1
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Pederson K, Meints GA, Drobny GP. Base Dynamics in the HhaI Protein Binding Site. J Phys Chem B 2023; 127:7266-7275. [PMID: 37561575 PMCID: PMC10461302 DOI: 10.1021/acs.jpcb.3c03687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.
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Affiliation(s)
- Kari Pederson
- Department
of Chemistry & Biochemistry, California
State University at Dominguez Hills, Carson, California 90747, United States
| | - Gary A. Meints
- Department
of Chemistry, Missouri State University, Springfield, Missouri 65897, United States
| | - Gary P. Drobny
- Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700, United
States
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2
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He S, Yang C, Peng S, Chen C, Zhao XS. Single-molecule study on conformational dynamics of M.HhaI. RSC Adv 2019; 9:14745-14749. [PMID: 35516350 PMCID: PMC9064139 DOI: 10.1039/c9ra00021f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/26/2019] [Indexed: 12/23/2022] Open
Abstract
We found that apo DNA methyltransferase M.HhaI under the physiological salt concentration does not possess the structure characterized by X-ray crystallography; instead, it interchanges between prefolded and unfolded states. Only after binding to the substrate, it transforms into a crystal-structure-like state. Flipping rates of its catalytic loop were directly measured. Huge conformational rearrangements in M.HhaI were observed by a single-molecule study.![]()
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Affiliation(s)
- Shanshan He
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
| | - Chen Yang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
| | - Sijia Peng
- School of Life Sciences
- Tsinghua-Peking Joint Center for Life Sciences
- Beijing Advanced Innovation Center for Structural Biology
- Tsinghua University
- Beijing 100084
| | - Chunlai Chen
- School of Life Sciences
- Tsinghua-Peking Joint Center for Life Sciences
- Beijing Advanced Innovation Center for Structural Biology
- Tsinghua University
- Beijing 100084
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
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3
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Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Comput Biol 2013; 9:e1003337. [PMID: 24244143 PMCID: PMC3828127 DOI: 10.1371/journal.pcbi.1003337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/27/2013] [Indexed: 11/25/2022] Open
Abstract
Bacterial chemotaxis is one of the best studied signal transduction pathways. CheW is a scaffold protein that mediates the association of the chemoreceptors and the CheA kinase in a ternary signaling complex. The effects of replacing conserved Arg62 of CheW with other residues suggested that the scaffold protein plays a more complex role than simply binding its partner proteins. Although R62A CheW had essentially the same affinity for chemoreceptors and CheA, cells expressing the mutant protein are impaired in chemotaxis. Using a combination of molecular dynamics simulations (MD), NMR spectroscopy, and circular dichroism (CD), we addressed the role of Arg62. Here we show that Arg62 forms a salt bridge with another highly conserved residue, Glu38. Although this interaction is unimportant for overall protein stability, it is essential to maintain the correct alignment of the chemoreceptor and kinase binding sites of CheW. Computational and experimental data suggest that the role of the salt bridge in maintaining the alignment of the two partner binding sites is fundamental to the function of the signaling complex but not to its assembly. We conclude that a key feature of CheW is to maintain the specific geometry between the two interaction sites required for its function as a scaffold. Signal transduction is a universal biological process and a common target of drug design. The chemotaxis machinery in Escherichia coli is a model signal transduction system, and the CheW protein is one of its core components. CheW is thought to work as a scaffold protein that mediates the formation of the signaling complex with the CheA histidine kinase and the chemoreceptors. A mutation targeting a highly conserved residue, Arg62, impairs chemotaxis while maintaining normal binding affinity for both partners, suggesting that CheW might play a more complex role than previously proposed. Using a series of molecular dynamics simulations, we found that the residue Arg62 can form a stable salt bridge with another highly conserved residue, Glu38. We determined that this bridge does not contribute to the overall stability of the protein. However, the bridge stabilizes the local backbone structure of CheW and stabilizes the relative position of the binding sites for the chemoreceptor and kinase. The geometry of these interactions appears to be vital for the function of the signaling complex. We validated and complemented our computational findings using NMR spectroscopy and circular dichroism analysis.
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Affiliation(s)
- Davi R. Ortega
- Joint Institute for Computational Sciences, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Guoya Mo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Kwangwoon Lee
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Jerome Baudry
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Molecular Biophysics, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Frederick W. Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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4
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Matje DM, Zhou H, Smith DA, Neely RK, Dryden DTF, Jones AC, Dahlquist FW, Reich NO. Enzyme-promoted base flipping controls DNA methylation fidelity. Biochemistry 2013; 52:1677-85. [PMID: 23409782 DOI: 10.1021/bi3012912] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quantitative understanding of how conformational transitions contribute to enzyme catalysis and specificity remains a fundamental challenge. A suite of biophysical approaches was used to reveal several transient states of the enzyme-substrate complexes of the model DNA cytosine methyltransferase M.HhaI. Multidimensional, transverse relaxation-optimized nuclear magnetic resonance (NMR) experiments show that M.HhaI has the same conformation with noncognate and cognate DNA sequences. The high-affinity cognatelike mode requires the formation of a subset of protein-DNA interactions that drive the flipping of the target base from the helix to the active site. Noncognate substrates lacking these interactions undergo slow base flipping, and fluorescence tracking of the catalytic loop corroborates the NMR evidence of a loose, nonspecific binding mode prior to base flipping and subsequent closure of the catalytic loop. This slow flipping transition defines the rate-limiting step for the methylation of noncognate sequences. Additionally, we present spectroscopic evidence of an intermediate along the base flipping pathway that has been predicted but never previously observed. These findings provide important details of how conformational rearrangements are used to balance specificity with catalytic efficiency.
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Affiliation(s)
- Douglas M Matje
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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5
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Jutras BL, Verma A, Stevenson B. Identification of novel DNA-binding proteins using DNA-affinity chromatography/pull down. CURRENT PROTOCOLS IN MICROBIOLOGY 2012; Chapter 1:Unit1F.1. [PMID: 22307548 PMCID: PMC3564586 DOI: 10.1002/9780471729259.mc01f01s24] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
This units presents methods through which one may isolate and identify novel bacterial DNA-binding proteins. Briefly, the DNA sequence of interest is affixed to beads, and then incubated with bacterial cytoplasmic extract. Washes with buffers containing nonspecific DNA and low-salt concentrations will remove non-adhering and low-specificity DNA-binding proteins, while subsequent washes with higher salt concentrations will elute more specific DNA-binding proteins. Eluted proteins may then be identified by standard proteomic techniques.
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Affiliation(s)
- Brandon L Jutras
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky
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6
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Mealman TD, Bagai I, Singh P, Goodlett DR, Rensing C, Zhou H, Wysocki VH, McEvoy MM. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry 2011; 50:2559-66. [PMID: 21323389 DOI: 10.1021/bi102012j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Escherichia coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane fusion protein CusB before metal extrusion from the periplasm to the extracellular space. Although previous in vitro experiments have demonstrated highly specific interactions between CusF and CusB that are crucial for metal transfer to occur, the structural details of the interaction have not been determined. Here, the interactions between CusF and CusB are mapped through nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled with high-resolution mass spectrometry to better understand how recognition and metal transfer occur between these proteins. The NMR (1)H-(15)N correlation spectra reveal that CusB interacts with the metal-binding face of CusF. In vitro chemical cross-linking with a 7.7 Å homobifunctional amine-reactive cross-linker, BS(2)G, was used to capture the CusF/CusB interaction site, and mass spectral data acquired on an LTQ-Orbitrap confirm the following two cross-links: CusF K31 to CusB K29 and CusF K58 to CusB K32, thus revealing that the N-terminal region of CusB interacts with the metal-binding face of CusF. The proteins transiently interact in a metal-dependent fashion, and contacts between CusF and CusB are localized to regions near their respective metal-binding sites.
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Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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7
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Matje DM, Coughlin DF, Connolly BA, Dahlquist FW, Reich NO. Determinants of precatalytic conformational transitions in the DNA cytosine methyltransferase M.HhaI. Biochemistry 2011; 50:1465-73. [PMID: 21229971 DOI: 10.1021/bi101446g] [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
The DNA methyltransferase M.HhaI is an excellent model for understanding how recognition of a nucleic acid substrate is translated into site-specific modification. In this study, we utilize direct, real-time monitoring of the catalytic loop position via engineered tryptophan fluorescence reporters to dissect the conformational transitions that occur in both enzyme and DNA substrate prior to methylation of the target cytosine. Using nucleobase analogues in place of the target and orphan bases, the kinetics of the base flipping and catalytic loop closure rates were determined, revealing that base flipping precedes loop closure as the rate-determining step prior to methyl transfer. To determine the mechanism by which individual specific hydrogen bond contacts at the enzyme-DNA interface mediate these conformational transitions, nucleobase analogues lacking hydrogen bonding groups were incorporated into the recognition sequence to disrupt the major groove recognition elements. The consequences of binding, loop closure, and catalysis were determined for four contacts, revealing large differences in the contribution of individual hydrogen bonds to DNA recognition and conformational transitions on the path to catalysis. Our results describe how M.HhaI utilizes direct readout contacts to accelerate extrication of the target base that offer new insights into the evolutionary history of this important class of enzymes.
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Affiliation(s)
- Douglas M Matje
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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8
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Zhou H, Purdy MM, Dahlquist FW, Reich NO. The Recognition Pathway for the DNA Cytosine Methyltransferase M.HhaI,. Biochemistry 2009; 48:7807-16. [DOI: 10.1021/bi900502g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106-9510
| | - Matthew M. Purdy
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106-9510
| | - Frederick W. Dahlquist
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106-9510
| | - Norbert O. Reich
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106-9510
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9
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Ricci F, Bonham AJ, Mason AC, Reich NO, Plaxco KW. Reagentless, electrochemical approach for the specific detection of double- and single-stranded DNA binding proteins. Anal Chem 2009; 81:1608-14. [PMID: 19199570 PMCID: PMC2692654 DOI: 10.1021/ac802365x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here we demonstrate a reagentless, electrochemical platform for the specific detection of proteins that bind to single- or double-stranded DNA. The sensor is composed of a double- or single-stranded, redox-tagged DNA probe which is covalently attached to an interrogating electrode. Upon protein binding the current arising from the redox tag is suppressed, indicating the presence of the target. Using this approach we have fabricated sensors against the double-stranded DNA binding proteins TATA-box binding protein and M.HhaI methyltransferase, and against the single-strand binding proteins Escherichia coli SSBP and replication protein A. All four targets are detected at nanomolar concentrations, in minutes, and in a convenient, general, readily reusable, electrochemical format. The approach is specific; we observed no significant cross-reactivity between the sensors. Likewise the approach is selective; it supports, for example, the detection of single strand binding protein directly in crude nuclear extracts. The generality of our approach (including its ability to detect both double- and single-strand binding proteins) and a strong, non-monotonic dependence of signal gain on probe density support a collisional signaling mechanism in which binding alters the collision efficiency, and thus electron transfer efficiency, of the attached redox tag. Given the ubiquity with which protein binding will alter the collisional dynamics of an oligonucleotide, we believe this approach may prove of general utility in the detection of DNA and RNA binding proteins.
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Affiliation(s)
- Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106
| | - Andrew J. Bonham
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106
| | - Aaron C. Mason
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242-1109
| | - Norbert O. Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106
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10
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Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage. Proc Natl Acad Sci U S A 2008; 105:10366-71. [PMID: 18653759 DOI: 10.1073/pnas.0800405105] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists of approximately 7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, S, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA-protein interface within a virus.
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11
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Shajani Z, Varani G. 13C relaxation studies of the DNA target sequence for hhai methyltransferase reveal unique motional properties. Biochemistry 2008; 47:7617-25. [PMID: 18578505 DOI: 10.1021/bi7020469] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The goal of this work was to examine if sequence-dependent conformational flexibility in DNA plays a role in base extrusion, a common conformational change induced by many DNA-modifying enzymes. We studied the dynamics of the double-stranded DNA target of the HhaI methyltransferase by recording an extensive set of (13)C NMR relaxation parameters. We observe that the cytidine furanose rings experience fast (picosecond to nanosecond) motions that are not present in other nucleotides; the methylation site experiences particularly high mobility. We also observe that the bases of guanosine and cytidine residues within the HhaI recognition sequence GCGC experience motions on a much slower (1-100 micros) time scale. We compare these observations with previous solution and solid-state NMR studies of the EcoRI nuclease target sequence, and solid-state NMR studies of a similar HhaI target construct. While an increased mobility of cytidine furanose rings compared to those of other nucleotides is observed for both sequences, the slower motions are only observed in the HhaI target DNA. We propose that this inherent flexibility lowers the energetic barriers that must occur when the DNA binds to the HhaI methyltransferase and for extrusion of the cytidine prior to its methylation.
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Affiliation(s)
- Zahra Shajani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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12
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Pederson K, Meints GA, Shajani Z, Miller PA, Drobny GP. Backbone dynamics in the DNA HhaI protein binding site. J Am Chem Soc 2008; 130:9072-9. [PMID: 18570423 DOI: 10.1021/ja801243d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dynamics of the phosphodiester backbone in the [5'-GCGC-3'] 2 moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5' methylene group of nucleotides within the [5'-GCGC-3'] 2 moiety indicated that all of these positions are structurally flexible. Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone and furanose ring of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through not only a loss of mobility but also a change of direction of motion. These NMR data indicate that the [5'-GCGC-3'] 2 moiety is dynamic, with the largest amplitude motions occurring nearest the methylation site. The change of orientation of this moiety in DNA upon methylation may make the molecule less amenable to binding to the HhaI endonuclease.
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Affiliation(s)
- Kari Pederson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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13
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Boyer JA, Lee AL. Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c. Biochemistry 2008; 47:4876-86. [PMID: 18393447 DOI: 10.1021/bi702330t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-range effects, such as allostery, have evolved in proteins as a means of regulating function via communication between distal sites. An NMR-based perturbation mapping approach was used to more completely probe the dynamic response of the core mutation V54A in the protein eglin c by monitoring changes in picosecond to nanosecond aromatic side-chain dynamics and H/D exchange stabilities. Previous side-chain dynamics studies on this mutant were limited to methyl-bearing residues, most of which were found to rigidify on the picosecond to nanosecond time scale in the form of a contiguous "network". Here, high precision (13)C relaxation data from 13 aromatic side chains were acquired by applying canonical relaxation experiments to a newly developed carbon labeling scheme [Teilum et al. (2006) J. Am. Chem. Soc. 128, 2506-2507]. The fitting of model-free parameters yielded S (2) variability which is intermediate with respect to backbone and methyl-bearing side-chain variability and tau e values that are approximately 1 ns. Inclusion of the aromatic dynamic response results in an expanded network of dynamically coupled residues, with some aromatics showing increases in flexibility, which partially offsets the rigidification in methyl side chains. Using amide hydrogen exchange, dynamic propagation on a slower time scale was probed in response to the V54A perturbation. Surprisingly, regional stabilization (slowed exchange) 10-12 A from the site of mutation was observed despite a global destabilization of 1.5 kcal x mol (-1). Furthermore, this unlikely pocket of stabilized residues colocalizes with increases in aromatic flexibility on the faster time scale. Because the converse is also true (destabilized residues colocalize with rigidification on the fast time scale), a plausible entropy-driven mechanism is discussed for relating colocalization of opposing dynamic trends on vastly different time scales.
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Affiliation(s)
- Joshua A Boyer
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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