Influence of Arrestin on the Photodecay of Bovine Rhodopsin

Continued activation of the photocycle of the dim‐light receptor rhodopsin leads to the accumulation of all‐trans‐retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre‐activated truncated bovine visual arrestin (Arr^Tr) with rhodopsin in 1,2‐diheptanoyl‐sn‐glycero‐3‐phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin–arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr^Tr leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all‐trans‐retinal from rhodopsin.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan–Cyanovirin Interactions by Using 19F NMR Spectroscopy

NMR spectroscopy and isothermal titration calorimetry (ITC) are powerful methods to investigate ligand–protein interactions. Here, we present a versatile and sensitive fluorine NMR spectroscopic approach that exploits the ¹⁹F nucleus of ¹⁹F‐labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin‐N, a mannose binding anti‐HIV lectin. Two fluoro‐deoxy sugar derivatives, methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside and methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside were utilized. Binding was studied by ¹⁹F NMR spectroscopy of the ligand and ¹H–¹⁵N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that the strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding, as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin.     

Light Dynamics of the Retinal‐Disease‐Relevant G90D Bovine Rhodopsin Mutant

The RHO gene encodes the G‐protein‐coupled receptor (GPCR) rhodopsin. Numerous mutations associated with impaired visual cycle have been reported; the G90D mutation leads to a constitutively active mutant form of rhodopsin that causes CSNB disease. We report on the structural investigation of the retinal configuration and conformation in the binding pocket in the dark and light‐activated state by solution and MAS‐NMR spectroscopy. We found two long‐lived dark states for the G90D mutant with the 11‐cis retinal bound as Schiff base in both populations. The second minor population in the dark state is attributed to a slight shift in conformation of the covalently bound 11‐cis retinal caused by the mutation‐induced distortion on the salt bridge formation in the binding pocket. Time‐resolved UV/Vis spectroscopy was used to monitor the functional dynamics of the G90D mutant rhodopsin for all relevant time scales of the photocycle. The G90D mutant retains its conformational heterogeneity during the photocycle.     

pH‐dependent Interaction of Rhodopsin with Cyanidin‐3‐glucoside. 1. Structural Aspects†

Anthocyanins are a class of natural compounds common in flowers and vegetables. Because of the increasing preference of consumers for food containing natural colorants and the demonstrated beneficial effects of anthocyanins on human health, it is important to decipher the molecular mechanisms of their action. Previous studies indicated that the anthocyanin cyanidin‐3‐glucoside (C3G) modulates the function of the photoreceptor rhodopsin. In this paper, we show using selective excitation ¹H NMR spectroscopy that C3G binds to rhodopsin. Ligand resonances broaden upon rhodopsin addition and rhodopsin resonances exhibit chemical shift changes as well as broadening effects in specific resonances, in an activation state‐dependent manner. Furthermore, dark‐adapted and light‐activated states of rhodopsin show preferences for different C3G species. Molecular docking studies of the flavylium cation, quinoidal base, carbinol pseudobase and chalcone forms of C3G to models of the dark, light‐activated and opsin structures of rhodopsin also support this conclusion. The results provide new insights into anthocyanin–protein interactions and may have relevance for the enhancement of night vision by this class of compounds. This work is also the first report of the study of ligand binding to a full‐length membrane receptor in detergent micelles by ¹H NMR spectroscopy. Such studies were previously hampered by the presence of detergent micelle resonances, a problem overcome by the selective excitation approach.     

1H,89Y HMQC and Further NMR Spectroscopic and X‐ray Diffraction Investigations on Yttrium‐Containing Complexes Exhibiting Various Nuclearities

2D ¹H,⁸⁹Y heteronuclear shift correlation through scalar coupling has been applied to the chemical‐shift determination of a set of yttrium complexes with various nuclearities. This method allowed the determination of ⁸⁹Y NMR data in a short period of time. Multinuclear NMR spectroscopy as function of temperature, PGSE NMR‐diffusion experiments, heteronuclear NOE measurements, and X‐ray crystallography were applied to determine the structures of [Y₅(OH)₅(L ‐Val)₄(Ph₂acac)₆] ( 1 ) (Ph₂acac=dibenzoylmethanide, L ‐Val=L ‐valine), [Y( 2 )(OTf)₃] ( 3 ), and [Y₂( 4 )(OTf)₅] ( 5 ) ( 2 : [(S)P{N(Me)N?C(H)Py}₃], 4 : [B{N(Me)N?C(H)Py}₄]^?) in solution and in the solid state. The structures found in the solid state are retained in solution, where averaged structures were observed. NMR diffusion measurements helped us to understand the nuclearity of compounds 3 and 5 in solution. ¹H,¹⁹F HOESY and ¹⁹F,¹⁹F EXSY data revealed that the anions are specifically located in particular regions of space, which nicely correlated with the geometries found in the X‐ray structures.     

Direct Observation of Ca2+‐Induced Calmodulin Conformational Transitions in Intact Xenopus laevis Oocytes by 19F NMR Spectroscopy

The Ca²⁺‐mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by ¹⁹F NMR spectroscopy of the transition of the Ca²⁺‐free and ‐bound forms in Xenopus laevis oocytes at different Ca²⁺ levels. We find that the Ca²⁺‐bound CaM population increased greatly upon binding the target protein myosin light‐chain kinase (MLCK) at the same Ca²⁺ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long‐range structural constraints in cells. Our study shows that ¹⁹F NMR spectroscopy can be used to obtain long‐range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants.     

Technical and practical aspects of 19F NMR‐based screening: toward sensitive high‐throughput screening with rapid deconvolution

The technical and practical aspects of ¹⁹F NMR‐based screening against a macromolecular target are analyzed in detail. A novel method utilizing the relaxation of ¹⁹F homonuclear double quantum coherence is proposed for performing NMR‐based binding assays in a direct‐ or competition‐mode format. A combined strategy based on ¹⁹F NMR chemical shift prediction, 2D ¹⁹F NMR DOSY, and 2D ¹⁹F–¹H NMR long‐range COSY experiments is presented for the deconvolution of complex mixtures of fluorinated molecules generated by either addition of single compounds or by chemical synthesis. The approaches presented here allow the screening of complex mixtures, even in the case where the exact composition is not known, and the rapid identification of the binders contained in the mixtures. Copyright © 2012 John Wiley & Sons, Ltd.     

1H‐19F REDOR‐filtered NMR spin diffusion measurements of domain size in heterogeneous polymers

Solid state NMR spectroscopy is inherently sensitive to chemical structure and composition and thus makes an ideal method to probe the heterogeneity of multicomponent polymers. Specifically, NMR spin diffusion experiments can be used to extract reliable information about spatial domain sizes on multiple length scales, provided that magnetization selection of one domain can be achieved. In this paper, we demonstrate the preferential filtering of protons in fluorinated domains during NMR spin diffusion experiments using ¹H‐¹⁹F heteronuclear dipolar dephasing based on rotational echo double resonance (REDOR) MAS NMR techniques. Three pulse sequence variations are demonstrated based on the different nuclei detected: direct ¹H detection, plus both ¹H?¹³C cross polarization and ¹H?¹⁹F cross polarization detection schemes. This ¹H‐¹⁹F REDOR‐filtered spin diffusion method was used to measure fluorinated domain sizes for a complex polymer blend. The efficacy of the REDOR‐based spin filter does not rely on spin relaxation behavior or chemical shift differences and thus is applicable for performing NMR spin diffusion experiments in samples where traditional magnetization filters may prove unsuccessful. This REDOR‐filtered NMR spin diffusion method can also be extended to other samples where a heteronuclear spin pair exists that is unique to the domain of interest.     

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

19F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis

Ligand‐based ¹⁹F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the ¹⁹F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the ¹⁹F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the ¹⁹F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment‐based screening. Copyright © 2016 John Wiley & Sons, Ltd.     

Complexes of Chlorin e6 with Pluronics and Polyvinylpyrrolidone: Structure and Photodynamic Activity in Cell Culture

Polymeric carriers are extensively used in photodynamic therapy (PDT) for increase of efficacy of photosensitizers. Here, we report the influence of nine Pluronic copolymers on phototoxicity of chlorin e6 (Ce6), in particular 5‐ to 7‐fold rise in the phototoxicity caused by hydrophilic Pluronics F127, F108, F68 and F87 and practically no influence on Ce6 of more hydrophobic polymers. The revealed value of 0.2 mg mL^?1 of Pluronic F127 concentration sufficient for half‐of‐maximal increase of Ce6 photodynamic activity proved to be close to 0.16 mg mL^?1 inherent in well‐documented carrier poly(N‐vinylpyrrolidone) (PVP). The dissociation constants of Ce6 complexes with Pluronic F127 and PVP that were estimated from UV spectra were 0.252 and 0.036 mg mL^?1, respectively, indicating higher stability of Ce6 complex with PVP. According to the results of ¹H‐NMR studies of Ce6 complexes, the porphyrin interacts not only with hydrophobic regions but also with hydrophilic sides of both polymers.     

pH‐dependent Interaction of Rhodopsin with Cyanidin‐3‐glucoside. 2. Functional Aspects†

Anthocyanins are a class of phytochemicals that confer color to flowers, fruits, vegetables and leaves. They are part of our regular diet and serve as dietary supplements because of numerous health benefits, including improved vision. Recent studies have shown that the anthocyanin cyanidin‐3‐O‐glucoside (C3G) increased regeneration of the dim‐light photoreceptor rhodopsin (Matsumoto et al. [2003] J. Agric. Food Chem., 51 , 3560–3563). In an accompanying study (Yanamala et al. [2009] Photochem. Photobiol.), we show that C3G directly binds to rhodopsin in a pH‐dependent manner. In this study, we investigated the functional consequences of C3G binding to rhodopsin. As observed previously in rod outer segments, regeneration of purified rhodopsin in detergent micelles is also accelerated in the presence of C3G. Thermal denaturation and stability studies using circular dichroism, fluorescence and UV/visible absorbance spectroscopy show that C3G exerts a destabilizing effect on rhodopsin structure while it only modestly alters G‐protein activation and the rates at which the light‐activated Metarhodopsin II state decays to opsin and free retinal. These results indicate that the mechanism of C3G‐enhanced regeneration may be based on changes in opsin structure promoting access to the retinal binding pocket.     

Aryl‐Phosphonate Lanthanide Complexes and Their Fluorinated Derivatives: Investigation of Their Unusual Relaxometric Behavior and Potential Application as Dual Frequency 1H/19F MRI Probes

A series of low molecular weight lanthanide complexes were developed that have high ¹H longitudinal relaxivities (r₁) and the potential to be used as dual frequency ¹H and ¹⁹F MR probes. Their behavior was investigated in more detail through relaxometry, pH‐potentiometry, luminescence, and multinuclear NMR spectroscopy. Fitting of the ¹H NMRD and ¹⁷O NMR profiles demonstrated a very short water residence lifetime (<10 ns) and an appreciable second sphere effect. At lower field strengths (20 MHz), two of the complexes displayed a peak in r₁ (21.7 and 16.3 mM ^?1 s^?1) caused by an agglomeration, that can be disrupted through the addition of phosphate anions. NMR spectroscopy revealed that at least two species are present in solution interconverting through an intramolecular binding process. Two complexes provided a suitable signal in ¹⁹F NMR spectroscopy and through the selection of optimized imaging parameters, phantom images were obtained in a MRI scanner at concentrations as low as 1 mM . The developed probes could be visualized through both ¹H and ¹⁹F MRI, showing their capability to function as dual frequency MRI contrast agents.     

Synthesis,Characterization, and Conformational Study of Acylhydrazones of α,β‐Unsaturated Aldehydes

New acylhydrazone derivatives 1–6 have been synthesized by condensation of tert‐butylphenoxyhydrazide and cinnamaldehyde A or β‐chloro‐α,β‐unsaturated aldehydes B–F . They were characterized by IR, (¹H, ¹³C, ¹⁹F) nuclear magnetic resonance (NMR), and high‐resolution mass spectroscopy. The NMR data show the existence of the cis/trans‐amide conformers due to N–C(O) bond rotation in addition to the E/Z isomers around the C=C bond of some of the starting aldehydes. The solvent polarity effects on the ratios of the cis/trans‐amide rotamers have also been investigated. Importantly, rotational barriers around the N–C(O) bond for all compounds 1–6 (62.9–68.8 kJ mol^–1) were calculated using the coalescence‐temperature method according to the Eyring equation. The results are discussed and compared with those previously reported for related acylhydrazones of aryl adehydes and acetone.     

Labeling Strategy and Signal Broadening Mechanism of Protein NMR Spectroscopy in Xenopus laevis Oocytes

We used Xenopus laevis oocytes, a paradigm for a variety of biological studies, as a eukaryotic model system for in‐cell protein NMR spectroscopy. The small globular protein GB1 was one of the first studied in Xenopus oocytes, but there have been few reports since then of high‐resolution spectra in oocytes. The scarcity of data is at least partly due to the lack of good labeling strategies and the paucity of information on resonance broadening mechanisms. Here, we systematically evaluate isotope enrichment and labeling methods in oocytes injected with five different proteins with molecular masses of 6 to 54 kDa. ¹⁹F labeling is more promising than ¹⁵N, ¹³C, and ²H enrichment. We also used ¹⁹F NMR spectroscopy to quantify the contribution of viscosity, weak interactions, and sample inhomogeneity to resonance broadening in cells. We found that the viscosity in oocytes is only about 1.2 times that of water, and that inhomogeneous broadening is a major factor in determining line width in these cells.     

Synthesis,Characterization, Optical and Electrochemical Properties of Fulleropyrrolidines Containing Trifluoromethyl Group

Four novel [60]fullerene pyrrolidines containing trifluoromethyl (? CF₃) group have been synthesized via 1,3‐dipolar cycloaddition reaction, which have been characterized by UV‐Vis spectroscopy, fourier transform infrared spectroscopy, matrix‐assisted laser desorption ionization‐time of flight mass spectroscopy, and ¹H, ¹³C, ¹⁹F nuclear magnetic resonance spectrometer (¹H NMR, ¹³C NMR, ¹⁹F NMR). Their optical and electrochemical properties have been studied, and the results show that those fulleropyrrolidines containing ? CF₃ group have good fluorescence and electrochemical properties. Compared with C₆₀, they have negative shifts in varying degrees for half‐wave potentials, and may have potential applications for photovoltaic conversion materials since their lowest unoccupied molecular orbital (LUMO) levels are close to that of [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester.     

Syntheses and Spectroscopic Study of Some New N‐4‐Fluorobenzoyl Phosphoric Triamides; Crystal Structures of 4‐F‐C6H4C(O)N(H)P(O)R2, R = NH‐C(CH3)3, NH‐CH2C6H5, N(CH3)(CH2C6H5)

Some new N‐4‐Fluorobenzoyl phosphoric triamides with formula 4‐F‐C₆H₄C(O)N(H)P(O)X₂, X = NH‐C(CH₃)₃ ( 1 ), NH‐CH₂‐CH=CH₂ ( 2 ), NH‐CH₂C₆H₅ ( 3 ), N(CH₃)(C₆H₅) ( 4 ), NH‐CH(CH₃)(C₆H₅) ( 5 ) were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR and Mass spectroscopy and elemental analysis. The structures of compounds 1 , 3 and 4 were investigated by X‐ray crystallography. The P=O and C=O bonds in these compounds are anti. Compounds 1 and 3 form one dimensional polymeric chain produced by intra‐ and intermolecular ‐P=O···H‐N‐ hydrogen bonds. Compound 4 forms only a centrosymmetric dimer in the crystalline lattice via two equal ‐P=O···H‐N‐ hydrogen bonds. ¹H and ¹³C NMR spectra show two series of signals for the two amine groups in compound 1 . This is also observed for the two α‐methylbenzylamine groups in 5 due to the presence of chiral carbon atom in molecule. ¹³C NMR spectrum of compound 4 shows that ²J(P,C_aliphatic) coupling constant for CH₂ group is greater than for CH₃ in agreement with our previous study. Mass spectra of compounds 1 ‐ 3 (containing 4‐F‐C₆H₄C(O)N(H)P(O) moiety) indicate the fragments of amidophosphoric acid and 4‐F‐C₆H₄CN⁺ that formed in a pseudo McLafferty rearrangement pathway. Also, the fragments of aliphatic amines have high intensity in mass spectra.     

19F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins

Fluorine NMR paramagnetic relaxation enhancement was evaluated as a versatile approach for extracting distance information in selectively F‐labeled proteins. Proof of concept and initial applications are presented for the HIV‐inactivating lectin cyanovirin‐N. Single F atoms were introduced at the 4‐, 5‐, 6‐ or 7 positions of Trp49 and the 4‐position of Phe4, Phe54, and Phe80. The paramagnetic nitroxide spin label was attached to Cys residues that were placed into the protein at positions 50 or 52. ¹⁹F‐T₂ NMR spectra with different relaxation delays were recorded and the transverse ¹⁹F‐PRE rate, ¹⁹F‐Γ₂, was used to determine the average distance between the F nucleus and the paramagnetic center. Our data show that experimental ¹⁹F PRE‐based distances correspond to 0.93 of the ¹H_N‐PRE distances, in perfect agreement with the gyromagnetic γ¹⁹F/γ¹H ratio, thereby demonstrating that ¹⁹F PREs are excellent alternative parameters for quantitative distance measurements in selectively F‐labeled proteins.