scholarly journals Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR

2021 ◽  
Author(s):  
◽  
Orawan Jakdetchai
Keyword(s):  
Schiff Base ◽  
Proton Transfer ◽  
Positive Charge ◽  
Chemical Shifts ◽  
Mas Nmr ◽  
Sodium Ion ◽  
Proton Acceptor ◽  
Magic Angle ◽  
Ion Pump ◽  
Dark State

KR2 is a light-driven sodium ion pump found in marine flavobacterium Krokinobacter Eikastus. The protein belongs to the microbial rhodopsin family, which is characterized by seven transmembrane helices and a retinal cofactor covalently bound to a conserved lysine residue through a Schiff base linkage. Specific features of KR2 and other sodium pumping rhodopsins are the NDQ motif, the N-terminal helix capping the protein at the extracellular side, and the sodium ion bound at the protomer interface in the pentameric structure. The ability to pump sodium ions was a surprising discovery since the positive charge at the Schiff base was long thought to hinder the transport of non-proton cations and the Grotthuss mechanism could not be applied to explain the Na+ transport. The photocycle of KR2 revealed by flashed photolysis and ultrafast femtosecond absorption spectroscopy consists of consecutive intermediates, named K, L, M, and O. Here, DNP-enhanced ssNMR was used to analyze various aspects of these intermediate states. The K/L-state can be generated and trapped by in-situ illumination inside the magnet at 110 K. The trapping of L-state together with the K-state at this temperature is unexpected as this usually leads to the trapping of only K-state in bacteriorhodopsin (BR), proteorhodopsin (PR), and channelrhodopsin 2 (ChR2). This observation suggests a lower energy barrier between K- and L-state in KR2. For the O-state, the intermediate was generated by illuminating outside the magnet, followed by rapid freezing in liquid nitrogen and transfer to the magnet. Based on these procedures, the retinal conformation, and the electrostatic environment at the Schiff base in KR2 dark, K-, L- and O-intermediates were probed using 13C-labeled retinals bound to 15N-labeled KR2 by both 1D and 2D magic angle spinning (MAS) NMR experiments. The obtained data show an all-trans retinal conformation with the distortion of 150° at H-C14-C15-H in the dark state whereas the retinal has a 13-cis, 15-anti conformation in the K- and L-state after light activation. Differences between K- and L-intermediates were observed. The retinal chemical shifts of the K-state show a large deviation from the model compound behavior between the middle and end part of the polyene chain. In the L-state, these differences are much less pronounced. These observations indicate that the light energy stored in the K-state dissipates into the protein in the subsequent photointermediate states. Furthermore, an additional shielding observed for C14 in L-state indicates the slight rotation toward a more compact 13-cis, 15-syn conformation. The distortion of the H-C14-C15-H angle in the L-state (136°) is larger than in the dark state. This twist of the retinal in the L-state would play an important role in lowering the pKa of the Schiff base, which is a prerequisite for the proton transfer from the Schiff base to the proton acceptor (D116). The electrostatic environments at the Schiff base in K- and L-states cause a de-shielding of the 15N nitrogen compared to the dark state. This indicates a stepwise stronger interaction with the counterion as the Schiff base proton moves away from the Schiff base and comes closer to the D116 in the transition from K- to L-state and approaches the proton transfer step during the M-state formation. In the O-state, the retinal was found to be in the all-trans conformation but differed to the dark state in the C13, C20, and Schiff base nitrogen chemical shifts. The largest effect (9 ppm) was observed for the Schiff base nitrogen, which could be explained by the effect of the positive charge of bound Na+ near the Schiff base in the O-state, coordinated by N112 and D116 as observed in the O-state crystal structure in the pentameric form. The structural change at the opsin followed the retinal isomerization and the energy transfer from the chromophore to the surrounding were also investigated in this thesis using various amino acids labeling schemes. Moreover, 1H-13C hNOE in combination with CE-DNP was applied to probe the dynamics of retinylidene methyl groups and 23Na MAS NMR was employed to detect the bound sodium ion at the protomer interface in KR2 dark state.

scholarly journals Photocycle-dependent conformational changes in the proteorhodopsin cross-protomer Asp–His–Trp triad revealed by DNP-enhanced MAS-NMR

2019 ◽  
Vol 116 (17) ◽  
pp. 8342-8349 ◽  
Author(s):  
Jakob Maciejko ◽  
Jagdeep Kaur ◽  
Johanna Becker-Baldus ◽  
Clemens Glaubitz
Keyword(s):  
Proton Transfer ◽  
Conformational Changes ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Proton Acceptor ◽  
Primary Proton ◽  
Magic Angle ◽  
Drastic Effect ◽  
Microbial Rhodopsin ◽  
Angle Spinning

Proteorhodopsin (PR) is a highly abundant, pentameric, light-driven proton pump. Proton transfer is linked to a canonical photocycle typical for microbial ion pumps. Although the PR monomer is able to undergo a full photocycle, the question arises whether the pentameric complex formed in the membrane via specific cross-protomer interactions plays a role in its functional mechanism. Here, we use dynamic nuclear polarization (DNP)-enhanced solid-state magic-angle spinning (MAS) NMR in combination with light-induced cryotrapping of photointermediates to address this topic. The highly conserved residue H75 is located at the protomer interface. We show that it switches from the (τ)- to the (π)-tautomer and changes its ring orientation in the M state. It couples to W34 across the oligomerization interface based on specific His/Trp ring orientations while stabilizing the pKaof the primary proton acceptor D97 within the same protomer. We further show that specific W34 mutations have a drastic effect on D97 and proton transfer mediated through H75. The residue H75 defines a cross-protomer Asp–His–Trp triad, which potentially serves as a pH-dependent regulator for proton transfer. Our data represent light-dependent, functionally relevant cross talk between protomers of a microbial rhodopsin homo-oligomer.

scholarly journals Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil

2017 ◽  
Vol 73 (3) ◽  
pp. 149-156 ◽  
Author(s):  
Ann-Christin Pöppler ◽  
Emily K. Corlett ◽  
Harriet Pearce ◽  
Mark P. Seymour ◽  
Matthew Reid ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Chemical Shifts ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Double Quantum ◽  
Magic Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Nmr Crystallography

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile–4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1H and 13C chemical shifts are determined from two-dimensional 1H–13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C—H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N—H...O and C—H...O hydrogen bonding, while changes of −2.7 and −1.5 ppm are due to ring current effects associated with C—H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

A multinuclear MAS NMR study of the short-range structure of fluorophosphate glass

1992 ◽  
Vol 7 (7) ◽  
pp. 1892-1899 ◽  
Author(s):  
R.K. Brow ◽  
Z.A. Osborne ◽  
R.J. Kirkpatrick
Keyword(s):  
Nmr Spectra ◽  
Chemical Shifts ◽  
Spectroscopic Studies ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Magic Angle ◽  
Nmr Studies ◽  
Nmr Study ◽  
Fluorophosphate Glass ◽  
Angle Spinning

We have examined the bonding arrangements in Na–P–O–F and Na–Al–P–O–F glasses using 19F, 27Al, and 31P solid-state magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy. For the Al-free series of glasses, the 19F NMR spectra are dominated by peaks near +90 ppm, representative of F terminating P-chains. The formation of these bonds has little effect on the 31P chemical shifts, indicating that F preferentially replaces bridging oxygen on the phosphate tetrahedra, consistent with previous NMR studies of crystalline fluorophosphates and other spectroscopic studies of fluorophosphate glass. For the Na–Al–P–O–F glasses, 27Al NMR detects only octahedral Al-sites, the 19F NMR spectra include a second peak near −12 ppm due to F bonded to Al, and the 31P NMR spectra contain signals due to Q1-sites with one or more Al next-nearest neighbors. The relative intensity of the two 19F peaks correlates well with previous spectroscopic studies and shows that a greater fraction of F–P bonds forms when the base glass is remelted in NH4HF2.

119Sn Magic Angle Spinning NMR of Nanocrystalline SnO2

2008 ◽  
Vol 8 (1) ◽  
pp. 321-328 ◽  
Author(s):  
V. Sabarinathan ◽  
C. Vinod Chandran ◽  
S. Ramasamy ◽  
S. Ganapathy
Keyword(s):  
Chemical Shifts ◽  
Life Time ◽  
Local Symmetry ◽  
Chemical Precipitation ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Precipitation Method ◽  
Magic Angle ◽  
Spin Lattice ◽  
Grain Sizes

Nanocrystalline SnO2 samples of different grain sizes, prepared by inert gas condensation technique (IGCT) and chemical precipitation method and conforming to the tetragonal phase, have been studied by variable speed (3–10 kHz) 119Sn MAS NMR at 11.74 Tesla field. 119Sn solid-state NMR results show that the IGCT prepared samples have good crystallinity and phase purity compared to the samples prepared by the chemical method. The determination of 119Sn chemical shielding parameters (δiso, Δδ and η) from slow MAS spectra shows that the 119Sn isotropic chemical shift (δiso) is strongly influenced at smaller grain sizes, attributable to the change in the O2− local symmetry for the surface 119Sn ions at smaller grain sizes. The observed line widths in MAS spectra are significantly larger than the life-time broadening due to spin–lattice (T1) and spin–spin (T2) relaxation. The 119Sn MAS NMR spectra are thus inhomogeneously broadened by a distribution of isotropic chemical shifts, the line broadening increasing with decrease in grain size.

scholarly journals Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR

2021 ◽  
Vol 7 (11) ◽  
pp. eabf4213
Author(s):  
Orawan Jakdetchai ◽  
Peter Eberhardt ◽  
Marvin Asido ◽  
Jagdeep Kaur ◽  
Clara Nassrin Kriebel ◽  
...  
Keyword(s):  
Solid State ◽  
Nuclear Polarization ◽  
Chemical Shifts ◽  
Three Dimensional ◽  
Sodium Ion ◽  
Resonance Spectroscopy ◽  
Proton Pumps ◽  
Ion Pump ◽  
Trans Conformation ◽  
Out Of Plane

The functional mechanism of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) raises fundamental questions since the transfer of cations must differ from the better-known principles of rhodopsin-based proton pumps. Addressing these questions must involve a better understanding of its photointermediates. Here, dynamic nuclear polarization–enhanced solid-state nuclear magnetic resonance spectroscopy on cryo-trapped photointermediates shows that the K-state with 13-cis retinal directly interconverts into the subsequent L-state with distinct retinal carbon chemical shift differences and an increased out-of-plane twist around the C14-C15 bond. The retinal converts back into an all-trans conformation in the O-intermediate, which is the key state for sodium transport. However, retinal carbon and Schiff base nitrogen chemical shifts differ from those observed in the KR2 dark state all-trans conformation, indicating a perturbation through the nearby bound sodium ion. Our findings are supplemented by optical and infrared spectroscopy and are discussed in the context of known three-dimensional structures.

The Spectroscopy Characterization of Kaolinite-Organic Intercalation Materials

2007 ◽  
Vol 353-358 ◽  
pp. 1362-1365 ◽  
Author(s):  
Lin Jiang Wang ◽  
Xiang Li Xie ◽  
Da Qing Wu
Keyword(s):  
Chemical Shifts ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
1H Mas Nmr ◽  
Surface Hydroxyl ◽  
Inner Surface ◽  
Ft Ir ◽  
Intercalation Materials

Kaolinite/formamide intercalation materials are characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy(FT-IR), Raman spectroscopy and 1H magic angle spinning nuclear magnetic resonance spectroscopy (1H MAS NMR). The d(001) spacing of kaolinite treated with formamide is 1.020nm, which is larger than that of the original clay. The 1H MAS NMR graphs show that the proton chemical shifts of the inner hydroxyl and inner surface hydroxyl of kaolinte are δ-1.3 and δ2.4 respectively. After formamide intercalation, the proton peaks of the inner surface hydroxyls shifted to high-field with δ2.3, the proton peak of the inner hydroxyl shifted to δ-0.3 toward low-field. In the hydroxyl stretching vibration region of Raman spectrum, the formamide intercalation resulted in the decrease of the intensities of kaolinite inner surface hydroxyl bands at 3699cm-1,3682cm-1, 3665cm-1 and 3642cm-1, and the appearance of additional bands at 3610cm-1,3628cm-1. In the NH stretching region of FT-IR spectrum, two bands are observed at 3336cm-1 and 3466cm-1 corresponding to the two types of the hydrogen bonds between formamide and kaolinite. In the carboxyl stretching region, an additional band at 1667cm-1 is assigned to C=O group that bonded to the inner surface hydroxyl of kaolinite.

scholarly journals Physicochemical properties and structural dynamics of organic–inorganic hybrid [NH3(CH2)3NH3]ZnX4 (X = Cl and Br) crystals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ae Ran Lim ◽  
Sun Ha Kim ◽  
Yong Lak Joo
Keyword(s):  
Structural Dynamics ◽  
Chemical Shifts ◽  
Lattice Relaxation ◽  
Magic Angle Spinning ◽  
Spin Lattice Relaxation ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Scanning Calorimetry ◽  
Inorganic Hybrid ◽  
Halogen Atoms

AbstractThe physical properties of the organic–inorganic hybrid crystals having the formula [NH3(CH2)3NH3]ZnX4 (X = Cl, Br) were investigated. The phase transition temperatures (TC; 268K for Cl and 272K for Br) of the two crystals bearing different halogen atoms in their skeletons were determined through differential scanning calorimetry. The thermodynamic properties of the two crystals were investigated through thermogravimetric analysis. The structural dynamics, particularly the role of the [NH3(CH2)3NH3] cation, were probed through 1H and 13C magic-angle spinning nuclear magnetic resonance spectroscopy as a function of temperature. The 1H and 13C NMR chemical shifts did not show any changes near TC. In addition, the 1H spin–lattice relaxation time (T1ρ) varied with temperature, whereas the 13C T1ρ values remained nearly constant at different temperatures. The T1ρ values of the atoms in [NH3(CH2)3NH3]ZnCl4 were higher than those in [NH3(CH2)3NH3]ZnBr4. The observed differences in the structural dynamics obtained from the chemical shifts and T1ρ values of the two compounds can be attributed to the differences in the bond lengths and halogen atoms. These findings can provide important insights or potential applications of these crystals.

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