1
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Henneman B, Erkelens AM, Heinsman J, Battjes J, Dame RT. Quantitation of DNA Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2024; 2819:497-518. [PMID: 39028521 DOI: 10.1007/978-1-0716-3930-6_23] [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: 07/20/2024]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered particle motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to measure binding constants of proteins binding to DNA reliably, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This change in bead motion makes it possible to measure the DNA-binding properties of proteins. We use the bacterial protein integration host factor (IHF) and the archaeal histone HMfA as examples to show how specific binding to DNA can be measured. Moreover, we show how the end-to-end distance can provide structural insights into protein-DNA binding.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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2
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Choi J, Kim R, Koh J. Quantitative Frameworks for Multivalent Macromolecular Interactions in Biological Linear Lattice Systems. Mol Cells 2022; 45:444-453. [PMID: 35754369 PMCID: PMC9260134 DOI: 10.14348/molcells.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.
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Affiliation(s)
- Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ryeonghyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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3
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K G, Thomas AR, T SV, Mandal SS. Structural and thermodynamic insights into the Cren7 mediated DNA organization in Crenarchaeota. Phys Chem Chem Phys 2022; 24:19401-19413. [DOI: 10.1039/d2cp02190k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Archaea have histone homologues and chromatin proteins to organize their DNA into a compact form and allow them to survive in extreme climatic conditions. Cren7 is one such chromatin protein...
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4
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Vo TD, Schneider AL, Wilson WD, Poon GMK. Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6. Phys Chem Chem Phys 2021; 23:13490-13502. [PMID: 34120158 PMCID: PMC8233815 DOI: 10.1039/d1cp01568k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to interfacial ion pairs with DNA. The role of extra-interfacial ionic interactions, particularly as dynamic drivers of DNA sequence selectivity, remain poorly known. The ETS family of transcription factors represents an attractive model for addressing this knowledge gap given their diverse ionic composition in primary structures that fold to a tightly conserved DNA-binding motif. To probe the importance of extra-interfacial salt bridges in DNA recognition, we compared the salt-dependent binding by Elk1 with ETV6, two ETS homologs differing markedly in ionic composition. While both proteins exhibit salt-dependent binding with cognate DNA that corresponds to interfacial phosphate contacts, their nonspecific binding diverges from cognate binding as well as each other. Molecular dynamics simulations in explicit solvent, which generated ionic interactions in agreement with the experimental binding data, revealed distinct salt-bridge dynamics in the nonspecific complexes formed by the two proteins. Impaired DNA contact by ETV6 resulted in fewer backbone contacts in the nonspecific complex, while Elk1 exhibited a redistribution of extra-interfacial salt bridges via residues that are non-conserved between the two ETS relatives. Thus, primary structure variation in ionic residues can encode highly differentiated specificity mechanisms in a highly conserved DNA-binding motif.
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Affiliation(s)
- Tam D Vo
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
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5
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Abstract
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Molecular association of proteins with nucleic
acids is required
for many biological processes essential to life. Electrostatic interactions
via ion pairs (salt bridges) of nucleic acid phosphates and protein
side chains are crucial for proteins to bind to DNA or RNA. Counterions
around the macromolecules are also key constituents for the thermodynamics
of protein–nucleic acid association. Until recently, there
had been only a limited amount of experiment-based information about
how ions and ionic moieties behave in biological macromolecular processes.
In the past decade, there has been significant progress in quantitative
experimental research on ionic interactions with nucleic acids and
their complexes with proteins. The highly negatively charged surfaces
of DNA and RNA electrostatically attract and condense cations, creating
a zone called the ion atmosphere. Recent experimental studies were
able to examine and validate theoretical models on ions and their
mobility and interactions with macromolecules. The ionic interactions
are highly dynamic. The counterions rapidly diffuse within the ion
atmosphere. Some of the ions are released from the ion atmosphere
when proteins bind to nucleic acids, balancing the charge via intermolecular
ion pairs of positively charged side chains and negatively charged
backbone phosphates. Previously, the release of counterions had been
implicated indirectly by the salt-concentration dependence of the
association constant. Recently, direct detection of counterion
release by NMR spectroscopy
has become possible and enabled more accurate and quantitative analysis
of the counterion release and its entropic impact on the thermodynamics
of protein–nucleic acid association. Recent studies also revealed
the dynamic nature of ion pairs of protein side chains and nucleic
acid phosphates. These ion pairs undergo transitions between two major
states. In one of the major states, the cation and the anion are in
direct contact and form hydrogen bonds. In the other major state,
the cation and the anion are separated by water. Transitions between
these states rapidly occur on a picosecond to nanosecond time scale.
When proteins interact with nucleic acids, interfacial arginine (Arg)
and lysine (Lys) side chains exhibit considerably different behaviors.
Arg side chains show a higher propensity to form rigid contacts with
nucleotide bases, whereas Lys side chains tend to be more mobile at
the molecular interfaces. The dynamic ionic interactions may facilitate
adaptive molecular recognition and play both thermodynamic and kinetic
roles in protein–nucleic acid interactions.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - B. Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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6
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Sreenivasan R, Shkel IA, Chhabra M, Drennan A, Heitkamp S, Wang HC, Sridevi MA, Plaskon D, McNerney C, Callies K, Cimperman CK, Record MT. Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex. Biochemistry 2020; 59:1565-1581. [PMID: 32216369 DOI: 10.1021/acs.biochem.0c00098] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
FRET (fluorescence resonance energy transfer) between far-upstream (-100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λPR promoter DNA on Escherichia coli RNA polymerase (RNAP) in closed and open complexes (CC and OC, respectively). Here we determine the kinetics and mechanism of DNA bending and wrapping by FRET and of formation of RNAP contacts with -100 and +14 DNA by single-dye protein-induced fluorescence enhancement (PIFE). FRET and PIFE kinetics exhibit two phases: rapidly reversible steps forming a CC ensemble ({CC}) of four intermediates [initial (RPC), early (I1E), mid (I1M), and late (I1L)], followed by conversion of {CC} to OC via I1L. FRET and PIFE are first observed for I1E, not RPc. FRET and PIFE together reveal large-scale bending and wrapping of upstream and downstream DNA as RPC advances to I1E, decreasing the Cy3-Cy5 distance to ∼75 Å and making RNAP-DNA contacts at -100 and +14. We propose that far-upstream DNA wraps on the upper β'-clamp while downstream DNA contacts the top of the β-pincer in I1E. Converting I1E to I1M (∼1 s time scale) reduces FRET efficiency with little change in -100 or +14 PIFE, interpreted as clamp opening that moves far-upstream DNA (on β') away from downstream DNA (on β) to increase the Cy3-Cy5 distance by ∼14 Å. FRET increases greatly in converting I1M to I1L, indicating bending of downstream duplex DNA into the clamp and clamp closing to reduce the Cy3-Cy5 distance by ∼21 Å. In the subsequent rate-determining DNA-opening step, in which the clamp may also open, I1L is converted to the initial unstable OC (I2). Implications for facilitation of CC-to-OC isomerization by upstream DNA and upstream binding, DNA-bending transcription activators are discussed.
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7
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Cuculis L, Zhao C, Abil Z, Zhao H, Shukla D, Schroeder CM. Divalent cations promote TALE DNA-binding specificity. Nucleic Acids Res 2020; 48:1406-1422. [PMID: 31863586 PMCID: PMC7026652 DOI: 10.1093/nar/gkz1174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/18/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR–Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.
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Affiliation(s)
| | - Chuankai Zhao
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA
| | - Zhanar Abil
- Department of Biochemistry, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Department of Biochemistry, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, Urbana, IL 61801, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles M Schroeder
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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8
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Blus BJ, Koh J, Krolak A, Seo HS, Coutavas E, Blobel G. Allosteric modulation of nucleoporin assemblies by intrinsically disordered regions. SCIENCE ADVANCES 2019; 5:eaax1836. [PMID: 31807700 PMCID: PMC6881172 DOI: 10.1126/sciadv.aax1836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/25/2019] [Indexed: 05/12/2023]
Abstract
Intrinsically disordered regions (IDRs) of proteins are implicated in key macromolecular interactions. However, the molecular forces underlying IDR function within multicomponent assemblies remain elusive. By combining thermodynamic and structural data, we have discovered an allostery-based mechanism regulating the soluble core region of the nuclear pore complex (NPC) composed of nucleoporins Nup53, Nic96, and Nup157. We have identified distinct IDRs in Nup53 that are functionally coupled when binding to partner nucleoporins and karyopherins (Kaps) involved in NPC assembly and nucleocytoplasmic transport. We show that the Nup53·Kap121 complex forms an ensemble of structures that destabilize Nup53 hub interactions. Our study provides a molecular framework for understanding how disordered and folded domains communicate within macromolecular complexes.
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Affiliation(s)
- Bartlomiej Jan Blus
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
- Corresponding author.
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Aleksandra Krolak
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elias Coutavas
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Günter Blobel
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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9
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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10
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Liao Q, Lüking M, Krüger DM, Deindl S, Elf J, Kasson PM, Lynn Kamerlin SC. Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition. J Phys Chem B 2019; 123:3576-3590. [PMID: 30952192 DOI: 10.1021/acs.jpcb.8b12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse-grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (LacI), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein-DNA interactions, as well as the behavior of the helix-turn-helix motif of LacI when interacting with the DNA. Our simulations suggest that stable LacI binding occurs primarily to bent A-form DNA, with a loss of LacI conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA-protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.
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Affiliation(s)
- Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Malin Lüking
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden.,Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, Bioinformatics Unit , German Center for Neurodegenerative Diseases, Göttingen , von Siebold Strasse 3A , 37075 Göttingen , Germany
| | - Sebastian Deindl
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Johan Elf
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
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11
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Henneman B, Heinsman J, Battjes J, Dame RT. Quantitation of DNA-Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2019; 1837:257-275. [PMID: 30109615 DOI: 10.1007/978-1-4939-8675-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered Particle Motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to reliably measure binding constants of proteins binding to DNA, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This makes it possible to measure binding properties. We use the bacterial protein Integration Host Factor (IHF) as an example to show how specific binding to DNA can be measured. Moreover, we show a new intuitive quantitative approach to displaying data obtained via TPM.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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12
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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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13
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Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B 2018; 122:11519-11534. [DOI: 10.1021/acs.jpcb.8b07405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Aline Arra
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Phoebe A. Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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14
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Wylie T, Garg R, Ridley AJ, Conte MR. Analysis of the interaction of Plexin-B1 and Plexin-B2 with Rnd family proteins. PLoS One 2017; 12:e0185899. [PMID: 29040270 PMCID: PMC5645086 DOI: 10.1371/journal.pone.0185899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/21/2017] [Indexed: 02/03/2023] Open
Abstract
The Rnd family of proteins, Rnd1, Rnd2 and Rnd3, are atypical Rho family GTPases, which bind to but do not hydrolyse GTP. They interact with plexins, which are receptors for semaphorins, and are hypothesised to regulate plexin signalling. We recently showed that each Rnd protein has a distinct profile of interaction with three plexins, Plexin-B1, Plexin-B2 and Plexin-B3, in mammalian cells, although it is unclear which region(s) of these plexins contribute to this specificity. Here we characterise the binary interactions of the Rnd proteins with the Rho-binding domain (RBD) of Plexin-B1 and Plexin-B2 using biophysical approaches. Isothermal titration calorimetry (ITC) experiments for each of the Rnd proteins with Plexin-B1-RBD and Plexin-B2-RBD showed similar association constants for all six interactions, although Rnd1 displayed a small preference for Plexin-B1-RBD and Rnd3 for Plexin-B2-RBD. Furthermore, mutagenic analysis of Rnd3 suggested similarities in its interaction with both Plexin-B1-RBD and Plexin-B2-RBD. These results suggest that Rnd proteins do not have a clear-cut specificity for different Plexin-B-RBDs, possibly implying the contribution of additional regions of Plexin-B proteins in conferring functional substrate selection.
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Affiliation(s)
- Thomas Wylie
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, United Kingdom
| | - Ritu Garg
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, United Kingdom
| | - Anne J. Ridley
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, United Kingdom
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, United Kingdom
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15
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Wieczór M, Czub J. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res 2017. [PMID: 28633355 PMCID: PMC5737604 DOI: 10.1093/nar/gkx534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
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Affiliation(s)
- Milosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
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16
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Dey D, Nagaraja V, Ramakumar S. Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF. Mol Phylogenet Evol 2016; 107:356-366. [PMID: 27894997 DOI: 10.1016/j.ympev.2016.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022]
Abstract
Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins. Yet, questions related to their DNA binding specificity, and differential ability to bend DNA thus affecting the binding site length remained unanswered. In addition, the problem has not been investigated from an evolutionary perspective. Our phylogenetic analysis revealed three major clades belonging to HU, IHFα and IHFβ like proteins with reference to E. coli. We carried out a comparative analysis of three-dimensional structures of HU/IHF proteins to gain insight into the structural basis of clade division. The present study revealed three major features which contribute to differential DNA binding specificity of HU/IHF proteins, (I) conformational restriction of DNA binding residues due to salt-bridge formation, (II) the enrichment of alanine in the DNA binding site increasing conformational space of flexible side chains in its vicinity and (III) nature of DNA binding residue (Arg to Lys bias in different clades) which interacts differentially to DNA bases. We observed an extended electropositive surface at the DNA draping site for IHF clade proteins compared to HU, which stabilizes the DNA bend. Differences in the dimer stabilization strategies between HU and IHF were also observed. Our analysis reveals a comprehensive evolutionary picture, which rationalizes the origin of multi-specificity of HU/IHF proteins using sequence and structure-based determinants, which could also be applied to understand differences in binding specificities of other nucleic acid binding proteins.
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Affiliation(s)
- Debayan Dey
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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17
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Zhang X, Daaboul GG, Spuhler PS, Dröge P, Ünlü MS. Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor. NANOSCALE 2016; 8:5587-5598. [PMID: 26890964 DOI: 10.1039/c5nr06785e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - George G Daaboul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA and Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA.
| | - Philipp S Spuhler
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - M Selim Ünlü
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA and Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA.
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18
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Jayaraman B, Mavor D, Gross JD, Frankel AD. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly. Biochemistry 2015; 54:6545-54. [PMID: 26422686 DOI: 10.1021/acs.biochem.5b00876] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev-ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev-IIB complex forms a stable interface, whereas the Rev-IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20-30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev-RRE assembly and disassembly, and consequently its function.
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Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - David Mavor
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - John D Gross
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
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19
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Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction. Biochemistry 2015; 54:4142-60. [DOI: 10.1021/acs.biochem.5b00447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Apoorva Ravishankar
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of
Biochemistry, Indian Institute of Science, Bangalore 560012, India
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20
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Abstract
Analytical ultracentrifugation (AUC) is a powerful tool that can provide thermodynamic information on associating systems. Here, we discuss how to use the two fundamental AUC applications, sedimentation velocity (SV), and sedimentation equilibrium (SE), to study nonspecific protein-nucleic acid interactions, with a special emphasis on how to analyze the experimental data to extract thermodynamic information. We discuss three specific applications of this approach: (i) determination of nonspecific binding stoichiometry of E. coli integration host factor protein to dsDNA, (ii) characterization of nonspecific binding properties of Adenoviral IVa2 protein to dsDNA using SE-AUC, and (iii) analysis of the competition between specific and nonspecific DNA-binding interactions observed for E. coli integration host factor protein assembly on dsDNA. These approaches provide powerful tools that allow thermodynamic interrogation and thus a mechanistic understanding of how proteins bind nucleic acids by both specific and nonspecific interactions.
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21
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Kim DH, Im H, Jee JG, Jang SB, Yoon HJ, Kwon AR, Kang SM, Lee BJ. β-Arm flexibility of HU fromStaphylococcus aureusdictates the DNA-binding and recognition mechanism. ACTA ACUST UNITED AC 2014; 70:3273-89. [DOI: 10.1107/s1399004714023931] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/30/2014] [Indexed: 12/11/2022]
Abstract
HU, one of the major nucleoid-associated proteins, interacts with the minor groove of DNA in a nonspecific manner to induce DNA bending or to stabilize bent DNA. In this study, crystal structures are reported for both free HU fromStaphylococcus aureusMu50 (SHU) and SHU bound to 21-mer dsDNA. The structures, in combination with electrophoretic mobility shift assays (EMSAs), isothermal titration calorimetry (ITC) measurements and molecular-dynamics (MD) simulations, elucidate the overall and residue-specific changes in SHU upon recognizing and binding to DNA. Firstly, structural comparison showed the flexible nature of the β-sheets of the DNA-binding domain and that the β-arms bend inwards upon complex formation, whereas the other portions are nearly unaltered. Secondly, it was found that the disruption and formation of salt bridges accompanies DNA binding. Thirdly, residue-specific free-energy analyses using the MM-PBSA method with MD simulation data suggested that the successive basic residues in the β-arms play a central role in recognizing and binding to DNA, which was confirmed by the EMSA and ITC analyses. Moreover, residue Arg55 resides in the hinge region of the flexible β-arms, exhibiting a remarkable role in their flexible nature. Fourthly, EMSAs with various DNAs revealed that SHU prefers deformable DNA. Taken together, these data suggest residue-specific roles in local shape and base readouts, which are primarily mediated by the flexible β-arms consisting of residues 50–80.
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22
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Sanyal SJ, Yang TC, Catalano CE. Integration host factor assembly at the cohesive end site of the bacteriophage lambda genome: implications for viral DNA packaging and bacterial gene regulation. Biochemistry 2014; 53:7459-70. [PMID: 25335823 PMCID: PMC4263431 DOI: 10.1021/bi501025s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Integration host factor (IHF) is
an Escherichia coli protein involved in (i) condensation
of the bacterial nucleoid and
(ii) regulation of a variety of cellular functions. In its regulatory
role, IHF binds to a specific sequence to introduce a strong bend
into the DNA; this provides a duplex architecture conducive to the
assembly of site-specific nucleoprotein complexes. Alternatively,
the protein can bind in a sequence-independent manner that weakly
bends and wraps the duplex to promote nucleoid formation. IHF is also
required for the development of several viruses, including bacteriophage
lambda, where it promotes site-specific assembly of a genome packaging
motor required for lytic development. Multiple IHF consensus sequences
have been identified within the packaging initiation site (cos), and we here interrogate IHF–cos binding interactions using complementary electrophoretic mobility
shift (EMS) and analytical ultracentrifugation (AUC) approaches. IHF
recognizes a single consensus sequence within cos (I1) to afford a strongly bent nucleoprotein complex.
In contrast, IHF binds weakly but with positive cooperativity to nonspecific
DNA to afford an ensemble of complexes with increasing masses and
levels of condensation. Global analysis of the EMS and AUC data provides
constrained thermodynamic binding constants and nearest neighbor cooperativity
factors for binding of IHF to I1 and to nonspecific
DNA substrates. At elevated IHF concentrations, the nucleoprotein
complexes undergo a transition from a condensed to an extended rodlike
conformation; specific binding of IHF to I1 imparts
a significant energy barrier to the transition. The results provide
insight into how IHF can assemble specific regulatory complexes in
the background of extensive nonspecific DNA condensation.
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Affiliation(s)
- Saurarshi J Sanyal
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington , H-172 Health Sciences Building, Box 357610, Seattle, Washington 98195, United States
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23
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Sharadamma N, Harshavardhana Y, Ravishankar A, Anand P, Chandra N, Muniyappa K. Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction. J Biol Chem 2014; 289:34325-40. [PMID: 25324543 DOI: 10.1074/jbc.m114.608596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.
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Affiliation(s)
| | | | - Apoorva Ravishankar
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Praveen Anand
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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24
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Harteis S, Schneider S. Making the bend: DNA tertiary structure and protein-DNA interactions. Int J Mol Sci 2014; 15:12335-63. [PMID: 25026169 PMCID: PMC4139847 DOI: 10.3390/ijms150712335] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 12/11/2022] Open
Abstract
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout") as well as the intrinsic DNA structure ("shape recognition"). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics.
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Affiliation(s)
- Sabrina Harteis
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
| | - Sabine Schneider
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
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25
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Wang S, Linde MH, Munde M, Carvalho VD, Wilson WD, Poon GMK. Mechanistic heterogeneity in site recognition by the structurally homologous DNA-binding domains of the ETS family transcription factors Ets-1 and PU.1. J Biol Chem 2014; 289:21605-16. [PMID: 24952944 DOI: 10.1074/jbc.m114.575340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a "dry" mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1 · DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
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Affiliation(s)
- Shuo Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Miles H Linde
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - Manoj Munde
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Victor D Carvalho
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - W David Wilson
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Gregory M K Poon
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
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26
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Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. J Chem Phys 2014; 139:121927. [PMID: 24089739 DOI: 10.1063/1.4818596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SK(bi) ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SK(uni) < 0.5. This result is counterintuitive because there are at least twice as many ionic protein-DNA contacts in the fully wrapped complex than in the weakly bent intermediate. The following picture emerges from this analysis: in the bimolecular step, the observed [KCl]-dependence is consistent with the number of DNA counterions expected to be released when IHF binds nonspecifically to DNA whereas in the unimolecular reorganization step, the weak [KCl]-dependence suggests that two effects cancel one another. On one hand, formation of additional protein-DNA contacts in the fully wrapped complex releases bound counterions into bulk solution, which is entropically favored by decreasing [salt]. On the other hand, formation of the fully wrapped complex also releases tightly bound water molecules, which is osmotically favored by increasing [salt]. More generally, our global analysis strategy is applicable to other protein-DNA complexes, and opens up the possibility of measuring DNA bending rates in complexes where the unimolecular and bimolecular steps are not easily separable.
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Affiliation(s)
- Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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27
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Winardhi RS, Gulvady R, Mellies JL, Yan J. Locus of enterocyte effacement-encoded regulator (Ler) of pathogenic Escherichia coli competes off histone-like nucleoid-structuring protein (H-NS) through noncooperative DNA binding. J Biol Chem 2014; 289:13739-50. [PMID: 24668810 DOI: 10.1074/jbc.m113.545954] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The locus of enterocyte effacement-encoded regulator (Ler) of enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC) functions to activate transcription of virulence genes silenced by the histone-like nucleoid-structuring protein (H-NS). Despite its important role in the bacterial gene regulation, the binding mode of Ler to DNA and its mechanism in alleviating genes repressed by H-NS are largely unknown. In this study, we use magnetic tweezers to demonstrate that Ler binds extended DNA through a largely noncooperative process, which results in DNA stiffening and DNA folding depending on protein concentration. We also show that Ler can replace prebound H-NS on DNA over a range of potassium and magnesium concentrations. Our findings reveal the DNA binding properties of Ler and shed light to further understand the anti-silencing activity of Ler.
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Affiliation(s)
- Ricksen S Winardhi
- From the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore, the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ranjit Gulvady
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jay L Mellies
- the Biology Department, Reed College, Portland, Oregon 97202, and
| | - Jie Yan
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore, the Department of Physics, National University of Singapore, Singapore 117542, Singapore
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28
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Mechanosensing of DNA bending in a single specific protein-DNA complex. Sci Rep 2013; 3:3508. [PMID: 24336435 PMCID: PMC3863814 DOI: 10.1038/srep03508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/29/2013] [Indexed: 01/10/2023] Open
Abstract
Many crucial biological processes are regulated by mechanical stimuli. Here, we report new findings that pico-Newton forces can drastically affect the stability of the site-specific DNA binding of a single transcription factor, the E. coli integration host factor (IHF), by stretching a short ~150 nm DNA containing a single IHF binding site. Dynamic binding and unbinding of single IHF were recorded and analyzed for the force-dependent stability of the IHF-DNA complex. Our results demonstrate that the IHF-DNA interaction is fine tuned by force in different salt concentration and temperature over physiological ranges, indicating that, besides other physiological factors, force may play equally important role in transcription regulation. These findings have broad implications with regard to general mechanosensitivity of site-specific DNA bending proteins.
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Gamba I, Salvadó I, Rama G, Bertazzon M, Sánchez MI, Sánchez-Pedregal VM, Martínez-Costas J, Brissos RF, Gamez P, Mascareñas JL, Vázquez López M, Vázquez ME. Custom-fit ruthenium(II) metallopeptides: a new twist to DNA binding with coordination compounds. Chemistry 2013; 19:13369-75. [PMID: 23943195 DOI: 10.1002/chem.201301629] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 12/20/2022]
Abstract
A new bipyridine building block has been used for the solid-phase synthesis of dinuclear DNA-binding ruthenium(II) metallopeptides. Detailed spectroscopic studies suggest that these compounds bind to the DNA by insertion into the DNA minor groove. Moreover, the potential of the solid-phase peptide synthesis approach is demonstrated by the straightforward synthesis of an octaarginine derivative that shows effective cellular internalization and cytotoxicity linked with strong DNA interaction, as evidenced by steady-state fluorescence spectroscopy and AFM studies.
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Affiliation(s)
- Ilaria Gamba
- Departamento de Química Inorgánica y Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago de Compostela (Spain)
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30
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Kuo TC, Lee PC, Tsai CW, Chen WY. Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer--thermodynamics and spectroscopic evidences. J Mol Recognit 2013; 26:149-59. [PMID: 23345105 DOI: 10.1002/jmr.2260] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 11/05/2012] [Accepted: 12/04/2012] [Indexed: 12/19/2022]
Abstract
Protein-nucleic acids binding driven by electrostatic interactions typically are characterized by the release of counter ions, and the salt-inhibited binding association constant (K(a)) and the magnitude of exothermic binding enthalpy (ΔH). Here, we report a non-classical thermodynamics of streptavidin (SA)-aptamer binding in NaCl (140-350 mM) solutions near room temperatures (23-27 °C). By using isothermal titration calorimetry (ITC) and circular dichroism (CD)/fluorescence spectroscopy, we found that the binding was enthalpy driven with a large entropy cost (ΔH -20.58 kcal mol(-1), TΔS -10.99 kcal mol(-1), and K(a) 1.08 × 10(7) M(-1) at 140 mM NaCl 25 °C). With the raise of salt concentrations, the ΔH became more exothermic, yet the K(a) was almost unchanged (ΔH -26.29 kcal mol(-1) and K(a) 1.50 × 10(7) M(-1) at 350 mM NaCl 25 °C). The data suggest that no counter Na(+) was released in the binding. Spectroscopy data suggest that the binding, with a stoichiometry of 2, was accompanied with substantial conformational changes on SA, and the changes were insensitive to the variation of salt concentrations. To account for the non-classical results, we propose a salt bridge exchange model. The intramolecular binding-site salt bridge(s) of the free SA and the charged phosphate group of aptamers re-organize to form the binding complex by forming a new intermolecular salt bridge(s). The salt bridge exchange binding process requires minimum amount of counter ions releasing but dehydration of the contacting surface of SA and the aptamer. The energy required for dehydration is reduced in the case of binding solution with higher salt concentration and account for the higher binding exothermic mainly.
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Affiliation(s)
- Tai-Chih Kuo
- Department of Biochemistry, Taipei Medical University, Taipei, 11031, Taiwan
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31
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Driessen RPC, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar UD, White MF, Schiessel H, van Noort J, Dame RT. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Res 2012; 41:196-205. [PMID: 23155062 PMCID: PMC3592393 DOI: 10.1093/nar/gks1053] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
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32
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Lin J, Chen H, Dröge P, Yan J. Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF). PLoS One 2012; 7:e49885. [PMID: 23166787 PMCID: PMC3498176 DOI: 10.1371/journal.pone.0049885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.
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Affiliation(s)
- Jie Lin
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Peter Dröge
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PD); (JY)
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (PD); (JY)
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Setny P, Bahadur RP, Zacharias M. Protein-DNA docking with a coarse-grained force field. BMC Bioinformatics 2012; 13:228. [PMID: 22966980 PMCID: PMC3522568 DOI: 10.1186/1471-2105-13-228] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/19/2012] [Indexed: 11/17/2022] Open
Abstract
Background Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy. Results We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location. Conclusions We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.
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Affiliation(s)
- Piotr Setny
- Physics Department T38, Technical University Munich, James Franck Str. 1, 85748 Garching, Germany.
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Lin HK, Chase SF, Laue TM, Jen-Jacobson L, Trakselis MA. Differential temperature-dependent multimeric assemblies of replication and repair polymerases on DNA increase processivity. Biochemistry 2012; 51:7367-82. [PMID: 22906116 DOI: 10.1021/bi300956t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Differentiation of binding accurate DNA replication polymerases over error prone DNA lesion bypass polymerases is essential for the proper maintenance of the genome. The hyperthermophilic archaeal organism Sulfolobus solfataricus (Sso) contains both a B-family replication (Dpo1) and a Y-family repair (Dpo4) polymerase and serves as a model system for understanding molecular mechanisms and assemblies for DNA replication and repair protein complexes. Protein cross-linking, isothermal titration calorimetry, and analytical ultracentrifugation have confirmed a previously unrecognized dimeric Dpo4 complex bound to DNA. Binding discrimination between these polymerases on model DNA templates is complicated by the fact that multiple oligomeric species are influenced by concentration and temperature. Temperature-dependent fluorescence anisotropy equilibrium binding experiments were used to separate discrete binding events for the formation of trimeric Dpo1 and dimeric Dpo4 complexes on DNA. The associated equilibria are found to be temperature-dependent, generally leading to improved binding at higher temperatures for both polymerases. At high temperatures, DNA binding of Dpo1 monomer is favored over binding of Dpo4 monomer, but binding of Dpo1 trimer is even more strongly favored over binding of Dpo4 dimer, thus providing thermodynamic selection. Greater processivities of nucleotide incorporation for trimeric Dpo1 and dimeric Dpo4 are also observed at higher temperatures, providing biochemical validation for the influence of tightly bound oligomeric polymerases. These results separate, quantify, and confirm individual and sequential processes leading to the formation of oligomeric Dpo1 and Dpo4 assemblies on DNA and provide for a concentration- and temperature-dependent discrimination of binding undamaged DNA templates at physiological temperatures.
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Affiliation(s)
- Hsiang-Kai Lin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Phelan MM, Goult BT, Clayton JC, Hautbergue GM, Wilson SA, Lian LY. The structure and selectivity of the SR protein SRSF2 RRM domain with RNA. Nucleic Acids Res 2012; 40:3232-44. [PMID: 22140111 PMCID: PMC3326313 DOI: 10.1093/nar/gkr1164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 11/10/2011] [Accepted: 11/11/2011] [Indexed: 11/26/2022] Open
Abstract
SRSF2 is a prototypical SR protein which plays important roles in the alternative splicing of pre-mRNA. It has been shown to be involved in regulatory pathways for maintaining genomic stability and play important roles in regulating key receptors in the heart. We report here the solution structure of the RNA recognition motifs (RRM) domain of free human SRSF2 (residues 9-101). Compared with other members of the SR protein family, SRSF2 structure has a longer L3 loop region. The conserved aromatic residue in the RNP2 motif is absent in SRSF2. Calorimetric titration shows that the RNA sequence 5'AGCAGAGUA3' binds SRSF2 with a K(d) of 61 ± 1 nM and a 1:1 stoichiometry. NMR and mutagenesis experiments reveal that for SFSF2, the canonical β1 and β3 interactions are themselves not sufficient for effective RNA binding; the additional loop L3 is crucial for RNA complex formation. A comparison is made between the structures of SRSF2-RNA complex with other known RNA complexes of SR proteins. We conclude that interactions involving the L3 loop, N- and C-termini of the RRM domain are collectively important for determining selectivity between the protein and RNA.
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Affiliation(s)
- Marie M. Phelan
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Benjamin T. Goult
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Jonathan C. Clayton
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Guillaume M. Hautbergue
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Stuart A. Wilson
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Lu-Yun Lian
- NMR Centre for Structural Biology, University of Liverpool, Institute of Integrative Biology, Crown Street, Liverpool L69 7ZB, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN and Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Martino L, Pennell S, Kelly G, Bui TTT, Kotik-Kogan O, Smerdon SJ, Drake AF, Curry S, Conte MR. Analysis of the interaction with the hepatitis C virus mRNA reveals an alternative mode of RNA recognition by the human La protein. Nucleic Acids Res 2012; 40:1381-94. [PMID: 22009680 PMCID: PMC3273827 DOI: 10.1093/nar/gkr890] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/29/2011] [Accepted: 10/01/2011] [Indexed: 12/31/2022] Open
Abstract
Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain IV of the hepatitis C virus (HCV) RNA, which is associated with viral translation stimulation. By systematic biophysical investigations, we have found that La binds to domain IV using an RNA recognition that is quite distinct from its mode of binding to RNAs with a 3' UUU(OH) trailer: although the La motif and first RNA recognition motif (RRM1) are sufficient for high-affinity binding to 3' oligoU, recognition of HCV domain IV requires the La motif and RRM1 to work in concert with the atypical RRM2 which has not previously been shown to have a significant role in RNA binding. This new mode of binding does not appear sequence specific, but recognizes structural features of the RNA, in particular a double-stranded stem flanked by single-stranded extensions. These findings pave the way for a better understanding of the role of La in viral translation initiation.
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Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Simon Pennell
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Geoff Kelly
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Tam T. T. Bui
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Olga Kotik-Kogan
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Stephen J. Smerdon
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Alex F. Drake
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Stephen Curry
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, Division of Molecular Structure, MRC Biomedical NMR Centre, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, Pharmaceutical Science Division, King's College London, The Wolfson Wing, Guy's Campus, London SE1 1UL and Department of Life Sciences, Division of Cell and Molecular Biology, Imperial College, London SW7 2AZ, UK
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SCHNURR BERNHARD, VORGIAS CONSTANTINOS, STAVANS JOEL. COMPACTION AND SUPERCOILING OF SINGLE, LONG DNA MOLECULES BY HU PROTEIN. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048006000021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The bacterial cell contains the highly conserved protein HU in abundance. To characterize its architectural role, we studied the elastic behavior of single, supercoilable DNA molecules (tens of kilobases long) in solution with HU from B. stearothermophilus (BstHU) by a micromanipulation assay. We point out quantitative yet notable differences to the behavior of HU from E. coli (EcoHU) observed by others. Our main contribution here, however, is to characterize the interaction of BstHU with single molecules of DNA in arbitrary states of supercoiling. BstHU clearly distinguishes under- and overwound substrates, breaking the characteristic symmetry in the elastic response of bare DNA. We demonstrate that BstHU shifts the preferred linking number of the complex, consistent with a model in which bound proteins untwist the double helix. The model qualitatively explains various features, such as overall compaction and weaker dependence on supercoiling, by a softening of the DNA to twist and bending. Previously reported reversal of binding effects at protein concentrations above a threshold also extends to supercoiling. All observed effects are highly sensitive to salt concentrations. Their range and magnitude lend HU great versatility in dynamically altering the physical properties and organization of the nucleoid.
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Affiliation(s)
- BERNHARD SCHNURR
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- Skirball Institute of Biomolecular Medicine, Program in Molecular Pathogenesis, NYU School of Medicine, New York, NY 10016, USA
| | - CONSTANTINOS VORGIAS
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis — Zographou, 157 84 Athens, Greece
| | - JOEL STAVANS
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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38
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Tsodikov OV, Biswas T. Structural and thermodynamic signatures of DNA recognition by Mycobacterium tuberculosis DnaA. J Mol Biol 2011; 410:461-76. [PMID: 21620858 DOI: 10.1016/j.jmb.2011.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/27/2011] [Accepted: 05/05/2011] [Indexed: 10/24/2022]
Abstract
An essential protein, DnaA, binds to 9-bp DNA sites within the origin of replication oriC. These binding events are prerequisite to forming an enigmatic nucleoprotein scaffold that initiates replication. The number, sequences, positions, and orientations of these short DNA sites, or DnaA boxes, within the oriCs of different bacteria vary considerably. To investigate features of DnaA boxes that are important for binding Mycobacterium tuberculosis DnaA (MtDnaA), we have determined the crystal structures of the DNA binding domain (DBD) of MtDnaA bound to a cognate MtDnaA-box (at 2.0 Å resolution) and to a consensus Escherichia coli DnaA-box (at 2.3 Å). These structures, complemented by calorimetric equilibrium binding studies of MtDnaA DBD in a series of DnaA-box variants, reveal the main determinants of DNA recognition and establish the [T/C][T/A][G/A]TCCACA sequence as a high-affinity MtDnaA-box. Bioinformatic and calorimetric analyses indicate that DnaA-box sequences in mycobacterial oriCs generally differ from the optimal binding sequence. This sequence variation occurs commonly at the first 2 bp, making an in vivo mycobacterial DnaA-box effectively a 7-mer and not a 9-mer. We demonstrate that the decrease in the affinity of these MtDnaA-box variants for MtDnaA DBD relative to that of the highest-affinity box TTGTCCACA is less than 10-fold. The understanding of DnaA-box recognition by MtDnaA and E. coli DnaA enables one to map DnaA-box sequences in the genomes of M. tuberculosis and other eubacteria.
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Affiliation(s)
- Oleg V Tsodikov
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
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Kozlov AG, Lohman TM. E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign. Biophys Chem 2011; 159:48-57. [PMID: 21636209 DOI: 10.1016/j.bpc.2011.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/02/2011] [Accepted: 05/02/2011] [Indexed: 11/17/2022]
Abstract
We have previously shown that formation of a 1:1 fully wrapped complex of Escherichia coli SSB tetramer with (dT)(70) displays a temperature-dependent sign reversal of the binding heat capacity (ΔC(P)). Here we examine SSB binding to shorter oligodeoxynucleotides ((dX)(35)) to probe whether this effect requires binding of one or two (dX)(35) molecules per SSB tetramer. We find that the ΔC(P) for the first molecule of (dX)(35) is always negative. However, a sign reversal of ΔC(P) from negative to positive occurs with increasing temperature for binding of the second (dX)(35). This striking behavior of ΔC(P) for the second (dX)(35) appears linked to conformational changes within the ssDNA-SSB complex that are required to form a fully wrapped (SSB)(65) binding mode. These results also underscore that binding heat capacities of macromolecular interactions have multiple origins that cannot be understood simply on the basis of examining static structures.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
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40
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Koh J, Shkel I, Saecker RM, Record MT. Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol 2011; 410:241-67. [PMID: 21513716 DOI: 10.1016/j.jmb.2011.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
Abstract
Previous isothermal titration calorimetry (ITC) and Förster resonance energy transfer studies demonstrated that Escherichia coli HU(αβ) binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34-bp mode that interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it by 140(o) and thereby increasing its flexibility, and two weaker, modestly cooperative small site-size modes (10 bp and 6 bp) that are useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and we deduce that DNA in the 34-bp mode is bent around-but not wrapped on-the body of HU, in contrast to specific binding of integration host factor. Analyses of binding isotherms (8-bp, 15-bp, and 34-bp DNA) and initial binding heats (34-bp, 38-bp, and 160-bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Sk(i)) even though their binding site sizes differ greatly; the most probable values of Sk(i) on 34-bp DNA or larger DNA are -7.5±0.5. From the similarity of Sk(i) values, we conclude that the binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent DNA 34-bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6-bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Sk(i) values are proposed.
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Affiliation(s)
- Junseock Koh
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA.
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41
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McLaughlin KJ, Jenkins JL, Kielkopf CL. Large favorable enthalpy changes drive specific RNA recognition by RNA recognition motif proteins. Biochemistry 2011; 50:1429-31. [PMID: 21261285 DOI: 10.1021/bi102057m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The RNA recognition motif (RRM) is a prevalent class of RNA binding domains. Although a number of RRM/RNA structures have been determined, thermodynamic analyses are relatively uncommon. Here, we use isothermal titration calorimetry to characterize single-stranded (ss)RNA binding by four representative RRM-containing proteins: (i) U2AF(65), (ii) SXL, (iii) TIA-1, and (iv) PAB. In all cases, ssRNA binding is accompanied by remarkably large favorable enthalpy changes (-30 to -60 kcal mol(-1)) and unfavorable entropy changes. Alterations of key RRM residues and binding sites indicate that under the nearly physiological conditions of these studies, large thermodynamic changes represent a signature of specific ssRNA recognition by RRMs.
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Affiliation(s)
- Krystle J McLaughlin
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
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42
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Böhm V, Hieb AR, Andrews AJ, Gansen A, Rocker A, Tóth K, Luger K, Langowski J. Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res 2010; 39:3093-102. [PMID: 21177647 PMCID: PMC3082900 DOI: 10.1093/nar/gkq1279] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleosomes are multi-component macromolecular assemblies which present a formidable obstacle to enzymatic activities that require access to the DNA, e.g. DNA and RNA polymerases. The mechanism and pathway(s) by which nucleosomes disassemble to allow DNA access are not well understood. Here we present evidence from single molecule FRET experiments for a previously uncharacterized intermediate structural state before H2A–H2B dimer release, which is characterized by an increased distance between H2B and the nucleosomal dyad. This suggests that the first step in nucleosome disassembly is the opening of the (H3–H4)2 tetramer/(H2A–H2B) dimer interface, followed by H2A–H2B dimer release from the DNA and, lastly, (H3–H4)2 tetramer removal. We estimate that the open intermediate state is populated at 0.2–3% under physiological conditions. This finding could have significant in vivo implications for factor-mediated histone removal and exchange, as well as for regulating DNA accessibility to the transcription and replication machinery.
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Affiliation(s)
- Vera Böhm
- Abteilung Biophysik der Makromoleküle, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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43
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Suryawanshi H, Sabharwal H, Maiti S. Thermodynamics of peptide-RNA recognition: the binding of a Tat peptide to TAR RNA. J Phys Chem B 2010; 114:11155-63. [PMID: 20687526 DOI: 10.1021/jp1000545] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
RNA-peptide interactions have been intensively studied at the structural level; however, in the absence of thermodynamic studies, the molecular forces that dictate the binding specificities and affinities remain elusive. Here we evaluate the thermodynamics (DeltaG, DeltaH, DeltaS) of HIV-1 TAR RNA hairpin and Tat peptide interaction as well as the hydration changes that accompany these interactions, through a series of calorimetric, spectroscopic, and osmotic stress studies. Tat peptide binding enhances the thermal stability of the TAR RNA hairpin; however, the thermal enhancement decreases with increasing Na(+) concentration. The equilibrium association constant (K(a)) is determined by fluorescence titrations and examined as a function of Na(+) concentration and temperature. The binding constant (K(a)) decreases with increasing Na(+) concentration. The binding free energy (DeltaG) is found to have a large nonpolyelectrolyte component with release of a single counterion upon binding. The ITC profiles showed two independent sites binding, indicating specific as well as nonspecific interactions. The enthalpy changes associated with both the binding sites are found to be more negative for the binding process at lower salt concentration of 20 mM Na(+). Our binding studies under osmotic stress conditions show that there is a release of 28 (+/-4) and 21 (+/-3) water molecules upon complex formation at 20 and 80 mM Na(+) concentration supporting the observed positive entropy contributions and accounting for discrepancies between DeltaH(cal) and DeltaH(vH). In aggregate, our results suggest that the hydrogen bonding of arginine to TAR RNA dictates the binding interaction.
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Affiliation(s)
- Hemant Suryawanshi
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis. Biochemistry 2010; 50:266-75. [PMID: 21121696 DOI: 10.1021/bi101096k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Revealing the thermodynamic driving force of protein-DNA interactions is crucial to the understanding of factors that dictate the properties and function of protein-DNA complexes. For the binding of DNA to DNA-wrapping proteins, such as the integration host factor (IHF), Record and co-workers proposed that the disruption of a large number of preexisting salt bridges is coupled with the binding process [Holbrook, J. A., et al. (2001) J. Mol. Biol. 310, 379]. To test this proposal, we have conducted explicit solvent MD simulations (multiple ∼25-50 ns trajectories for each salt concentration) to examine the behavior of charged residues in IHF, especially concerning their ability to form salt bridges at different salt concentrations. Of the 17 cationic residues noted by Record and co-workers, most are engaged in salt bridge interactions for a significant portion of the trajectories, especially in the absence of salt. This observation suggests that, from a structural point of view, their proposal is plausible. However, the complex behaviors of charged residues observed in the MD simulations also suggest that the unusual thermodynamic characteristics of IHF-DNA binding likely arise from the interplay between complex dynamics of charged residues both in and beyond the DNA binding site. Moreover, a comparison of MD simulations at different salt concentrations suggests that the strong dependence of the IHF-DNA binding enthalpy on salt concentration may not be due to a significant decrease in the number of stable salt bridges in apo IHF at high salt concentrations. In addition to the Hofmeister effects quantified in more recent studies of IHF-DNA binding, we recommend consideration of the variation of the enthalpy change of salt bridge disruption at different salt concentrations. Finally, the simulation study presented here explicitly highlights the fact that the electrostatic properties of DNA-binding proteins can be rather different in the apo and DNA-bound states, which has important implications for the design of robust methods for predicting DNA binding sites in proteins.
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Affiliation(s)
- L Ma
- Graduate Program in Biophysics, University of Wisconsin, Madison, 53706, United States
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45
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An easy-to-use tool for planning and modeling a calorimetric titration. Anal Biochem 2010; 406:91-3. [DOI: 10.1016/j.ab.2010.06.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 06/29/2010] [Accepted: 06/30/2010] [Indexed: 02/01/2023]
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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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Yang TC, Yang Q, Maluf NK. Interaction of the adenoviral IVa2 protein with a truncated viral DNA packaging sequence. Biophys Chem 2008; 140:78-90. [PMID: 19150169 DOI: 10.1016/j.bpc.2008.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/25/2008] [Accepted: 11/25/2008] [Indexed: 10/21/2022]
Abstract
Adenoviral (Ad) infection typically poses little health risk for immunosufficient individuals. However, for immunocompromised individuals, such as AIDS patients and organ transplant recipients, especially pediatric heart transplant recipients, Ad infection is common and can be lethal. Ad DNA packaging is the process whereby the Ad genome becomes encapsulated by the viral capsid. Specific packaging is dependent upon the packaging sequence (PS), which is composed of seven repeated elements called A repeats. The Ad protein, IVa2, which is required for viral DNA packaging, has been shown to bind specifically to synthetic DNA probes containing A repeats I and II, however, the molecular details of this interaction have not been investigated. In this work we have studied the binding of a truncated form of the IVa2 protein, that has previously been shown to be sufficient for virus viability, to a DNA probe containing A repeats I and II. We find that the IVa2 protein exists as a monomer in solution, and that a single IVa2 monomer binds to this DNA with high affinity (K(d)< approximately 10 nM), and moderate specificity, and that the trIVa2 protein interacts in a fundamentally different way with DNA containing A repeats than it does with non-specific DNA. We also find that at elevated IVa2 concentrations, additional binding, beyond the singly ligated complex, is observed. When this reaction is modeled as representing the binding of a second IVa2 monomer to the singly ligated complex, the K(d) is 1.4+/-0.7 microM, implying a large degree of negative cooperativity exists for placing two IVa2 monomers on a DNA with adjacent A repeats.
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Affiliation(s)
- Teng-Chieh Yang
- University of Colorado Denver, Department of Pharmaceutical Sciences, School of Pharmacy C238-P15, P.O Box 6511, Aurora, CO 80045, USA
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Koh J, Saecker RM, Record MT. DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA. J Mol Biol 2008; 383:324-46. [PMID: 18657548 DOI: 10.1016/j.jmb.2008.07.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Escherichia coli HU(alphabeta), a major nucleoid-associated protein, organizes chromosomal DNA and facilitates numerous DNA transactions. Using isothermal titration calorimetry, fluorescence resonance energy transfer and a series of DNA lengths (8 bp, 15 bp, 34 bp, 38 bp and 160 bp) we established that HU(alphabeta) interacts with duplex DNA using three different nonspecific binding modes. Both the HU to DNA molar ratio ([HU]/[DNA]) and DNA length dictate the dominant HU binding mode. On sufficiently long DNA (> or =34 bp), at low [HU]/[DNA], HU populates a noncooperative 34 bp binding mode with a binding constant of 2.1+/-0.4x10(6) M(-1), and a binding enthalpy of +7.7+/-0.6 kcal/mol at 15 degrees C and 0.15 M Na(+). With increasing [HU]/[DNA], HU bound in the noncooperative 34 bp mode progressively converts to two cooperative (omega approximately 20) modes with site sizes of 10 bp and 6 bp. These latter modes exhibit smaller binding constants (1.1+/-0.2x10(5) M(-1) for the 10 bp mode, 3.5+/-1.4x10(4) M(-1) for the 6 bp mode) and binding enthalpies (4.2+/-0.3 kcal/mol for the 10 bp mode, -1.6+/-0.3 kcal/mol for the 6 bp mode). As DNA length increases to 34 bp or more at low [HU]/[DNA], the small modes are replaced by the 34 bp binding mode. Fluorescence resonance energy transfer data demonstrate that the 34 bp mode bends DNA by 143+/-6 degrees whereas the 6 bp and 10 bp modes do not. The model proposed in this study provides a novel quantitative and comprehensive framework for reconciling previous structural and solution studies of HU, including single molecule (force extension measurement), fluorescence, and electrophoretic gel mobility-shift assays. In particular, it explains how HU condenses or extends DNA depending on the relative concentrations of HU and DNA.
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Affiliation(s)
- Junseock Koh
- Program in Biophysics, University of Wisconsin, Madison WI 53706, USA
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Vivas P, Kuznetsov SV, Ansari A. New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor. J Phys Chem B 2008; 112:5997-6007. [PMID: 18461910 DOI: 10.1021/jp076042s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.
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Affiliation(s)
- Paula Vivas
- Department of Physics (M/C 273), and Department of Bioengineering (M/C 063), University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
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Mukherjee A, Sokunbi AO, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res 2008; 36:3956-68. [PMID: 18515342 PMCID: PMC2475624 DOI: 10.1093/nar/gkn348] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid organization as well as in regulation of DNA-dependent processes. Little is known about nucleoid organization in thermophilic eubacteria. We show here that HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and constrains negative DNA supercoils in the presence of topoisomerase I. However, while binding to a single site occludes approximately 35 bp, association of T. maritima HU with DNA of sufficient length to accommodate multiple protomers results in an apparent shorter occluded site size. Such complexes consist of ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. Association of TmHU with plasmid DNA yields a complex that is remarkably resistant to DNase I-mediated degradation. TmHU is the only member of this protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we propose that this property allows TmHU to form exceedingly stable associations in which DNA flanking the kinks is sandwiched between adjacent proteins. We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA.
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Affiliation(s)
- Anirban Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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