Dissection of Environmental Changes at the Cytoplasmic Surface of Light-activated Bacteriorhodopsin and Visual Rhodopsin: Sequence of Spectrally Silent Steps

Transient Deprotonation of the Chromophore Affects Protein Dynamics Proximal and Distal to the Linear Tetrapyrrole Chromophore in Phytochrome Cph1

Phytochromes are biological red/far-red light sensors found in many organisms. Prototypical phytochromes, including Cph1 from the cyanobacterium Synechocystis 6803, act as photochemical switches that interconvert between stable red (Pr)- and metastable far-red (Pfr)-absorbing states induced by photoisomerization of the bilin chromophore. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY) and the C-terminal transmitter (output) module, usually a histidine kinase, as in the case of Cph1. The chromophore deprotonates transiently during the Pr → Pfr photoconversion in association with extensive global structural changes required for signal transmission. Here, we performed equilibrium studies in the Pr state, involving pH titration of the linear tetrapyrrole chromophore in different Cph1 constructs, and measurement of pH-dependent structural changes at various positions in the protein using picosecond time-resolved fluorescence anisotropy. The fluorescent reporter group was attached at positions 371 (PHY domain), 305 (GAF domain), and 120 (PAS domain), as well as at sites in the PAS-GAF bidomain. We show direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains. Our results suggest that chromophore deprotonation is closely associated with a higher protein mobility (conformational space) both in proximal and in distal protein sites, implying a causal relationship that might be important for the global large protein arrangements and thus intramolecular signal transduction.

Light and pH-induced Changes in Structure and Accessibility of Transmembrane Helix B and Its Immediate Environment in Channelrhodopsin-2

A variant of the cation channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) was selectively labeled at position Cys-79 at the end of the first cytoplasmic loop and the beginning of transmembrane helix B with the fluorescent dye fluorescein (acetamidofluorescein). We utilized (i) time-resolved fluorescence anisotropy experiments to monitor the structural dynamics at the cytoplasmic surface close to the inner gate in the dark and after illumination in the open channel state and (ii) time-resolved fluorescence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4. The light-induced increase in final anisotropy for acetamidofluorescein bound to the channel variant with a prolonged conducting state clearly shows that the formation of the open channel state is associated with a large conformational change at the cytoplasmic surface, consistent with an outward tilt of helix B. Furthermore, results from solute accessibility studies of the cytoplasmic end of helix B suggest a pH-dependent structural heterogeneity that appears below pH 7. At pH 7.4 conformational homogeneity was observed, whereas at pH 6.0 two protein fractions exist, including one in which residue 79 is buried. This inaccessible fraction amounts to 66% in nanodiscs and 82% in micelles. Knowledge about pH-dependent structural heterogeneity may be important for CrChR2 applications in optogenetics.

Interactions of hyaluronic Acid with the skin and implications for the dermal delivery of biomacromolecules

Hyaluronic acid (HA) hydrogels are interesting delivery systems for topical applications. Besides moisturizing the skin and improving wound healing, HA facilitates topical drug absorption and is highly compatible with labile biomacromolecules. Hence, in this study we investigated the influence of HA hydrogels with different molecular weights (5 kDa, 100 kDa, 1 MDa) on the skin absorption of the model protein bovine serum albumin (BSA) using fluorescence lifetime imaging microscopy (FLIM). To elucidate the interactions of HA with the stratum corneum and the skin absorption of HA itself, we combined FLIM and Fourier-transform infrared (FTIR) spectroscopy. Our results revealed distinct formulation and skin-dependent effects. In barrier deficient (tape-stripped) skin, BSA alone penetrated into dermal layers. When BSA and HA were applied together, however, penetration was restricted to the epidermis. In normal skin, penetration enhancement of BSA into the epidermis was observed when applying low molecular weight HA (5 kDa). Fluorescence resonance energy transfer analysis indicated close interactions between HA and BSA under these conditions. FTIR spectroscopic analysis of HA interactions with stratum corneum constituents showed an α-helix to β-sheet interconversion of keratin in the stratum corneum, increased skin hydration, and intense interactions between 100 kDa HA and the skin lipids resulting in a more disordered arrangement of the latter. In conclusion, HA hydrogels restricted the delivery of biomacromolecules to the stratum corneum and viable epidermis in barrier deficient skin, and therefore seem to be potential topical drug vehicles. In contrast, HA acted as an enhancer for delivery in normal skin, probably mediated by a combination of cotransport, increased skin hydration, and modifications of the stratum corneum properties.

Nanodynamics of dendritic core-multishell nanocarriers

The molecular dynamics of polymeric nanocarriers is an important parameter for controlling the interaction of nanocarrier branches with cargo. Understanding the interplay of dendritic polymer dynamics, temperature, and cargo molecule interactions should provide valuable new insight for tailoring the dendritic architecture to specific needs in nanomedicine, drug, dye, and gene delivery. Here, we have investigated polyglycerol-based core-multishell (CMS) nanotransporters with incorporated Nile Red as a fluorescent drug mimetic and CMS nanotransporters with a covalently bound fluorophore (Indocarbocyanine) using fluorescence spectroscopy methods. From time-resolved fluorescence depolarization we have obtained the rotational diffusion dynamics of the incorporated dye, the nanocarrier, and its branches as a function of temperature. UV/vis and fluorescence lifetime measurements provided additional information on the local dye environment. Our results show a distribution of the cargo Nile Red within the nanotransporter shells that depends on solvent and temperature. In particular, we show that the flexibility of the polymer branches in the unimolecular state of the nanotransporter undergoes a temperature-dependent transition which correlates with a larger space for the mobility of the incorporated hydrophobic drug mimetic Nile Red and a higher probability of cargo-solvent interactions at temperatures above 31 °C. The measurements have further revealed that a loss of the cargo molecule Nile Red occurred neither upon dilution of the CMS nanotransporters nor upon heating. Thus, the unimolecular preloaded CMS nanotransporters retain their cargo and are capable to transport and respond to temperature, thereby fulfilling important requirements for biomedical applications.

Fluorescence spectroscopy of rhodopsins: insights and approaches

Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

Optimization of a malachite green assay for detection of ATP hydrolysis by solubilized membrane proteins

We studied the activity of the fluorescently labeled membrane transporter MalGFK(2), which transports maltose at the expense of ATP hydrolysis. We used a commercially available malachite green assay (SensoLyte MG phosphate assay kit; Anaspec) to quantify the liberated phosphate upon ATP hydrolysis. However, strong variations in phosphate concentration were measured when using the supplier's handling protocol. We optimized the protocol, taking into account the effects mediated by glycerol, SDS, and fluorescent label on the sample. As a result we obtained highly reproducible phosphate concentration values under conditions optimal for solubilized membrane proteins.

Conformational dynamics of helix 8 in the GPCR rhodopsin controls arrestin activation in the desensitization process

Arrestins are regulatory molecules for G-protein coupled receptor function. In visual rhodopsin, selective binding of arrestin to the cytoplasmic side of light-activated, phosphorylated rhodopsin (P-Rh*) terminates signaling via the G-protein transducin. While the "phosphate-sensor" of arrestin for the recognition of receptor-attached phosphates is identified, the molecular mechanism of arrestin binding and the involvement of receptor conformations in this process are still largely hypothetic. Here we used fluorescence pump-probe and time-resolved fluorescence depolarization measurements to investigate the kinetics of arrestin conformational changes and the corresponding nanosecond dynamical changes at the receptor surface. We show that at least two sequential conformational changes of arrestin occur upon interaction with P-Rh*, thus providing a kinetic proof for the suggested multistep nature of arrestin binding. At the cytoplasmic surface of P-Rh*, the structural dynamics of the amphipathic helix 8 (H8), connecting transmembrane helix 7 and the phosphorylated C-terminal tail, depends on the arrestin interaction state. We find that a high mobility of H8 is required in the low-affinity (prebinding) but not in the high-affinity binding state. High-affinity arrestin binding is inhibited when a bulky, inflexible group is bound to H8, indicating close interaction. We further show that this close steric interaction of H8 with arrestin is mandatory for the transition from prebinding to high-affinity binding; i.e., for arrestin activation. This finding implies a regulatory role for H8 in activation of visual arrestin, which shows high selectivity to P-Rh* in contrast to the broad receptor specificity displayed by the two nonvisual arrestins.

Exploiting Fluorescence Lifetime Plasticity in FLIM: Target Molecule Localization in Cells and Tissues

The mechanisms of drug-receptor interactions and the controlled delivery of drugs via biodegradable and biocompatible nanoparticulate carriers are active research fields in nanomedicine. Many clinically used drugs target G-protein coupled receptors (GPCRs) due to the fact that signaling via GPCRs is crucial in physiological and pathological processes and thus central for the function of biological systems. In this letter, a fast and reliable ratiometric fluorescence lifetime imaging microscopy (rmFLIM) approach is described to analyze the distribution of protein-ligand complexes in the cellular context. Binding of the fluorescently labeled antagonist naloxone to the G-protein coupled μ-opioid receptor is used as an example. To show the broad applicability of the rmFLIM method, we extended this approach to investigate the distribution of polymer-based nanocarriers in histological liver sections.

Activation and molecular recognition of the GPCR rhodopsin--insights from time-resolved fluorescence depolarisation and single molecule experiments

The cytoplasmic surface of the G-protein coupled receptor (GPCR) rhodopsin is a key element in membrane receptor activation, molecular recognition by signalling molecules, and receptor deactivation. Understanding of the coupling between conformational changes in the intramembrane domain and the membrane-exposed surface of the photoreceptor rhodopsin is crucial for the elucidation of the molecular mechanism in GPCR activation. As little is known about protein dynamics, particularly the conformational dynamics of the cytoplasmic surface elements on the nanoseconds timescale, we utilised time-resolved fluorescence anisotropy experiments and site-directed fluorescence labelling to provide information on both, conformational space and motion. We summarise our recent advances in understanding rhodopsin dynamics and function using time-resolved fluorescence depolarisation and single molecule fluorescence experiments, with particular focus on the amphipathic helix 8, lying parallel to the cytoplasmic membrane surface and connecting transmembrane helix 7 with the long C-terminal tail.

Characterization of membrane protein non-native states. 2. The SDS-unfolded states of rhodopsin

Little is known about the molecular nature of residual structure in unfolded states of membrane proteins. A screen of chemical denaturants to maximally unfold the mammalian membrane protein and prototypic G protein coupled receptor rhodopsin, without interference from aggregation, described in an accompanying paper (DOI 10.1021/bi100338e ), identified sodium dodecyl sulfate (SDS), alone or in combination with other chemicals, as the most suitable denaturant. Here, we initiate the biophysical characterization of SDS-denatured states of rhodopsin. Using absorption, steady-state and time-resolved fluorescence spectroscopy, dynamic light scattering, and cysteine accessibility studies, tertiary structure of denatured states was characterized. In agreement with the pattern of secondary structure changes detected by circular dichroism described in the accompanying paper (DOI 10.1021/bi100338e ), tertiary structure changes are distinct over four SDS concentration ranges based on the expected predominant micellar structures. Dodecyl maltoside (DM)/SDS mixed micelle spheres (0.05-0.3% SDS) turn into SDS spheres (0.3-3% SDS) that gradually (3-15% SDS) become cylindrical (above 15% SDS). Denatured states in SDS spheres and cylinders show a relatively greater burial of cysteine and tryptophan residues and are more compact as compared to the states observed in mixed micellar structures. Protein structural changes at the membrane/water interface region are most prominent at very low SDS concentrations but reach transient stability in the compact conformations in SDS spheres. This is the first experimental evidence for the formation of a compact unfolding intermediate state with flexible surface elements in a membrane protein.

The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations

Rhodopsin, the prototype class A G-protein-coupled receptor, is a very important model system for all seven-transmembrane domain proteins. Characterization of the interactions between rhodopsin and transducin, its intracellular G-protein counterpart, and the fluctuations in these interactions due to thermal motions is required for an understanding of early events in the mechanism of signal transduction. In this study, we used all-atom molecular dynamics simulations of a transmembrane protein complex between rhodopsin and the heterotrimeric transducin (G alpha beta gamma) in an all-atom DOPC (1,2-dioleoylsn-glycero-3-phosphocholine) membrane-water environment. Based on the analysis of a microsecond-timescale simulation trajectory, we characterized the dynamics of the system and its effects in the structural features of the protein subunits. Our simulations describe a highly dynamic interaction interface where the system is alternating between distinct domain orientations at the 10- to 100-ns timescale that can be further classified into interaction modes involving contacts between distinct structural features on the protein subunits. We related our results with experimental measurements from a variety of studies and high-resolution models of activated rhodopsin. Monitoring key structural features that are involved in the activation process along our simulation trajectory indicates the presence of extensive dynamics in the dark-adapted state, including a motion of Y223 from helix 3 toward the "ionic-lock" interactions of the conserved ERY motif. The dynamic picture shown here is consistent with a framework in which the dark-state fluctuations sample conformations consistent with the activated state. These results provide an atomic-level description of the dynamics of the full complex and further suggest novel mutagenesis experiments that can be used to investigate the stability and dynamics of this model membrane protein receptor system.

Functional interaction structures of the photochromic retinal protein rhodopsin

We studied functional interaction structures of the vertebrate membrane photoreceptor rhodopsin containing retinal as a chromophore. Using time-resolved fluorescence depolarization we analyzed real-time dynamics and conformational changes of the cytoplasmic helix 8 (H8) preceding the long C-terminal tail of rhodopsin. H8 runs parallel to the membrane surface and extends from transmembrane helix 7 whose highly conserved NPxxY(x)F motif connects that region of rhodopsin with the retinal binding pocket. Our measurements indicate that photo-induced retinal isomerization from 11-cis to all-trans provokes conformational changes of H8, including slower motion and reduced flexibility, that are specific for the active metarhodopsin-II photo-intermediate. These conformational changes are absent in the retinal-devoid state opsin and in the phosphorylated metarhodopsin-II state upon receptor deactivation. Furthermore we show that membrane rim effects can influence interfacial reactions at the cytoplasmic rhodopsin surface such as proton transfer reactions between surface and aqueous bulk phase or binding of the signaling protein transducin visualized with single-molecule widefield microscopy. These findings are important for an understanding of the effects of membrane structure on the photo-transduction mechanism.