Expression systems for bovine rhodopsin: a review of the progress made in the Khorana laboratory.

Here I will review the development of gene expression systems for production of bovine rhodopsin in the Khorana laboratory with particular focus on stable mammalian cell lines made using human embryonic kidney cells (HEK293S). The synthesis of a gene encoding bovine rhodopsin was completed in 1986. This gene was expertly designed with the built-in capacity for DNA duplex cassette replacement mutagenesis which made site-directed mutagenesis relatively straightforward. Intense effort was expended over several years in order to identify a gene expression system capable of producing rhodopsin in milligram amounts as required for biophysical studies. Mammalian expression systems, both transient and stable, were found to be the most favourable based on several criteria including receptor expression levels, correct folding and post translational processing, and capacity for purification of fully functional receptor. Transient expression using COS-1 cells was preferred for routine small-scale production of rhodopsin mutants, while HEK293S stable cell lines were used when milligram amounts of rhodopsin mutants were needed; for example, when conducting NMR studies.

17O NMR Spectroscopy in Lithium-Ion Battery Cathode Materials: Challenges and Interpretation.

Modern studies of lithium-ion battery (LIB) cathode materials employ a large range of experimental and theoretical techniques to understand the changes in bulk and local chemical and electronic structures during electrochemical cycling (charge and discharge). Despite its being rich in useful chemical information, few studies to date have used 17O NMR spectroscopy. Many LIB cathode materials contain paramagnetic ions, and their NMR spectra are dominated by hyperfine and quadrupolar interactions, giving rise to broad resonances with extensive spinning sideband manifolds. In principle, careful analysis of these spectra can reveal information about local structural distortions, magnetic exchange interactions, structural inhomogeneities (Li+ concentration gradients), and even the presence of redox-active O anions. In this Perspective, we examine the primary interactions governing 17O NMR spectroscopy of LIB cathodes and outline how 17O NMR may be used to elucidate the structure of pristine cathodes and their structural evolution on cycling, providing insight into the challenges in obtaining and interpreting the spectra. We also discuss the use of 17O NMR in the context of anionic redox and the role this technique may play in understanding the charge compensation mechanisms in high-capacity cathodes, and we provide suggestions for employing 17O NMR in future avenues of research.

Differences in SMA-like polymer architecture dictate the conformational changes exhibited by the membrane protein rhodopsin encapsulated in lipid nano-particles.

Membrane proteins are of fundamental importance to cellular processes and nano-encapsulation strategies that preserve their native lipid bilayer environment are particularly attractive for studying and exploiting these proteins. Poly(styrene-co-maleic acid) (SMA) and related polymers poly(styrene-co-(N-(3-N',N'-dimethylaminopropyl)maleimide)) (SMI) and poly(diisobutylene-alt-maleic acid) (DIBMA) have revolutionised the study of membrane proteins by spontaneously solubilising membrane proteins direct from cell membranes within nanoscale discs of native bilayer called SMA lipid particles (SMALPs), SMILPs and DIBMALPs respectively. This systematic study shows for the first time, that conformational changes of the encapsulated protein are dictated by the solubilising polymer. The photoactivation pathway of rhodopsin (Rho), a G-protein-coupled receptor (GPCR), comprises structurally-defined intermediates with characteristic absorbance spectra that revealed conformational restrictions with styrene-containing SMA and SMI, so that photoactivation proceeded only as far as metarhodopsin-I, absorbing at 478 nm, in a SMALP or SMILP. In contrast, full attainment of metarhodopsin-II, absorbing at 382 nm, was observed in a DIBMALP. Consequently, different intermediate states of Rho could be generated readily by simply employing different SMA-like polymers. Dynamic light-scattering and analytical ultracentrifugation revealed differences in size and thermostability between SMALP, SMILP and DIBMALP. Moreover, encapsulated Rho exhibited different stability in a SMALP, SMILP or DIBMALP. Overall, we establish that SMA, SMI and DIBMA constitute a 'toolkit' of solubilising polymers, so that selection of the appropriate solubilising polymer provides a spectrum of useful attributes for studying membrane proteins.

Structural Origins of Voltage Hysteresis in the Na-Ion Cathode P2-Na0.67[Mg0.28Mn0.72]O2: A Combined Spectroscopic and Density Functional Theory Study.

P2-layered sodium-ion battery (NIB) cathodes are a promising class of Na-ion electrode materials with high Na+ mobility and relatively high capacities. In this work, we report the structural changes that take place in P2-Na0.67[Mg0.28Mn0.72]O2. Using ex situ X-ray diffraction, Mn K-edge extended X-ray absorption fine structure, and 23Na NMR spectroscopy, we identify the bulk phase changes along the first electrochemical charge-discharge cycle-including the formation of a high-voltage "Z phase", an intergrowth of the OP4 and O2 phases. Our ab initio transition state searches reveal that reversible Mg2+ migration in the Z phase is both kinetically and thermodynamically favorable at high voltages. We propose that Mg2+ migration is a significant contributor to the observed voltage hysteresis in Na0.67[Mg0.28Mn0.72]O2 and identify qualitative changes in the Na+ ion mobility.

Construction of Recombinant Cell Lines for GPCR Expression.

Large-scale recombinant expression of G protein-coupled receptors (GPCRs) is required for structure and function studies where there is a need for milligram amounts of protein in pure form. Here we describe a procedure for the construction of human embryonic kidney 293S (HEK293S) stable cell lines for inducible expression of the gene encoding bovine rhodopsin. The HEK293S cell line is particularly suitable for this application because of several favorable properties as a recombinant host including: its ease of transfection, its capacity for handling large amounts of protein cargo, and its ability to perform the necessary co- and post-translational modifications required for correct folding and processing of complex membrane proteins such as GPCRs. The procedures described here will focus on the HEK293S GnTI- cell line, an HEK293S derivative that is widely used for the production of glycoproteins modified homogeneously with truncated N-glycans.

Bulk fatigue induced by surface reconstruction in layered Ni-rich cathodes for Li-ion batteries.

Ni-rich layered cathode materials are among the most promising candidates for high-energy-density Li-ion batteries, yet their degradation mechanisms are still poorly understood. We report a structure-driven degradation mechanism for NMC811 (LiNi0.8Mn0.1Co0.1O2), in which a proportion of the material exhibits a lowered accessible state of charge at the end of charging after repetitive cycling and becomes fatigued. Operando synchrotron long-duration X-ray diffraction enabled by a laser-thinned coin cell shows the emergence and growth in the concentration of this fatigued phase with cycle number. This degradation is structure driven and is not solely due to kinetic limitations or intergranular cracking: no bulk phase transformations, no increase in Li/Ni antisite mixing and no notable changes in the local structure or Li-ion mobility of the bulk are seen in aged NMCs. Instead, we propose that this degradation stems from the high interfacial lattice strain between the reconstructed surface and the bulk layered structure that develops when the latter is at states of charge above a distinct threshold of approximately 75%. This mechanism is expected to be universal in Ni-rich layered cathodes. Our findings provide fundamental insights into strategies to help mitigate this degradation process.

Bulk and Surface Chemistry of the Niobium MAX and MXene Phases from Multinuclear Solid-State NMR Spectroscopy.

MXenes, derived from layered MAX phases, are a class of two-dimensional materials with emerging applications in energy storage, electronics, catalysis, and other fields due to their high surface areas, metallic conductivity, biocompatibility, and attractive optoelectronic properties. MXene properties are heavily influenced by their surface chemistry, but a detailed understanding of the surface functionalization is still lacking. Solid-state nuclear magnetic resonance (NMR) spectroscopy is sensitive to the interfacial chemistry, the phase purity including the presence of amorphous/nanocrystalline phases, and the electronic properties of the MXene and MAX phases. In this work, we systematically study the chemistry of Nb MAX and MXene phases, Nb2AlC, Nb4AlC3, Nb2CTx, and Nb4C3Tx, with their unique electronic and mechanical properties, using solid-state NMR spectroscopy to examine a variety of nuclei (1H, 13C, 19F, 27Al, and 93Nb) with a range of one- and two-dimensional correlation, wide-line, high-sensitivity, high-resolution, and/or relaxation-filtered experiments. Hydroxide and fluoride terminations are identified, found to be intimately mixed, and their chemical shifts are compared with other MXenes. This multinuclear NMR study demonstrates that diffraction alone is insufficient to characterize the phase composition of MAX and MXene samples as numerous amorphous or nanocrystalline phases are identified including NbC, AlO6 species, aluminum nitride or oxycarbide, AlF3·nH2O, Nb metal, and unreacted MAX phase. To the best of our knowledge, this is the first study to examine the transition-metal resonances directly in MXene samples, and the first 93Nb NMR of any MAX phase. The insights from this work are employed to enable the previously elusive assignment of the complex overlapping 47/49Ti NMR spectrum of Ti3AlC2. The results and methodology presented here provide fundamental insights on MAX and MXene phases and can be used to obtain a more complete picture of MAX and MXene chemistry, to prepare realistic structure models for computational screening, and to guide the analysis of property measurements.

A Conserved Proline Hinge Mediates Helix Dynamics and Activation of Rhodopsin.

Despite high-resolution crystal structures of both inactive and active G protein-coupled receptors (GPCRs), it is still not known how ligands trigger the large structural change on the intracellular side of the receptor since the conformational changes that occur within the extracellular ligand-binding region upon activation are subtle. Here, we use solid-state NMR and Fourier transform infrared spectroscopy on rhodopsin to show that Trp2656.48 within the CWxP motif on transmembrane helix H6 constrains a proline hinge in the inactive state, suggesting that activation results in unraveling of the H6 backbone within this motif, a local change in dynamics that allows helix H6 to swing outward. Notably, Tyr3017.48 within activation switch 2 appears to mimic the negative allosteric sodium ion found in other family A GPCRs, a finding that is broadly relevant to the mechanism of receptor activation.

Intrinsic Kinetic Limitations in Substituted Lithium-Layered Transition-Metal Oxide Electrodes.

Substituted Li-layered transition-metal oxide (LTMO) electrodes such as LixNiyMnzCo1-y-zO2 (NMC) and LixNiyCo1-y-zAlzO2 (NCA) show reduced first cycle Coulombic efficiency (90-87% under standard cycling conditions) in comparison with the archetypal LixCoO2 (LCO; ∼98% efficiency). Focusing on LixNi0.8Co0.15Al0.05O2 as a model compound, we use operando synchrotron X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) spectroscopy to demonstrate that the apparent first-cycle capacity loss is a kinetic effect linked to limited Li mobility at x > 0.88, with near full capacity recovered during a potentiostatic hold following the galvanostatic charge-discharge cycle. This kinetic capacity loss, unlike many capacity losses in LTMOs, is independent of the cutoff voltage during delithiation and it is a reversible process. The kinetic limitation manifests not only as the kinetic capacity loss during discharge but as a subtle bimodal compositional distribution early in charge and, also, a dramatic increase of the charge-discharge voltage hysteresis at x > 0.88. 7Li NMR measurements indicate that the kinetic limitation reflects limited Li transport at x > 0.86. Electrochemical measurements on a wider range of LTMOs including Lix(Ni,Fe)yCo1-yO2 suggest that 5% substitution is sufficient to induce the kinetic limitation and that the effect is not limited to Ni substitution. We outline how, in addition to a reduction in the number of Li vacancies and shrinkage of the Li-layer size, the intrinsic charge storage mechanism (two-phase vs solid-solution) and localization of charge give rise to additional kinetic barriers in NCA and nonmetallic LTMOs in general.

Short-range ordering in a battery electrode, the 'cation-disordered' rocksalt Li1.25Nb0.25Mn0.5O2.

Cation order, with a local structure related to γ-LiFeO2, is observed in the nominally cation-disordered Li-excess rocksalt Li1.25Nb0.25Mn0.5O2via X-ray diffraction, neutron pair distribution function analysis, magnetic susceptibility and NMR spectroscopy. The correlation length of ordering depends on synthesis conditions and has implications for the electrochemistry of these phases.

Electrochemical Performance of Nanosized Disordered LiVOPO4.

ε-LiVOPO4 is a promising multielectron cathode material for Li-ion batteries that can accommodate two electrons per vanadium, leading to higher energy densities. However, poor electronic conductivity and low lithium ion diffusivity currently result in low rate capability and poor cycle life. To enhance the electrochemical performance of ε-LiVOPO4, in this work, we optimized its solid-state synthesis route using in situ synchrotron X-ray diffraction and applied a combination of high-energy ball-milling with electronically and ionically conductive coatings aiming to improve bulk and surface Li diffusion. We show that high-energy ball-milling, while reducing the particle size also introduces structural disorder, as evidenced by 7Li and 31P NMR and X-ray absorption spectroscopy. We also show that a combination of electronically and ionically conductive coatings helps to utilize close to theoretical capacity for ε-LiVOPO4 at C/50 (1 C = 153 mA h g-1) and to enhance rate performance and capacity retention. The optimized ε-LiVOPO4/Li3VO4/acetylene black composite yields the high cycling capacity of 250 mA h g-1 at C/5 for over 70 cycles.

The molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy.

Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration.

G Protein-Coupled Receptors Contain Two Conserved Packing Clusters.

G protein-coupled receptors (GPCRs) have evolved a seven-transmembrane helix framework that is responsive to a wide range of extracellular signals. An analysis of the interior packing of family A GPCR crystal structures reveals two clusters of highly packed residues that facilitate tight transmembrane helix association. These clusters are centered on amino acid positions 2.47 and 4.53, which are highly conserved as alanine and serine, respectively. Ala2.47 mediates the interaction between helices H1 and H2, while Ser4.53 mediates the interaction between helices H3 and H4. The helical interfaces outside of these clusters are lined with residues that are more loosely packed, a structural feature that facilitates motion of helices H5, H6, and H7, which is required for receptor activation. Mutation of the conserved small side chain at position 4.53 within packing cluster 2 is shown to disrupt the structure of the visual receptor rhodopsin, whereas sites in packing cluster 1 (e.g., positions 1.46 and 2.47) are more tolerant to mutation but affect the overall stability of the protein. These findings reveal a common structural scaffold of GPCRs that is important for receptor folding and activation.

Rescue of mutant rhodopsin traffic by metformin-induced AMPK activation accelerates photoreceptor degeneration.

Protein misfolding caused by inherited mutations leads to loss of protein function and potentially toxic 'gain of function', such as the dominant P23H rhodopsin mutation that causes retinitis pigmentosa (RP). Here, we tested whether the AMPK activator metformin could affect the P23H rhodopsin synthesis and folding. In cell models, metformin treatment improved P23H rhodopsin folding and traffic. In animal models of P23H RP, metformin treatment successfully enhanced P23H traffic to the rod outer segment, but this led to reduced photoreceptor function and increased photoreceptor cell death. The metformin-rescued P23H rhodopsin was still intrinsically unstable and led to increased structural instability of the rod outer segments. These data suggest that improving the traffic of misfolding rhodopsin mutants is unlikely to be a practical therapy, because of their intrinsic instability and long half-life in the outer segment, but also highlights the potential of altering translation through AMPK to improve protein function in other protein misfolding diseases.

Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation.

The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its ß-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff's base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation.

The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs.

The disruption of ionic and H-bond interactions between the cytosolic ends of transmembrane helices TM3 and TM6 of class-A (rhodopsin-like) G protein-coupled receptors (GPCRs) is a hallmark for their activation by chemical or physical stimuli. In the bovine photoreceptor rhodopsin, this is accompanied by proton uptake at Glu(134) in the class-conserved D(E)RY motif. Studies on TM3 model peptides proposed a crucial role of the lipid bilayer in linking protonation to stabilization of an active state-like conformation. However, the molecular details of this linkage could not be resolved and have been addressed in this study by molecular dynamics (MD) simulations on TM3 model peptides in a bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We show that protonation of the conserved glutamic acid alters the peptide insertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helical structure. These factors contribute to the rise of the side-chain pKa (> 6) and to reduced polarity around the TM3 C terminus as confirmed by fluorescence spectroscopy. Helix stabilization requires the protonated carboxyl group; unexpectedly, this stabilization could not be evoked with an amide in MD simulations. Additionally, time-resolved Fourier transform infrared (FTIR) spectroscopy of TM3 model peptides revealed a different kinetics for lipid ester carbonyl hydration, suggesting that the carboxyl is linked to more extended H-bond clusters than an amide. Remarkably, this was seen as well in DOPC-reconstituted Glu(134)- and Gln(134)-containing bovine opsin mutants and demonstrates that the D(E)RY motif is a hydrated microdomain. The function of the D(E)RY motif as a proton switch is suggested to be based on the reorganization of the H-bond network at the membrane interface.

Free backbone carbonyls mediate rhodopsin activation.

Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins.

Construction of stable mammalian cell lines for inducible expression of G protein-coupled receptors.

The large-scale expression of many membrane proteins, including the members of the G protein-coupled receptor superfamily, in a correctly folded and fully functional form remains a formidable challenge. In this chapter, we focus on the construction of stable mammalian cell lines to overcome this hurdle. First, we will outline the steps for establishing a tightly regulated gene expression system in human HEK293S cells. This system utilizes separate plasmids containing components of well-defined genetic control elements from the Escherichia coli tetracycline operon to control the powerful cytomegalovirus immediate early enhancer/promoter. Next, we describe the assembly of this expression system into HEK293S cells and a derivative cell line devoid of complex N-glycosylation. Finally, we describe methods for the growth of these cells lines in scalable suspension culture for the preparation of milligram amounts of recombinant protein.

Uncovering the triggers for GPCR activation using solid-state NMR spectroscopy.

G protein-coupled receptors (GPCRs) span cell membranes with seven transmembrane helices and respond to a diverse array of extracellular signals. Crystal structures of GPCRs have provided key insights into the architecture of these receptors and the role of conserved residues. However, the question of how ligand binding induces the conformational changes that are essential for activation remains largely unanswered. Since the extracellular sequences and structures of GPCRs are not conserved between receptor subfamilies, it is likely that the initial molecular triggers for activation vary depending on the specific type of ligand and receptor. In this article, we describe NMR studies on the rhodopsin subfamily of GPCRs and propose a mechanism for how retinal isomerization switches the receptor to the active conformation. These results suggest a general approach for determining the triggers for activation in other GPCR subfamilies using NMR spectroscopy.

Sequential structural changes in rhodopsin occurring upon photoactivation.

We describe the use of solid-state magic angle spinning NMR spectroscopy for characterizing the structure and dynamics of dark, inactive rhodopsin and the active metarhodopsin II intermediate. Solid-state NMR spectroscopy is well suited for structural measurements in both detergent micelles and membrane bilayer environments. We first outline the methods for large-scale production of stable, functional rhodopsin containing (13)C- and (15)N-labeled amino acids. The expression methods make use of eukaryotic HEK293S cell lines that produce correctly folded, fully functional receptors. We subsequently describe the basic methods used for solid-state magic angle spinning NMR measurements of chemical shifts and dipolar couplings, which provide information on rhodopsin structure and dynamics, and describe the use of low-temperature methods to trap the active metarhodopsin II intermediate.