1
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Kurle-Tucholski P, Köhler L, Zhao Z, Link G, Wiebeler C, Matysik J. Stabilization of a flavoprotein for solid-state photo-CIDNP MAS NMR at room temperature by embedding in a glassy sugar matrix. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107497. [PMID: 37295281 DOI: 10.1016/j.jmr.2023.107497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Hyperpolarization via the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect can be detected in frozen solutions of electron transfer proteins generating a radical-pair upon illumination. The effect has been observed in various natural photosynthetic reaction centers and in light-oxygen-voltage (LOV) sensing domains incorporating a flavin mononucleotide (FMN) as chromophore. In LOV domains, where a highly conserved cysteine is mutated to a flavin to interrupt its natural photochemistry, a radical-pair is generated by electron transfer from a nearby tryptophan to the photoexcited triplet state of FMN. During the photocycle, both the LOV domain and the chromophore are photochemically degraded, e.g., by the formation of singlet oxygen. This limits the time for collection of hyperpolarized nuclear magnetic resonance (NMR) data. We show that embedding of the protein into a trehalose sugar glass matrix stabilizes the protein for 13C solid-state photo-CIDNP NMR experiments which can be conducted at room temperature in a powder sample. Additionally, this preparation allows for incorporation of high amounts of protein further boosting the intensity of the detected signals from FMN and tryptophan at natural abundance. Signal assignment is aided by quantum chemical calculations of absolute shieldings. The underlying mechanism for the surprising absorption-only signal pattern is not yet understood. Comparison to calculated isotropic hyperfine couplings imply that the enhancement is not due to the classical radical-pair mechanism (RPM). Analysis of the anisotropic hyperfine couplings associated with solid-state photo-CIDNP mechanisms also show no simple correlation, suggesting a more complex underlying mechanism.
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Affiliation(s)
- Patrick Kurle-Tucholski
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Lisa Köhler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Ziyue Zhao
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Gerhard Link
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 21, D-79104 Freiburg, Germany
| | - Christian Wiebeler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany; Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstraße 2, D-04103 Leipzig, Germany; Institut für Physik, Universität Augsburg, Universitätsstraße 1, D-86159 Augsburg, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany.
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2
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Kaushik M, Lingua H, Stevanato G, Elokova M, Lelli M, Lesage A, Ouari O. Trehalose Matrices for High Temperature Dynamic Nuclear Polarization Enhanced Solid State NMR. Phys Chem Chem Phys 2022; 24:12167-12175. [DOI: 10.1039/d2cp00970f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic Nuclear Polarization (DNP) at cryogenic temperatures has proved to be a valuable technique to enhance the sensitivity of solid-state NMR spectroscopy. Over the years, sample formulations have been optimized...
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3
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Köhler L, Gärtner W, Matysik J, Song C. Long‐Term Preservation of Short‐Lived Photoproducts of Phytochromes at Room Temperature. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lisa Köhler
- Institut für Analytische Chemie Fakultät für Chemie und Mineralogie Universität Leipzig 04103 Leipzig Germany
| | - Wolfgang Gärtner
- Institut für Analytische Chemie Fakultät für Chemie und Mineralogie Universität Leipzig 04103 Leipzig Germany
| | - Jörg Matysik
- Institut für Analytische Chemie Fakultät für Chemie und Mineralogie Universität Leipzig 04103 Leipzig Germany
| | - Chen Song
- Institut für Analytische Chemie Fakultät für Chemie und Mineralogie Universität Leipzig 04103 Leipzig Germany
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4
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Singh J, Singh V, Sharma PC. Elucidating the role of osmotic, ionic and major salt responsive transcript components towards salinity tolerance in contrasting chickpea ( Cicer arietinum L.) genotypes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:441-453. [PMID: 29692552 PMCID: PMC5911262 DOI: 10.1007/s12298-018-0517-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 01/23/2018] [Accepted: 01/31/2018] [Indexed: 05/25/2023]
Abstract
The growth of chickpea (Cicer arietinum L.) is extremely hampered by salt stress. Understanding of physio-biochemical and molecular attributes along with morphological traits contributing to the salinity tolerance is important for developing salt tolerant chickpea varieties. To explore these facts, two genotypes CSG8962 and HC5 with contrasting salt tolerance were evaluated in the salinity stress (Control and 120 mM NaCl) conditions. CSG8962 maintained lower Na/K ratio in root and shoot, trammeled Na translocation to the shoots from roots compared to HC5 which ascribed to better exclusion of salt from its roots and compartmentation in the shoot. In chickpea, salt stress specifically induced genes/sequences involved at several levels in the salt stress signaling pathway. Higher induction of trehalose 6 phosphate synthase and protein kinase genes pertaining to the osmotic and signaling modules, respectively, were evident in CSG8962 compared to HC5. Further transcripts of late embryogenesis abundant, non-specific lipid transfer protein, HI and 219 genes/sequences were also highly induced in CSG8962 compared to HC5 which emphasizes the better protection of cellular membranous network and membrane-bound macromolecules under salt stress. This further suppressed the stress enhanced electrolyte leakage, loss of turgidity, promoted the higher compatible solute accumulation and maintained better cellular ion homoeostasis in CSG8962 compared to HC5. Our study further adds to the importance of these genes in salt tolerance by comparing their behavior in contrasting chickpea genotypes.
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Affiliation(s)
- Jogendra Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Vijayata Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - P. C. Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
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5
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Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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6
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Bärenwald R, Achilles A, Lange F, Ferreira TM, Saalwächter K. Applications of Solid-State NMR Spectroscopy for the Study of Lipid Membranes with Polyphilic Guest (Macro)Molecules. Polymers (Basel) 2016; 8:E439. [PMID: 30974716 PMCID: PMC6432237 DOI: 10.3390/polym8120439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022] Open
Abstract
The incorporation of polymers or smaller complex molecules into lipid membranes allows for property modifications or the introduction of new functional elements. The corresponding molecular-scale details, such as changes in dynamics or features of potential supramolecular structures, can be studied by a variety of solid-state NMR techniques. Here, we review various approaches to characterizing the structure and dynamics of the guest molecules as well as the lipid phase structure and dynamics by different high-resolution magic-angle spinning proton and 13C NMR experiments as well as static 31P NMR experiments. Special emphasis is placed upon the incorporation of novel synthetic polyphilic molecules such as shape-persistent T- and X-shaped molecules as well as di- and tri-block copolymers. Most of the systems studied feature dynamic heterogeneities, for instance those arising from the coexistence of different phases; possibilities for a quantitative assessment are of particular concern.
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Affiliation(s)
- Ruth Bärenwald
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Anja Achilles
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Frank Lange
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Tiago Mendes Ferreira
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany.
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7
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Shukla N, Pomarico E, Chen L, Chergui M, Othon CM. Retardation of Bulk Water Dynamics by Disaccharide Osmolytes. J Phys Chem B 2016; 120:9477-83. [DOI: 10.1021/acs.jpcb.6b07751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nimesh Shukla
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Enrico Pomarico
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Lee Chen
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Christina M. Othon
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06457, United States
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8
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Achilles A, Bärenwald R, Lechner BD, Werner S, Ebert H, Tschierske C, Blume A, Bacia K, Saalwächter K. Self-Assembly of X-Shaped Bolapolyphiles in Lipid Membranes: Solid-State NMR Investigations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:673-682. [PMID: 26735449 DOI: 10.1021/acs.langmuir.5b03712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel class of rigid-rod bolapolyphilic molecules with three philicities (rigid aromatic core, mobile aliphatic side chains, polar end groups) has recently been demonstrated to incorporate into and span lipid membranes, and to exhibit a rich variety of self-organization modes, including macroscopically ordered snowflake structures with 6-fold symmetry. In order to support a structural model and to better understand the self-organization on a molecular scale, we here report on proton and carbon-13 high-resolution magic-angle spinning solid-state NMR investigations of two different bolapolyphiles (BPs) in model membranes of two different phospholipids (DPPC, DOPC). We elucidate the changes in molecular dynamics associated with three new phase transitions detected by calorimetry in composite membranes of different composition, namely, a change in π-π-packing, the melting of lipid tails associated with the superstructure, and the dissolution and onset of free rotation of the BPs. We derive dynamic order parameters associated with different H-H and C-H bond directions of the BPs, demonstrating that the aromatic cores are well packed below the final phase transition, showing only 180° flips of the phenyl ring, and that they perform free rotations with additional oscillations of the long axis when dissolved in the fluid membrane. Our data suggests that BPs not only form ordered superstructures, but also rather homogeneously dispersed π-packed filaments within the lipid gel phase, thus reducing the corrugation of large vesicles.
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Affiliation(s)
- Anja Achilles
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Ruth Bärenwald
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Bob-Dan Lechner
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Stefan Werner
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Helgard Ebert
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Carsten Tschierske
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Alfred Blume
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Kirsten Bacia
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
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9
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Abstract
Protein aggregation and loss of protein's biological functionality are manifestations of protein instability. Cosolvents, in particular trehalose, are widely accepted antidotes against such destabilization. Although numerous theories have been promulgated in the literature with regard to its mechanism of stabilization, the present scenario is still elusive in view of the discrepancies existing in them. To this end, we have revisited the conundrum and attempted to rationalize the mechanism by conducting thorough investigation of the effect of trehalose on the native, partially unfolded and denatured states of protein "Lysozyme" by means of molecular dynamic (MD) simulations under different temperature and concentration regimes. Two-dimensional contour plots along with principal component analysis suggest that trehalose molecules offer on-pathway stabilization unaltering the principal direction of protein's motion, although it slows down protein dynamics so that the protein gets trapped in the homogeneous ensemble of conformations closer to the native state. Free energy landscape reveals higher population of native compared to intermediate and denatured states. Delphi results and calculation of the preferential interaction parameter demonstrate that this relative stabilization of the native state can be ascribed to be the consequence of favourable interactions of trehalose with side chains of certain loci on the protein surface encompassing polar flexible residues. Stability of protein results from the observed difference in binding affinity of trehalose for native and denatured states of protein. Our findings are at variance with the common conception of relative destabilization of the denatured state. Rather, we provide evidence for relative stabilization of the native state. This stabilization is due to interplay of protein-trehalose, water-trehalose, water-water, protein-water and trehalose-trehalose interactions.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, 110016, India.
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10
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Malferrari M, Francia F, Venturoli G. Retardation of Protein Dynamics by Trehalose in Dehydrated Systems of Photosynthetic Reaction Centers. Insights from Electron Transfer and Thermal Denaturation Kinetics. J Phys Chem B 2015; 119:13600-18. [DOI: 10.1021/acs.jpcb.5b02986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale
Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o
Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
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11
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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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12
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Bärenwald R, Goerlitz S, Godehardt R, Osichow A, Tong Q, Krumova M, Mecking S, Saalwächter K. Local Flips and Chain Motion in Polyethylene Crystallites: A Comparison of Melt-Crystallized Samples, Reactor Powders, and Nanocrystals. Macromolecules 2014. [DOI: 10.1021/ma500691k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ruth Bärenwald
- Institut
für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.
7, D-06120 Halle, Germany
| | - Sylvia Goerlitz
- Institut
für Physik − Allgemeine Werkstoffwissenschaften, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 3, D-06120 Halle, Germany
| | - Reinhold Godehardt
- Institut
für Physik − Allgemeine Werkstoffwissenschaften, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 3, D-06120 Halle, Germany
| | - Anna Osichow
- Chemische
Materialwissenschaft, Fachbereich Chemie, Universität Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
| | - Qiong Tong
- Chemische
Materialwissenschaft, Fachbereich Chemie, Universität Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
| | - Marina Krumova
- Chemische
Materialwissenschaft, Fachbereich Chemie, Universität Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
| | - Stefan Mecking
- Chemische
Materialwissenschaft, Fachbereich Chemie, Universität Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
| | - Kay Saalwächter
- Institut
für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.
7, D-06120 Halle, Germany
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13
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Zinkevich T, Chevelkov V, Reif B, Saalwächter K, Krushelnitsky A. Internal protein dynamics on ps to μs timescales as studied by multi-frequency (15)N solid-state NMR relaxation. JOURNAL OF BIOMOLECULAR NMR 2013; 57:219-35. [PMID: 24048638 DOI: 10.1007/s10858-013-9782-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/06/2013] [Indexed: 05/14/2023]
Abstract
A comprehensive analysis of the dynamics of the SH3 domain of chicken alpha-spectrin is presented, based upon (15)N T1 and on- and off-resonance T1ρ relaxation times obtained on deuterated samples with a partial back-exchange of labile protons under a variety of the experimental conditions, taking explicitly into account the dipolar order parameters calculated from (15)N-(1)H dipole-dipole couplings. It is demonstrated that such a multi-frequency approach enables access to motional correlation times spanning about 6 orders of magnitude. We asses the validity of different motional models based upon orientation autocorrelation functions with a different number of motional components. We find that for many residues a "two components" model is not sufficient for a good description of the data and more complicated fitting models must be considered. We show that slow motions with correlation times on the order of 1-10 μs can be determined reliably in spite of rather low apparent amplitudes (below 1 %), and demonstrate that the distribution of the protein backbone mobility along the time scale axis is pronouncedly non-uniform and non-monotonic: two domains of fast (τ < 10(-10) s) and intermediate (10(-9) s < τ < 10(-7) s) motions are separated by a gap of one order of magnitude in time with almost no motions. For slower motions (τ > 10(-6) s) we observe a sharp ~1 order of magnitude decrease of the apparent motional amplitudes. Such a distribution obviously reflects different nature of backbone motions on different time scales, where the slow end may be attributed to weakly populated "excited states." Surprisingly, our data reveal no clearly evident correlations between secondary structure of the protein and motional parameters. We also could not notice any unambiguous correlations between motions in different time scales along the protein backbone emphasizing the importance of the inter-residue interactions and the cooperative nature of protein dynamics.
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Affiliation(s)
- Tatiana Zinkevich
- NMRGroup, Faculty of Natural Sciences II, Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, Saale, 06120, Halle, Germany
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14
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Chen W, Sun HJ, Miyoshi T. Unique molecular dynamics of structural elements in an asymmetric Janus bisamide supramolecule characterized by solid-state NMR. J Phys Chem B 2013; 117:13698-709. [PMID: 24102116 DOI: 10.1021/jp4081492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An asymmetric tapered Janus bisamide supramolecule consisting of 1,4-bis[3,4,5-tris(alkan-1-yloxy)benzamido]benzene bisamide (abbreviated as C22PhBAEO3) can possess three-dimensional (3D) long-range order under mild thermal treatment conditions. To understand its structural formation and unique phase-transition processes, the locally detailed structure and molecular dynamics of its structural elements in disordered and ordered phases of C22PhBAEO3 were investigated using various solid-state (SS) NMR techniques at the atomic level. On the basis of the determined conformations and packing structures of the alkyl chains in ordered and disordered crystalline phases, along with the geometry and kinetic parameters of the structural elements' dynamics, this study addresses the self-assembly, the phase-transition mechanisms, and the relationship between the structure and dynamics of these asymmetric Janus bisamide supramolecules.
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Affiliation(s)
- Wei Chen
- Department of Polymer Science, The University of Akron , Akron, Ohio 44325-3909, United States
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15
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Schäler K, Achilles A, Bärenwald R, Hackel C, Saalwächter K. Dynamics in Crystallites of Poly(ε-caprolactone) As Investigated by Solid-State NMR. Macromolecules 2013. [DOI: 10.1021/ma401532v] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kerstin Schäler
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße
7, D-06120 Halle/Saale, Germany
| | - Anja Achilles
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße
7, D-06120 Halle/Saale, Germany
| | - Ruth Bärenwald
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße
7, D-06120 Halle/Saale, Germany
| | - Christiane Hackel
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße
7, D-06120 Halle/Saale, Germany
| | - Kay Saalwächter
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße
7, D-06120 Halle/Saale, Germany
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Krushelnitsky A, Reichert D, Saalwächter K. Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds. Acc Chem Res 2013; 46:2028-36. [PMID: 23875699 DOI: 10.1021/ar300292p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has matured to the point that it is possible to determine the structure of proteins in immobilized states, such as within microcrystals or embedded in membranes. Currently, researchers continue to develop and apply NMR techniques that can deliver site-resolved dynamic information toward the goal of understanding protein function at the atomic scale. As a widely-used, natural approach, researchers have mostly measured longitudinal (T1) relaxation times, which, like in solution-state NMR, are sensitive to picosecond and nanosecond motions, and motionally averaged dipolar couplings, which provide an integral amplitude of all motions with a correlation time of up to a few microseconds. While overall Brownian tumbling in solution mostly precludes access to slower internal dynamics, dedicated solid-state NMR approaches are now emerging as powerful new options. In this Account, we give an overview of the classes of solid-state NMR experiments that have expanded the accessible range correlation times from microseconds to many milliseconds. The measurement of relaxation times in the rotating frame, T1ρ, now allows researchers to access the microsecond range. Using our recent theoretical work, researchers can now quantitatively analyze this data to distinguish relaxation due to chemical-shift anisotropy (CSA) from that due to dipole-dipole couplings. Off-resonance irradiation allows researchers to extend the frequency range of such experiments. We have built multidimensional analogues of T2-type or line shape experiments using variants of the dipolar-chemical shift correlation (DIPSHIFT) experiment that are particularly suited to extract intermediate time scale motions in the millisecond range. In addition, we have continuously improved variants of exchange experiments, mostly relying on the recoupling of anisotropic interactions to address ultraslow motions in the ms to s ranges. The NH dipolar coupling offers a useful probe of local dynamics, especially with proton-depleted samples that suppress the adverse effect of strong proton dipolar couplings. We demonstrate how these techniques have provided a concise picture of the internal dynamics in a popular model system, the SH3 domain of α-spectrin. T1-based methods have shown that large-amplitude bond orientation fluctuations in the picosecond range and slower 10 ns low-amplitude motions coexist in these structures. When we include T1ρ data, we observe that many residues undergo low amplitude motions slower than 100 ns. On the millisecond to second scale, mostly localized but potentially cooperative motions occur. Comparing different exchange experiments, we found that terminal NH2 groups in side chains can even undergo a combination of ultraslow large-angle two-site jumps accompanied by small-angle fluctuations that occur 10 times more quickly.
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Affiliation(s)
- Alexey Krushelnitsky
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Detlef Reichert
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Kay Saalwächter
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
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