approach that treats mobile ions via Boltzmann distribution with an added desolvation penalty. Thus, ion concentration near macromolecules is governed by the local electrostatic potential and the desolvation penalty (from being partially desolvated). The approach is tested against the experimental salt dependence of binding free energy on 7 protein-protein complexes and 12 DNA-protein complexes, resulting in Pearson correlations of 0.95 and 0.88, respectively. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
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20
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Busa VF, Rector MJ, Russell R. The DEAD-Box Protein CYT-19 Uses Arginine Residues in Its C-Tail To Tether RNA Substrates. Biochemistry 2017. [PMID: 28650145 DOI: 10.1021/acs.biochem.7b00362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich "C-tail" that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the 11 arginines reduced RNA unwinding activity (kcat/KM) to a degree equivalent to that seen upon removal of the C-tail, suggesting that a minimum or "threshold" number of arginines is required. In addition, a mutant with 16 arginines displayed RNA unwinding activity greater than that of wild-type CYT-19. The C-tail modifications impacted unwinding only of RNA helices within constructs that included an adjacent helix or structured RNA element that would allow C-tail binding, indicating that the helicase core remained active in the mutants. In addition, changes in RNA unwinding efficiency of the mutants were mirrored by changes in functional RNA affinity, as determined from the RNA concentration dependence of ATPase activity, suggesting that the C-tail functions primarily to increase RNA affinity. Interestingly, the salt concentration dependence of RNA unwinding activity is unaffected by C-tail composition, suggesting that the C-tail uses primarily hydrogen bonding, not electrostatic interactions, to bind double-stranded RNA. Our results provide insights into how an unstructured C-tail contributes to DEAD-box protein activity and suggest parallels with other families of RNA- and DNA-binding proteins.
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Affiliation(s)
- Veronica F Busa
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
| | - Maxwell J Rector
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
| | - Rick Russell
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
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21
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Dragan AI, Read CM, Crane-Robinson C. Enthalpy-entropy compensation: the role of solvation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:301-308. [PMID: 27796417 PMCID: PMC5384952 DOI: 10.1007/s00249-016-1182-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 11/24/2022]
Abstract
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy–entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation—an intrinsically compensatory process—can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.
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Affiliation(s)
- Anatoliy I Dragan
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64, Volodymyrs'ka St., Kiev, 01601, Ukraine.,Institute of Molecular Biology and Genetics, NASU, 150, Zabolotnogo St., Kiev, 03680, Ukraine
| | - Christopher M Read
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK.
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22
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Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J. Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. Biophys J 2016; 109:1026-37. [PMID: 26331260 DOI: 10.1016/j.bpj.2015.07.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022] Open
Abstract
Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.
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Affiliation(s)
- Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Kurtis M Anderson
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - David G Gorenstein
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
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23
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Iwahara J, Esadze A, Zandarashvili L. Physicochemical Properties of Ion Pairs of Biological Macromolecules. Biomolecules 2015; 5:2435-63. [PMID: 26437440 PMCID: PMC4693242 DOI: 10.3390/biom5042435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/23/2022] Open
Abstract
Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic moieties are important for proteins and nucleic acids to perform their function. Although numerous three-dimensional structures show ion pairs at functionally important sites of biological macromolecules and their complexes, the physicochemical properties of the ion pairs are not well understood. Crystal structures typically show a single state for each ion pair. However, recent studies have revealed the dynamic nature of the ion pairs of the biological macromolecules. Biomolecular ion pairs undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. This dynamic behavior is reasonable in light of the fundamental concepts that were established for small ions over the last century. In this review, we introduce the physicochemical concepts relevant to the ion pairs and provide an overview of the recent advancement in biophysical research on the ion pairs of biological macromolecules.
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Affiliation(s)
- Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Alexandre Esadze
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Levani Zandarashvili
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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24
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Merino F, Bouvier B, Cojocaru V. Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery. PLoS Comput Biol 2015; 11:e1004287. [PMID: 26067358 PMCID: PMC4465831 DOI: 10.1371/journal.pcbi.1004287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/15/2015] [Indexed: 12/19/2022] Open
Abstract
Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions. Pluripotent stem cells can give rise to all somatic lineages. When taken out of the context of the embryo they can be maintained and for this a core transcriptional regulatory circuitry is crucial. OCT4 and SOX2, two factors of this network, are also critical for the induction of pluripotency in somatic cells. In pluripotent cells, OCT4 and SOX2 associate on DNA regulatory regions, enhancing or modifying each other's sequence specificity. In contrast, in the early stages during induction of pluripotency, it was proposed that OCT4 explores the genome independent of SOX2. Here we report the mechanism by which SOX2 influences the orientation, dynamics, and unbinding free energy profile of OCT4. This involves an interplay of protein-protein interactions and DNA-mediated allostery. We consider that this mechanism enables OCT4 to use its DNA binding domains and the interaction partners available in a certain biological context to access alternative genome exploration routes. This study enhances the understanding of the context specific function of OCT4 and provides a general perspective on how DNA-binding cooperativity is modulated by different types of interactions.
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Affiliation(s)
- Felipe Merino
- Computational Structural Biology Group, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
| | - Benjamin Bouvier
- Bioinformatics: Structures and Interactions, Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR5086, IBCP, Lyon, France
| | - Vlad Cojocaru
- Computational Structural Biology Group, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
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25
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26
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Cravens SL, Hobson M, Stivers JT. Electrostatic properties of complexes along a DNA glycosylase damage search pathway. Biochemistry 2014; 53:7680-92. [PMID: 25408964 PMCID: PMC4263432 DOI: 10.1021/bi501011m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human uracil DNA glycosylase (hUNG) follows an extended reaction coordinate for locating rare uracil bases in genomic DNA. This process begins with diffusion-controlled engagement of undamaged DNA, followed by a damage search step in which the enzyme remains loosely associated with the DNA chain (translocation), and finally, a recognition step that allows the enzyme to efficiently bind and excise uracil when it is encountered. At each step along this coordinate, the enzyme must form DNA interactions that are highly specialized for either rapid damage searching or catalysis. Here we make extensive measurements of hUNG activity as a function of salt concentration to dissect the thermodynamic, kinetic, and electrostatic properties of key enzyme states along this reaction coordinate. We find that the interaction of hUNG with undamaged DNA is electrostatically driven at a physiological concentration of potassium ions (ΔGelect = -3.5 ± 0.5 kcal mol(-1)), with only a small nonelectrostatic contribution (ΔGnon = -2.0 ± 0.2 kcal mol(-1)). In contrast, the interaction with damaged DNA is dominated by the nonelectrostatic free energy term (ΔGnon = -7.2 ± 0.1 kcal mol(-1)), yet retains the nonspecific electrostatic contribution (ΔGelect = -2.3 ± 0.2 kcal mol(-1)). Stopped-flow kinetic experiments established that the salt sensitivity of damaged DNA binding originates from a reduction of kon, while koff is weakly dependent on salt. Similar findings were obtained from the salt dependences of the steady-state kinetic parameters, where the diffusion-controlled kcat/Km showed a salt dependence similar to kon, while kcat (limited by product release) was weakly dependent on salt. Finally, the salt dependence of translocation between two uracil sites separated by 20 bp in the same DNA chain was indistinguishable from that of kon. This result suggests that the transition-state for translocation over this spacing resembles that for DNA association from bulk solution and that hUNG escapes the DNA ion cloud during translocation. These findings provide key insights into how the ionic environment in cells influences the DNA damage search pathway.
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Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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27
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Babin V, Wang D, Rose RB, Sagui C. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PLoS Comput Biol 2013; 9:e1003160. [PMID: 23950697 PMCID: PMC3738460 DOI: 10.1371/journal.pcbi.1003160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022] Open
Abstract
The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold. This is one of several small DNA binding motifs that, in spite of limited DNA binding specificity, adopts crucial, specific roles when incorporated in a transcription factor. The homeodomain is composed of a 3-helix domain and a mobile N-terminal arm. Helix 3 (the recognition helix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered upon binding a specific sequence through the minor groove. Although many structural studies have characterized the DNA binding properties of homeodomains, the factors behind the binding specificity are still difficult to elucidate. A crystal structure of the Pdx1 homeodomain bound to DNA (PDB 2H1K) obtained previously in our lab shows two complexes with differences in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising new questions about the DNA recognition process by homeodomains. Here, we carry out fully atomistic Molecular Dynamics simulations both in crystal and aqueous environments in order to elucidate the nature of the difference in binding contacts. The crystal simulations reproduce the X-ray experimental structures well. In the absence of crystal packing constraints, the differences between the two complexes increase during the solution simulations. Thus, the conformational differences are not an artifact of crystal packing. In solution, the homeodomain with a disordered N-terminal arm repositions to a partially specific orientation. Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity. We propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. This flexibility in DNA binding may facilitate multiple functions for the same transcription factor.
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Affiliation(s)
- Volodymyr Babin
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, United States of America
| | - Dongli Wang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert B. Rose
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
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28
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Anderson KM, Esadze A, Manoharan M, Brüschweiler R, Gorenstein DG, Iwahara J. Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. J Am Chem Soc 2013; 135:3613-9. [PMID: 23406569 PMCID: PMC3721336 DOI: 10.1021/ja312314b] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR (15)N relaxation and hydrogen-bond scalar (15)N-(31)P J-couplings ((h3)J(NP)), we have investigated the dynamics of the ion pairs between lysine side-chain NH3(+) amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain-DNA complex. We have determined the order parameters and the correlation times for C-N bond rotation and reorientation of the lysine NH3(+) groups. Our data indicate that the NH3(+) groups in the intermolecular ion pairs are highly dynamic at the protein-DNA interface, which should lower the entropic costs for protein-DNA association. Judging from the C-N bond-rotation correlation times along with experimental and quantum-chemically derived (h3)J(NP) hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond time scale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3(+) group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein-DNA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.
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Affiliation(s)
- Kurtis M. Anderson
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
- Department of NanoMedicine and Biomedical Engineering, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225
| | - Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Mariappan Manoharan
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306
| | - Rafael Brüschweiler
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306
| | - David G. Gorenstein
- Department of NanoMedicine and Biomedical Engineering, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
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29
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Pica A, Russo Krauss I, Castellano I, La Cara F, Graziano G, Sica F, Merlino A. Effect of NaCl on the conformational stability of the thermophilic γ-glutamyltranspeptidase from Geobacillus thermodenitrificans: Implication for globular protein halotolerance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:149-57. [DOI: 10.1016/j.bbapap.2012.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/10/2012] [Accepted: 09/27/2012] [Indexed: 12/28/2022]
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30
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Hu W, Blecking C, Kralj M, Šuman L, Piantanida I, Schrader T. Dimeric calixarenes: a new family of major-groove binders. Chemistry 2012; 18:3589-97. [PMID: 22336964 DOI: 10.1002/chem.201100634] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 11/26/2011] [Indexed: 01/26/2023]
Abstract
A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl-protected calix[4]arene tetramines in relatively short synthetic sequences (3-5 steps). The compounds attach themselves to double-stranded nucleic acids in a noncovalent fashion, with micro- to nanomolar affinities. Guanidinium headgroups with their extended hydrogen-bonding "fingers" are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K(d))<AT-rich (1 μM)<GC-rich DNA double strands (100-10 nM). Ethidium bromide displacement studies confirm this order. CE(50) values are remarkably low (1-4 μM), and are more than 300 times lower than that of spermine, which is a typical backbone binder. Stoichiometries are rather high (one calixarene dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye-loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A-form to a perfect B-signature, providing further experimental evidence for major-groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte-Carlo simulations on 1:1 complexes in water.
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Affiliation(s)
- Wenbin Hu
- Department of Chemistry, Universität Duisburg-Essen, Universitätsstr. 7, 45117 Essen, Germany
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31
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Doerdelmann T, Kojetin DJ, Baird-Titus JM, Solt LA, Burris TP, Rance M. Structural and biophysical insights into the ligand-free Pitx2 homeodomain and a ring dermoid of the cornea inducing homeodomain mutant. Biochemistry 2012; 51:665-76. [PMID: 22224469 PMCID: PMC3264736 DOI: 10.1021/bi201639x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The homeodomain-containing transcription factor Pitx2 (pituitary homeobox protein 2) is present in many developing embryonic tissues, including the heart. Its homeodomain is responsible for the recognition and binding to target DNA sequences and thus constitutes a major functional unit in the Pitx2 protein. Nuclear magnetic resonance techniques were employed to determine the solution structure of the native Pitx2 homeodomain and a R24H mutant that causes autosomal dominantly inherited ring dermoid of the cornea syndrome. The structures reveal that both isoforms possess the canonical homeodomain fold. However, the R24H mutation results in a 2-fold increase in DNA binding affinity and a 5 °C decrease in thermal stability, while changing the dynamic environment of the homeodomain only locally. When introduced into full-length Pitx2c, the mutation results in an only 25% loss of transactivation activity. Our data correlate well with clinical observations suggesting a milder deficiency for the R24H mutation compared to those of other Pitx2 homeodomain mutations.
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Affiliation(s)
- Thomas Doerdelmann
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Douglas J. Kojetin
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jamie M. Baird-Titus
- College of Mount St. Joseph, Department of Chemistry, 5701 Delhi Road, Cincinnati, OH 45233, USA
| | - Laura A. Solt
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas P. Burris
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mark Rance
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
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32
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Vuzman D, Levy Y. Intrinsically disordered regions as affinity tuners in protein–DNA interactions. ACTA ACUST UNITED AC 2012; 8:47-57. [DOI: 10.1039/c1mb05273j] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Recognition of DNA by the helix-turn-helix global regulatory protein Lrp is modulated by the amino terminus. J Bacteriol 2011; 193:3794-803. [PMID: 21642464 DOI: 10.1128/jb.00191-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The AsnC/Lrp family of regulatory proteins links bacterial and archaeal transcription patterns to metabolism. In Escherichia coli, Lrp regulates approximately 400 genes, over 200 of them directly. In earlier studies, lrp genes from Vibrio cholerae, Proteus mirabilis, and E. coli were introduced into the same E. coli background and yielded overlapping but significantly different regulons. These differences were seen despite amino acid sequence identities of 92% (Vibrio) and 98% (Proteus) to E. coli Lrp, including complete conservation of the helix-turn-helix motifs. The N-terminal region contains many of the sequence differences among these Lrp orthologs, which led us to investigate its role in Lrp function. Through the generation of hybrid proteins, we found that the N-terminal diversity is responsible for some of the differences between orthologs in terms of DNA binding (as revealed by mobility shift assays) and multimerization (as revealed by gel filtration, dynamic light scattering, and analytical ultracentrifugation). These observations indicate that the N-terminal tail plays a significant role in modulating Lrp function, similar to what is seen for a number of other regulatory proteins.
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34
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DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail. Proc Natl Acad Sci U S A 2010; 107:21004-9. [PMID: 21078959 DOI: 10.1073/pnas.1011775107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered tails are common in DNA-binding proteins and can affect their search efficiency on nonspecific DNA by promoting the brachiation dynamics of intersegment transfer. During brachiation, the protein jumps between distant DNA regions via an intermediate state in which the tail and globular moieties are bound to different DNA segments. While the disordered tail must be long and positively charged to facilitate DNA search, the effect of its residue sequence on brachiation is unknown. We explored this issue using the NK-2 and Antp homeodomain transcription factors. We designed 566 NK-2 tail-variants and 55 Antp tail-variants having different net charges and positive charge distributions and studied their dynamics and DNA search efficiencies using coarse-grained molecular dynamics simulations. More intersegment transfers occur when the tail is moderately positively charged and the positive charges are clustered together in the middle of the tail or towards its N terminus. The presence of a negatively charged residue does not significantly affect protein brachiation, although it is likely that the presence of many negatively charged residues will complicate the DNA search mechanism. A bioinformatic analysis of 1,384 wild-type homeodomains illustrates that the charge composition and distribution in their N-tail sequences are consistent with an optimal charge pattern to promote intersegment transfer. Our study thus indicates that the residue sequence of the disordered tails of DNA-binding proteins has unique characteristics that were evolutionarily selected to achieve optimized function and suggests that the sequence-structure-function paradigm known for structured proteins is valid for intrinsically disordered proteins as well.
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35
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Privalov PL, Dragan AI, Crane-Robinson C. Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components. Nucleic Acids Res 2010; 39:2483-91. [PMID: 21071403 PMCID: PMC3074165 DOI: 10.1093/nar/gkq984] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We discuss the effectiveness of existing methods for understanding the forces driving the formation of specific protein-DNA complexes. Theoretical approaches using the Poisson-Boltzmann (PB) equation to analyse interactions between these highly charged macromolecules to form known structures are contrasted with an empirical approach that analyses the effects of salt on the stability of these complexes and assumes that release of counter-ions associated with the free DNA plays the dominant role in their formation. According to this counter-ion condensation (CC) concept, the salt-dependent part of the Gibbs energy of binding, which is defined as the electrostatic component, is fully entropic and its dependence on the salt concentration represents the number of ionic contacts present in the complex. It is shown that although this electrostatic component provides the majority of the Gibbs energy of complex formation and does not depend on the DNA sequence, the salt-independent part of the Gibbs energy--usually regarded as non-electrostatic--is sequence specific. The CC approach thus has considerable practical value for studying protein/DNA complexes, while practical applications of PB analysis have yet to demonstrate their merit.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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36
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Corry GN, Raghuram N, Missiaen KK, Hu N, Hendzel MJ, Underhill DA. The PAX3 Paired Domain and Homeodomain Function as a Single Binding Module In Vivo to Regulate Subnuclear Localization and Mobility by a Mechanism That Requires Base-Specific Recognition. J Mol Biol 2010; 402:178-93. [DOI: 10.1016/j.jmb.2010.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/05/2010] [Accepted: 07/07/2010] [Indexed: 10/19/2022]
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37
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Kontur WS, Capp MW, Gries TJ, Saecker RM, Record MT. Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate. Biochemistry 2010; 49:4361-73. [PMID: 20201585 DOI: 10.1021/bi100092a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transcription by all RNA polymerases (RNAPs) requires a series of large-scale conformational changes to form the transcriptionally competent open complex RP(o). At the lambdaP(R) promoter, Escherichia coli sigma(70) RNAP first forms a wrapped, closed 100 bp complex I(1). The subsequent step opens the entire DNA bubble, creating the relatively unstable (open) complex I(2). Additional conformational changes convert I(2) to the stable RP(o). Here we probe these events by dissecting the effects of Na(+) salts of Glu(-), F(-), and Cl(-) on each step in this critical process. Rapid mixing and nitrocellulose filter binding reveal that the binding constant for I(1) at 25 degrees C is approximately 30-fold larger in Glu(-) than in Cl(-) at the same Na(+) concentration, with the same log-log salt concentration dependence for both anions. In contrast, both the rate constant and equilibrium constant for DNA opening (I(1) to I(2)) are only weakly dependent on salt concentration, and the opening rate constant is insensitive to replacement of Cl(-) with Glu(-). These very small effects of salt concentration on a process (DNA opening) that is strongly dependent on salt concentration in solution may indicate that the backbones of both DNA strands interact with polymerase throughout the process and/or that compensation is present between ion uptake and release. Replacement of Cl(-) with Glu(-) or F(-) at 25 degrees C greatly increases the lifetime of RP(o) and greatly reduces its salt concentration dependence. By analogy to Hofmeister salt effects on protein folding, we propose that the excluded anions Glu(-) and F(-) drive the folding and assembly of the RNAP clamp/jaw domains in the conversion of I(2) to RP(o), while Cl(-) does not. Because the Hofmeister effect of Glu(-) or F(-) largely compensates for the destabilizing Coulombic effect of any salt on the binding of this assembly to downstream promoter DNA, RP(o) remains long-lived even at 0.5 M Na(+) in Glu(-) or F(-) salts. The observation that Esigma(70) RP(o) complexes are exceedingly long-lived at moderate to high Glu(-) concentrations argues that Esigma(70) RNAP does not dissociate from strong promoters in vivo when the cytoplasmic glutamate concentration increases during osmotic stress.
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Affiliation(s)
- Wayne S Kontur
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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38
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Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails. J Mol Biol 2009; 396:674-84. [PMID: 19958775 DOI: 10.1016/j.jmb.2009.11.056] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/22/2022]
Abstract
The search through nonspecific DNA for a specific site by proteins is known to be facilitated by sliding, hopping, and intersegment transfer between separate DNA strands, yet the driving forces of these protein dynamics from the molecular perspective are unclear. In this study, molecular features of the DNA search mechanism were explored for three homologous proteins (the HoxD9, Antp, and NK-2 homeodomains) using a simple computational model in which protein-DNA interactions are represented solely by electrostatic forces. In particular, we studied the impact that disordered N-terminal tails (N-tails), which are more common in DNA-binding proteins than in other proteins, have on the efficiency of DNA search. While the three homeodomain proteins were found to use similar binding interfaces in specific and nonspecific interactions with DNAs, their different electrostatic potentials affect the nature of their sliding dynamics. The different lengths and net charges of the N-tails of the homeodomains affect their motion along the DNA. The presence of an N-tail increases sliding propensity but slows linear diffusion along the DNA. When the search is performed in the presence of two parallel DNA molecules, a direct transfer, which is facilitated by the protein tail, from one nonspecific DNA to another occurs. The tailed proteins jump between two DNA molecules through an intermediate in which the recognition helix of the protein is adsorbed to one DNA fragment and the N-tail is adsorbed to the second, suggesting a "monkey bar" mechanism. Our study illustrates how the molecular architecture of proteins controls the efficiency of DNA scanning.
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39
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Tóth-Petróczy Á, Simon I, Fuxreiter M, Levy Y. Disordered Tails of Homeodomains Facilitate DNA Recognition by Providing a Trade-Off between Folding and Specific Binding. J Am Chem Soc 2009; 131:15084-5. [DOI: 10.1021/ja9052784] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ágnes Tóth-Petróczy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary
| | - Istvan Simon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary
| | - Monika Fuxreiter
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, and Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary
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40
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Privalov PL, Dragan AI, Crane-Robinson C. The cost of DNA bending. Trends Biochem Sci 2009; 34:464-70. [PMID: 19726198 DOI: 10.1016/j.tibs.2009.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 12/22/2022]
Abstract
Experimental data on protein-DNA interactions highlight a surprising peculiarity of protein binding to the minor groove: in contrast to major groove binding, which proceeds with heat release and does not induce substantial deformation of DNA, minor groove binding takes place at AT-rich sites, proceeds with heat absorption and results in significant DNA bending. By forming a highly ordered and dense spine in the minor groove of AT-rich DNA, water plays an essential role in defining the energetic signature of protein-minor groove binding. Removal of this water requires minimal work and results in significant loss of rigidity in the DNA, which can then easily acquire the conformation imposed by the bound protein. Therefore the introduction of substantial bends into the DNA is not energetically expensive.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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41
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Favicchio R, Dragan AI, Kneale GG, Read CM. Fluorescence spectroscopy and anisotropy in the analysis of DNA-protein interactions. Methods Mol Biol 2009; 543:589-611. [PMID: 19378154 DOI: 10.1007/978-1-60327-015-1_35] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Fluorescence spectroscopy can be used as a sensitive non-destructive technique for the characterisation of protein-DNA interactions. A comparison of the intrinsic emission spectra obtained for a protein-DNA complex and for free protein can be informative about the environment of tryptophan and tyrosine residues in the two states. Often there is quenching of the fluorescence intensity of an intrinsic emission spectrum and/or a shift in the wavelength maximum on protein binding to DNA. A step-by-step protocol describes the determination of a DNA-binding curve by measurement of the quenching of the intrinsic protein fluorescence.Fluorescence anisotropy can also be used to obtain a DNA-binding curve if the molecular size of the protein-DNA complex is sufficiently different from the free fluorescing component. Typically an extrinsic fluorophore attached to one or both 5' ends of single-stranded or duplex DNA is used, for this increases the sensitivity of measurement.Fitting of the binding curves, assuming a model, can often yield the stoichiometry and association constant of the interaction. The approach is illustrated using the interaction of the DNA-binding domains (HMG boxes) of mouse Sox-5 and mammalian HMGB1 with short DNA duplexes.
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Affiliation(s)
- Rosy Favicchio
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
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42
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Abstract
Understanding the forces driving formation of protein/DNA complexes requires measurement of the Gibbs energy of association, DeltaG, and its component enthalpic, DeltaH, and entropic, DeltaS, contributions. Isothermal titration calorimetry provides the enthalpy (heat) of the binding reaction and an estimate of the association constant, if not too high. Repeating the ITC experiment at several temperatures yields DeltaC ( p ), the change in heat capacity, an important quantity permitting extrapolation of enthalpies and entropies to temperatures outside the experimental range. Binding constants, i.e. Gibbs energies, are best obtained by optical methods such as fluorescence at temperatures where the components are maximally folded. Since DNA-binding domains are often partially unfolded at physiological temperatures, the ITC-observed enthalpy of binding may need to be corrected for the negative contribution from protein refolding. This correction is obtained by differential scanning calorimetric melting of the free DNA-binding domain. Corrected enthalpies are finally combined with accurate Gibbs energies to yield the entropy factor (TDeltaS) at various temperatures. Gibbs energies can be separated into electrostatic and non-electrostatic contributions from the ionic strength dependence of the binding constant.
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43
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Baranauskienė L, Petrikaitė V, Matulienė J, Matulis D. Titration calorimetry standards and the precision of isothermal titration calorimetry data. Int J Mol Sci 2009; 10:2752-2762. [PMID: 19582227 PMCID: PMC2705514 DOI: 10.3390/ijms10062752] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 06/01/2009] [Accepted: 06/15/2009] [Indexed: 11/16/2022] Open
Abstract
Current Isothermal Titration Calorimetry (ITC) data in the literature have relatively high errors in the measured enthalpies of protein-ligand binding reactions. There is a need for universal validation standards for titration calorimeters. Several inorganic salt co-precipitation and buffer protonation reactions have been suggested as possible enthalpy standards. The performances of several commercial calorimeters, including the VP-ITC, ITC200, and Nano ITC-III, were validated using these suggested standard reactions.
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Affiliation(s)
| | | | | | - Daumantas Matulis
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +370-5-269-1884; Fax: +370-5-260-2116
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44
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Abstract
Ultrasensitive microcalorimetric techniques for measuring the heat capacities of proteins in dilute solutions over a broad temperature range (DSC) and the heats of protein reactions at fixed temperatures (ITC) are described and the methods of working with these instruments are considered. Particular attention is paid to analyzing the thermal properties of individual proteins, their stability, the energetics of their folding, and their association with specific macromolecular partners. Use of these calorimetric methods is illustrated with examples of small compact globular proteins, small proteins having loose noncompact structure, multidomain proteins, and protein complexes, particularly with DNA.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, John Hopkins University, Baltimore, MD, USA
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45
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Hargreaves VV, Schleif RF. The salt dependence of the interferon regulatory factor 1 DNA binding domain binding to DNA reveals ions are localized around protein and DNA. Biochemistry 2008; 47:4119-28. [PMID: 18324782 DOI: 10.1021/bi702082q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The equilibrium dissociation constant of the DNA binding domain of interferon regulatory factor 1 (IRF1 DBD) for its DNA binding site depends strongly on salt concentration and salt type. These dependencies are consistent with IRF1 DBD binding to DNA, resulting in the release of cations from the DNA and both release of anions from the protein and uptake of a cation by the protein. We demonstrated this by utilizing the fact that the release of fluoride from protein upon complex formation does not contribute to the salt concentration dependence of binding and by studying mutants in which charged residues in IRF1 DBD that form salt bridges with DNA phosphates are changed to alanine. The salt concentration dependencies of the dissociation constants of wild-type IRF1 DBD and the mutants R64A, D73A, K75A, and D73A/K75A were measured in buffer containing NaF, NaCl, or NaBr. The salt concentration and type dependencies of the mutants relative to wild-type IRF1 DBD provide evidence of charge neutralization by solution ions for R64 and by a salt bridge between D73 and K75 in buffer containing chloride or bromide salts. These data also allowed us to determine the number, type, and localization of condensed ions around both IRF1 DBD and its DNA binding site.
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46
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Niiranen L, Altermark B, Brandsdal BO, Leiros HS, Helland R, Smalås AO, Willassen NP. Effects of salt on the kinetics and thermodynamic stability of endonuclease I from
Vibrio salmonicida
and
Vibrio cholerae. FEBS J 2008; 275:1593-1605. [DOI: 10.1111/j.1742-4658.2008.06317.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Laila Niiranen
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Norway
| | - Bjørn Altermark
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Bjørn O. Brandsdal
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Hanna‐Kirsti S. Leiros
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Ronny Helland
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Arne O. Smalås
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, Norway
| | - Nils P. Willassen
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Norway
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47
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Del Vecchio P, Carullo P, Barone G, Pagano B, Graziano G, Iannetti A, Acquaviva R, Leonardi A, Formisano S. Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain. Proteins 2008; 70:748-60. [PMID: 17729273 DOI: 10.1002/prot.21552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The conformational stability of the rat thyroid transcription factor 1 homeodomain, TTF-1HD, has been investigated by means of circular dichroism (CD) and differential scanning calorimetry (DSC) measurements at pH 5.0 as a function of KCl concentration. Thermal unfolding of TTF-1HD is a reversible two-state transition. The protein is not stable against temperature, showing a denaturation temperature of 32 degrees C in the absence of salt and 50 degrees C at 75 mM KCl. The binding energetics of TTF-1HD to its target DNA sequence has been characterized by means of isothermal titration calorimetry (ITC) measurements, complemented with CD data. At 25 degrees C, pH 5.0 and 75 mM KCl, the binding constant amounts to 1.5 x 10(8)M(-1) and the binding enthalpy change amounts to -41 kJ mol(-1). The process is enthalpy driven, but also the entropy change is favorable to complex formation. To gain a molecular level understanding of the interactions determining the association of TTF-1HD to the target DNA sequence structural information would be requested, but it is not yet available. Therefore, structural models of two complexes, TTF-1HD with the target DNA sequence and TTF-1HD with a modified DNA sequence, have been constructed by using as a template the NMR structure of the complex between NK-2 HD and its target DNA, and by performing molecular dynamics simulations 3.5 ns long. Analysis of these models allows one to shed light on the origin of the DNA binding specificity characteristic of TTF-1HD.
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Affiliation(s)
- Pompea Del Vecchio
- Dipartimento di Chimica, Università di Napoli Federico II, Via Cintia, 80126, Napoli, Italy.
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48
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Gümral D, Nadalin L, Corazza A, Fogolari F, Damante G, Viglino P, Esposito G. Helix mobility and recognition function of the rat thyroid transcription factor 1 homeodomain - hints from 15N-NMR relaxation studies. FEBS J 2007; 275:435-48. [DOI: 10.1111/j.1742-4658.2007.06208.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bello M, Pérez-Hernández G, Fernández-Velasco DA, Arreguín-Espinosa R, García-Hernández E. Energetics of protein homodimerization: Effects of water sequestering on the formation of β-lactoglobulin dimer. Proteins 2007; 70:1475-87. [PMID: 17910061 DOI: 10.1002/prot.21639] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transient protein-protein interactions are functionally relevant as a control mechanism in a variety of biological processes. Analysis of the 3D structure of protein-protein complexes indicates that water molecules trapped at the interface are very common; however, their role in the stability and specificity of protein homodimer interactions has been not addressed yet. To provide new insights into the energetic bases that govern the formation of highly hydrated interfaces, the dissociation process of bovine beta lg variant A at a neutral pH was characterized here thermodynamically by conducting dilution experiments with an isothermal titration calorimeter. Association was enthalpically driven throughout the temperature range spanned. DeltaH and deltaC(p) were significantly more negative than estimates based on surface area changes, suggesting the occurrence of effects additional to the dehydration of the contact surfaces between subunits. Near-UV CD spectra proved to be independent of protein concentration, indicating a rigid body-like association. Furthermore, the process proved not to be coupled to significant changes in the protonation state of ionizable groups or counterion exchange. In contrast, both osmotic stress experiments and a computational analysis of the dimer's 3D structure indicated that a large number of water molecules are incorporated into the interface upon association. Numerical estimates considering the contributions of interface area desolvation and water immobilization accounted satisfactorily for the experimental deltaC(p). Thus, our study highlights the importance of explicitly considering the effects of water sequestering to perform a proper quantitative analysis of the formation of homodimers with highly hydrated interfaces.
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Affiliation(s)
- Martiniano Bello
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, México
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