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Meirovitch E, Liang Z, Schurko RW, Loeb SJ, Freed JH. Structural Dynamics by NMR in the Solid State: II. The MOMD Perspective of the Dynamic Structure of Metal-Organic Frameworks Comprising Several Mobile Components. J Phys Chem B 2022; 126:2452-2465. [PMID: 35333061 PMCID: PMC9055879 DOI: 10.1021/acs.jpcb.1c10120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the application of the microscopic-order-macroscopic-disorder (MOMD) approach, developed for the analysis of dynamic 2H NMR lineshapes in the solid state, to unravel interactions among the constituents of metal-organic frameworks (MOFs) that comprise mobile components. MOMD was applied recently to University of Windsor Dynamic Material (UWDM) MOFs with one mobile crown ether per cavity. In this work, we study UWDM-9-d4, which comprises a mobile 2H-labeled phenyl-ring residue along with an isotopically unlabeled 24C8 crown ether. We also study UiO-68-d4, which is structurally similar to UWDM-9-d4 but lacks the crown ether. The physical picture consists of the NMR probe─the C-D bonds of the phenyl-d4 rotor─diffusing locally (diffusion tensor R) in the presence of a local ordering potential, u. For UiO-68-d4, we find it sufficient to expand u in terms of four real Wigner functions, D0|K|L, overall 2-3 kT in magnitude, with R∥ relatively fast, and R⊥ in the (2.8-5.0) × 102 s-1 range. For UWDM-9-d4, u requires only two terms 2-3 kT in magnitude and slower rate constants R∥ and R⊥. In the more crowded macrocycle-containing UWDM-9-d4 cavity, phenyl-d4 dynamics is more isotropic and is described by a simpler ordering potential. This is ascribed to cooperative phenyl-ring/macrocycle motion, which yields a dynamic structure more uniform in character. The experimental 2H spectra used here were analyzed previously with a multi-simple-mode (MSM) approach where several independent simple motional modes are combined. Where possible, similar features have been identified and used to compare the two approaches.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Robert W Schurko
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Stephen J Loeb
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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Meirovitch E, Liang Z, Freed JH. Structural Dynamics by NMR in the Solid State: The Unified MOMD Perspective Applied to Organic Frameworks with Interlocked Molecules. J Phys Chem B 2020; 124:6225-6235. [PMID: 32584038 DOI: 10.1021/acs.jpcb.0c03687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microscopic-order-macroscopic-disorder (MOMD) approach for NMR lineshape analysis has been applied to the University of Windsor Dynamic Materials (UWDM) of types 1, 2, α-3, β-3, and 5, which are metal-organic frameworks (MOFs) comprising mobile mechanically interlocked molecules (MIMs). The mobile MIM components are selectively deuterated crown ether macrocycles - 24C6, 22C6, and B24C6. Their motion is described in MOMD by an effective/collective dynamic mode characterized by a diffusion tensor, R, a restricting/ordering potential, u, expanded in the Wigner rotation matrix elements, D0, KL, and features of local geometry. Experimental 2H lineshapes are available over 220 K (on average) and in some cases 320 K. They are reproduced with axial R, u given by the terms D0,02 and D0,|2|2, and established local geometry. For UWDM of types 1, β-3, and 5, where the macrocycle resides in a relatively loose space, u is in the 1-3 kT, R∥ in the (1.0-2.5) × 106 s-1, and R⊥ in the (0.4-2.5) × 104 s-1 range; the deuterium atom is bonded to a carbon atom with tetrahedral coordination character. For UWDM of types 2 and α-3, where the macrocycle resides in a much tighter space, a substantial change in the symmetry of u and the coordination character of the 2H-bonded carbon are detected at higher temperatures. The activation energies for R∥ and R⊥ are characteristic of each system. The MOMD model is general; effective/collective dynamic modes are treated. The characteristics of motion, ordering, and geometry are physically well-defined; they differ from case to case in extent and symmetry but not in essence. Physical clarity and consistency provide new insights. A previous interpretation of the same experimental data used models consisting of collections of independent simple motions. These models are specific to each case and temperature. Within their scope, generating consistent physical pictures and comparing cases are difficult; possible collective modes are neglected.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences. Biochemistry 2020; 59:1909-1926. [PMID: 32352758 PMCID: PMC7253346 DOI: 10.1021/acs.biochem.0c00253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recognition of the epigenetic mark 5-methylcytosine (mC) at CpG sites in DNA has emerged as a novel function of many eukaryotic transcription factors (TFs). It remains unclear why the sequence specificity of these TFs differs for CpG-methylated motifs and consensus motifs. Here, we dissect the structural and dynamic basis for this differential DNA binding specificity in the human zinc finger TF Kaiso, which exhibits high affinity for two consecutive mCpG sites in variable contexts and also for a longer, sequence-specific Kaiso binding site (KBS). By integrating structural analysis and DNA binding studies with targeted protein mutagenesis and nucleotide substitutions, we identify distinct mechanisms for readout of methylated and KBS motifs by Kaiso. We show that a key glutamate residue (E535), critical for mCpG site recognition, adopts different conformations in complexes with specific and methylated DNA. These conformational differences, together with intrinsic variations in DNA flexibility and/or solvation at TpG versus mCpG sites, contribute to the different DNA affinity and sequence specificity. With methylated DNA, multiple direct contacts between E535 and the 5' mCpG site dominate the binding affinity, allowing for tolerance of different flanking DNA sequences. With KBS, Kaiso employs E535 as part of an indirect screen of the 5' flanking sequence, relying on key tyrosine-DNA interactions to stabilize an optimal DNA conformation and select against noncognate sites. These findings demonstrate how TFs use conformational adaptation and exploit variations in DNA flexibility to achieve distinct DNA readout outcomes and target a greater variety of regulatory and epigenetic sites than previously appreciated.
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Meirovitch E, Freed JH. Local ordering and dynamics in anisotropic media by magnetic resonance: from liquid crystals to proteins. LIQUID CRYSTALS 2019; 47:1926-1954. [PMID: 32435078 PMCID: PMC7239324 DOI: 10.1080/02678292.2019.1622158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 06/11/2023]
Abstract
Magnetic resonance methods have been used extensively for over 50 years to elucidate molecular structure and dynamics of liquid crystals (LCs), providing information quite unique in its rigour and extent. The ESR- or NMR-active probe is often a solute molecule reporting on characteristics associated with the surrounding (LC) medium, which exerts the spatial restrictions on the probe. The theoretical approaches developed for LCs are applicable to anisotropic media in general. Of particular interest is the interior space of a globular protein labelled, e.g. with a nitroxide moiety or a 15N-1H bond. The ESR or NMR label plays the role of the probe and the internal protein surroundings the role of the anisotropic medium. A general feature of the restricted motions is the local ordering, i.e. the nature, magnitude and symmetry of the spatial restraints exerted at the site of the moving probe. This property is the main theme of the present review article. We outline its treatment in our work from both the theoretical and the experimental points of view, highlighting the new physical insights gained. Our illustrations include studies on thermotropic (nematic and smectic) and lyotropic liquid crystals formed by phospholipids, in addition to studies of proteins.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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Meirovitch E, Liang Z, Freed JH. Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective. J Phys Chem B 2018; 122:8675-8684. [PMID: 30141954 DOI: 10.1021/acs.jpcb.8b06330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a potential, u, and the "local geometry" by the relative orientation of the model-related and nuclear magnetic resonance-related tensors. Here, we apply MOMD to phenyl-ring dynamics in several Αβ40-amyloid-fibrils, and the villin headpiece subdomain (HP36). Because the available data are limited in extent and sensitivity, we adjust u and R in the relevant parameter ranges, fixing the "local geometry" in accordance with standard stereochemistry. This yields a physically well-defined and consistent picture of phenyl-ring dynamics, enabling comparison between different systems. In the temperature range of 278-308 K, u has a strength of (1.7-1.8) kT and a rhombicity of (2.4-2.6) kT, and R has components of 5.0 × 102 ≤ R⊥ ≤ 2.0 × 103 s-1 and 6.3 × 105 ≤ R∥ ≤ 2.0 × 106 s-1. At 278 K, fibril hydration increases the axiality of both u and R; HP36 hydration has a similar effect at 295 K, reducing R⊥ considerably. The D23N mutation slows down the motion of the probe; Aβ40 polymorphism affects both this motion and the related local potential. The present study identifies the impact of various factors on phenyl-ring mobility in amyloid fibrils and globular proteins; the difference between the two protein forms is considerable. The distinctive impact of hydration on phenyl-ring motion and previously studied methyl-group motion is also examined. The 2H lineshapes considered here were analyzed previously with various multi-simple-mode (MSM) models, where several simple motional modes are combined. The MOMD and MSM interpretations differ in essence.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
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Meirovitch E, Liang Z, Freed JH. MOMD Analysis of NMR Line Shapes from Aβ-Amyloid Fibrils: A New Tool for Characterizing Molecular Environments in Protein Aggregates. J Phys Chem B 2018; 122:4793-4801. [PMID: 29624402 DOI: 10.1021/acs.jpcb.8b02181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The microscopic-order-macroscopic-disorder (MOMD) approach for 2H NMR line shape analysis is applied to dry and hydrated 3-fold- and 2-fold-symmetric amyloid-Aβ40 fibrils and protofibrils of the D23N mutant. The methyl moieties of L17, L34, V36 (C-CD3), and M35 (S-CD3) serve as probes. Experimental 2H spectra acquired previously in the 147-310 K range are used. MOMD describes local probe motion as axial diffusion ( R tensor) in the presence of a potential, u, which represents the spatial restrictions exerted by the molecular surroundings. We find that R∥ = (0.2-3.3) × 104 s-1, R⊥ = (2.2-2.5) × 102 s-1, and R is tilted from the 2H quadrupolar tensor at 60-75°. The strength of u is in the (2.0-2.4) kT range; its rhombicity is substantial. The only methyl moieties affected by fibril hydration are those of M35, located at fibril interfaces. The associated local potentials change form abruptly around 260 K, where massive water freezing occurs. An independent study revealed unfrozen "tightly-peptide-bound" water residing at the interfaces of the 3-fold-symmetric Aβ40 fibrils and at the interfaces of the E22G and E22Δ Aβ40-mutant fibrils. Considering this to be the case in general for Aβ40-related fibrils, the following emerges. The impact of water freezing is transmitted selectively to the fibril structure through interactions with tightly-peptide-bound water, in this case of M35 methyl moieties. The proof that such waters reside at the interfaces of the 2-fold-symmetric fibril, and the protofibril of the D23N mutant, is new. MOMD provides information on the surroundings of the NMR probe directly via the potential, u, which is inherent to the model; a prior interpretation of the same experimental data does so partially and indirectly (see below). Thus, MOMD analysis of NMR line shapes as applied to amyloid fibrils/protein aggregates emerges as a consistent new tool for elucidating the properties of, and processes associated with, molecular environments in the fibril.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid-state from 2H NMR lineshape analysis. III. MOMD in the presence of Magic Angle Spinning. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 89:35-44. [PMID: 29208317 PMCID: PMC5772661 DOI: 10.1016/j.ssnmr.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
We report on a new approach to the analysis of dynamic NMR lineshapes from polycrystalline (i.e., macroscopically disordered) samples in the presence of Magic Angle Spinning (MAS). This is an application of the Stochastic Liouville Equation developed by Freed and co-workers for treating restricted (i.e., microscopically ordered) motions. The 2H nucleus in an internally-mobile C-CD3 moiety serves as a prototype probe. The acronym is 2H/MOMD/MAS, where MOMD stands for "microscopic-order-macroscopic-disorder." The key elements describing internal motions - their type, the local spatial restrictions, and related features of local geometry - are treated in MOMD generally, within their rigorous three-dimensional tensorial requirements. Based on this representation a single physically well-defined model of local motion has the capability of reproducing experimental spectra. There exist other methods for analyzing dynamic 2H/MAS spectra which advocate simple motional modes. Yet, to reproduce satisfactorily the experimental lineshapes, one has either to use unusual parameter values, or combine several simple motional modes. The multi-simple-mode reasoning assumes independence of the constituent modes, features ambiguity as different simple modes may be used, renders inter-system comparison difficult as the overall models differ, and makes possible model-improvement only by adding yet another simple mode, i.e., changing the overall model. 2H/MOMD/MAS is free of such limitations and inherently provides a clear physical interpretation. These features are illustrated. The advantage of 2H/MOMD/MAS in dealing with sensitive but hardly investigated slow-motional lineshapes is demonstrated by applying it to actual experimental data. The results differ from those obtained previously with a two-site exchange scheme that yielded unusual parameters.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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8
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Meirovitch E, Liang Z, Freed JH. Protein Dynamics in the Solid State from (2)H NMR Line Shape Analysis. II. MOMD Applied to C-D and C-CD3 Probes. J Phys Chem B 2015; 119:14022-32. [PMID: 26402431 PMCID: PMC4676681 DOI: 10.1021/acs.jpcb.5b07434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Deuterium
line shape analysis from mobile C–D and C–CD3 groups has emerged as a particularly useful tool for studying
dynamics in the solid state. The theoretical models devised so far
consist typically of sets of independent dynamic modes. Each such
mode is simple and usually case-specific. In this scenario, model
improvement entails adding yet another mode (thereby changing the
overall model), comparison of different cases is difficult, and ambiguity
is unavoidable. We recently developed the microscopic order macroscopic
disorder (MOMD) approach as a single-mode alternative. In MOMD, the
local spatial restrictions are expressed by an anisotropic potential,
the local motion by a diffusion tensor, and the local molecular geometry
by relative (magnetic and model-related) tensor orientations, all
of adjustable symmetry. This approach provides a consistent method
of analysis, thus resolving the issues above. In this study, we apply
MOMD to PS-adsorbed LKα14 peptide and dimethylammonium tetraphenylborate
(C–CD3 and N–CD3 dynamics, respectively),
as well as HhaI methyltransferase target DNA and
phase III of benzene-6-hexanoate (C–D dynamics). The success
with fitting these four disparate cases, as well as the two cases
in the previous report, demonstrates the generality of this MOMD-based
approach. In this study, C–D and C–CD3 are
both found to execute axial diffusion (rates R⊥ and R∥) in the
presence of a rhombic potential given by the L =
2 spherical harmonics (coefficients c02 and c22). R⊥ (R∥) is in the 102–103 (104–105) s–1 range, and c02 and c22 are on the
order of 2–3 kBT. Specific parameter values are determined for each mobile site.
The diffusion and quadrupolar tensors are tilted at either 120°
(consistent with trans–gauche isomerization) or nearly 110.5° (consistent with methyl exchange).
Future prospects include extension of the MOMD formalism to include
MAS, and application to 15N and 13C nuclei.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
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9
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective. J Phys Chem B 2015; 119:2857-68. [PMID: 25594631 DOI: 10.1021/jp511386b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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10
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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11
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Emani PS, Bardaro MF, Huang W, Aragon S, Varani G, Drobny GP. Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles. J Phys Chem B 2014; 118:1726-42. [PMID: 24479561 PMCID: PMC3983377 DOI: 10.1021/jp409386t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Complex RNA structures are constructed
from helical segments connected
by flexible loops that move spontaneously and in response to binding
of small molecule ligands and proteins. Understanding the conformational
variability of RNA requires the characterization of the coupled time
evolution of interconnected flexible domains. To elucidate the collective
molecular motions and explore the conformational landscape of the
HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized
structures generated by the program “Fragment Assembly of RNA
with Full-Atom Refinement (FARFAR)”. We apply structural filters
in the form of experimental residual dipolar couplings (RDCs) to select
a subset of discrete energy-minimized conformers and carry out principal
component analyses (PCA) to corroborate the choice of the filtered
subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule
using two simulation protocols that we previously published. We match
the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results
introduce a protocol to construct viable dynamic trajectories for
RNA molecules that accord well with experimental NMR data and support
the notion that the motions of the helical portions of this small
RNA can be described by a relatively small number of discrete conformations
exchanging over time scales longer than 1 μs.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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12
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Morag O, Abramov G, Goldbourt A. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell. J Am Chem Soc 2014; 136:2292-301. [PMID: 24447194 DOI: 10.1021/ja412178n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Ramat Aviv 69978, Tel Aviv, Israel
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13
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Nikolova EN, Bascom GD, Andricioaei I, Al-Hashimi HM. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry 2012; 51:8654-64. [PMID: 23035755 DOI: 10.1021/bi3009517] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet few studies have experimentally explored the sequence dependence of DNA dynamics that occur on biologically relevant time scales. Here, we use nuclear magnetic resonance (NMR) carbon spin relaxation combined with molecular dynamics (MD) simulations to examine the picosecond to nanosecond dynamics in a variety of dinucleotide steps as well as in varying length homopolymeric A(n)·T(n) repeats (A(n)-tracts, where n = 2, 4, or 6) that exhibit unusual structural and mechanical properties. We extend the NMR spin relaxation time scale sensitivity deeper into the nanosecond regime by using glycerol and a longer DNA duplex to slow overall tumbling. Our studies reveal a structurally unique A-tract core (for n > 3) that is uniformly rigid, flanked by junction steps that show increasing sugar flexibility with A-tract length. High sugar mobility is observed at pyrimidine residues at the A-tract junctions, which is encoded at the dinucleotide level (CA, TG, and CG steps) and increases with A-tract length. The MD simulations reproduce many of these trends, particularly the overall rigidity of A-tract base and sugar sites, and suggest that the sugar-backbone dynamics could involve transitions in sugar pucker and phosphate backbone BI ↔ BII equilibria. Our results reinforce an emerging view that sequence-specific DNA flexibility can be imprinted in dynamics occurring deep within the nanosecond time regime that is difficult to characterize experimentally at the atomic level. Such large-amplitude sequence-dependent backbone fluctuations might flag the genome for specific DNA recognition.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
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14
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Emani PS, Olsen GL, Echodu DC, Varani G, Drobny GP. Slow exchange model of nonrigid rotational motion in RNA for combined solid-state and solution NMR studies. J Phys Chem B 2010; 114:15991-6002. [PMID: 21067190 PMCID: PMC3246393 DOI: 10.1021/jp107193z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Functional RNA molecules are conformationally dynamic and sample a multitude of dynamic modes over a wide range of frequencies. Thus, a comprehensive description of RNA dynamics requires the inclusion of a broad range of motions across multiple dynamic rates which must be derived from multiple spectroscopies. Here we describe a slow conformational exchange theoretical approach to combining the description of local motions in RNA that occur in the nanosecond to microsecond window and are detected by solid-state NMR with nonrigid rotational motion of the HIV-1 transactivation response element (TAR) RNA in solution as observed by solution NMR. This theoretical model unifies the experimental results generated by solution and solid-state NMR and provides a comprehensive view of the dynamics of HIV-1 TAR RNA, a well-known paradigm of an RNA where function requires extensive conformational rearrangements. This methodology provides a quantitative atomic level view of the amplitudes and rates of the local and collective displacements of the TAR RNA molecule and provides directly motional parameters for the conformational capture hypothesis of this classical RNA-ligand interaction.
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Affiliation(s)
- Prashant S. Emani
- Department of Physics, University of Washington, Box 351560, Seattle, USA 98195
| | - Gregory L. Olsen
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
| | - Dorothy C. Echodu
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
- Department of Biochemistry, University of Washington, Box 357350, Seattle, USA 98195
| | - Gary P. Drobny
- Department of Chemistry, University of Washington, Box 351700, Seattle, USA 98195
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15
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Kinde-Carson MN, Ferguson C, Oyler NA, Harbison GS, Meints GA. Solid state 2H NMR analysis of furanose ring dynamics in DNA containing uracil. J Phys Chem B 2010; 114:3285-93. [PMID: 20151717 DOI: 10.1021/jp9091656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions, such as uracil, in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Increased dynamic properties in lesion-containing DNAs have been suggested to assist recognition and specificity. Deuterium solid-state nuclear magnetic resonance (SSNMR) has been used to directly observe local dynamics of the furanose ring within a uracil:adenine (U:A) base pair and compared to a normal thymine:adenine (T:A) base pair. Quadrupole echo lineshapes, <T(1Z)>, and <T(2e)> relaxation data were collected, and computer modeling was performed. The results indicate that the relaxation times are identical within the experimental error, the solid lineshapes are essentially indistinguishable above the noise level, and our lineshapes are best fit with a model that does not have significant local motions. Therefore, U:A base pair furanose rings appear to have essentially identical dynamic properties as a normal T:A base pair, and the local dynamics of the furanose ring are unlikely to be the sole arbiter for uracil recognition and specificity in U:A base pairs.
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16
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:360-405. [PMID: 20625480 PMCID: PMC2899824 DOI: 10.1016/j.pnmrs.2010.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
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17
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Nikolova EN, Al-Hashimi HM. Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR. JOURNAL OF BIOMOLECULAR NMR 2009; 45:9-16. [PMID: 19636798 DOI: 10.1007/s10858-009-9350-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 06/19/2009] [Indexed: 05/28/2023]
Abstract
DNA is a highly flexible molecule that undergoes functionally important structural transitions in response to external cellular stimuli. Atomic level spin relaxation NMR studies of DNA dynamics have been limited to short duplexes in which sensitivity to biologically relevant fluctuations occurring at nanosecond timescales is often inadequate. Here, we introduce a method for preparing residue-specific (13)C/(15)N-labeled elongated DNA along with a strategy for establishing resonance assignments and apply the approach to probe fast inter-helical bending motions induced by an adenine tract. Preliminary results suggest the presence of elevated A-tract independent end-fraying internal motions occurring at nanosecond timescales, which evade detection in short DNA constructs and that penetrate deep (7 bp) within the DNA helix and gradually fade away towards the helix interior.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry, Biophysics and Chemical Biology Program, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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