Design of an Ultrafast G Protein Switch Based on a Mouse Melanopsin Variant.

The primary goal of optogenetics is the light-controlled noninvasive and specific manipulation of various cellular processes. Herein, we present a hybrid strategy for targeted protein engineering combining computational techniques with electrophysiological and UV/visible spectroscopic experiments. We validated our concept for channelrhodopsin-2 and applied it to modify the less-well-studied vertebrate opsin melanopsin. Melanopsin is a promising optogenetic tool that functions as a selective molecular light switch for G protein-coupled receptor pathways. Thus, we constructed a model of the melanopsin Gq protein complex and predicted an absorption maximum shift of the Y211F variant. This variant displays a narrow blue-shifted action spectrum and twofold faster deactivation kinetics compared to wild-type melanopsin on G protein-coupled inward rectifying K+ (GIRK) channels in HEK293 cells. Furthermore, we verified the in vivo activity and optogenetic potential for the variant in mice. Thus, we propose that our developed concept will be generally applicable to designing optogenetic tools.

Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy.

Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully benchmarked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several Gαi1 point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for α-GTP (Gαi1-T48A), γ-GTP (Gαi1-R178S), and for both ß-GTP/γ-GTP (Gαi1-K46A, Gαi1-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding Gαi1: we show that the GDP state of Gαi1 carries a Mg2+, which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.

Simulations of a G protein-coupled receptor homology model predict dynamic features and a ligand binding site.

A computational approach to predict structures of rhodopsin-like G protein-coupled receptors (GPCRs) is presented and evaluated by comparison to the X-ray structural models. By combining sequence alignment, the rhodopsin crystal structure, and point mutation data on the beta2 adrenoreceptor (b2ar), we predict a (-)-epinephrine-bound computational model of the beta2 adrenoreceptor. The model is evaluated by molecular dynamics simulations and by comparison with the recent X-ray structures of b2ar. The overall correspondence between the predicted and the X-ray structural model is high. Especially the prediction of the ligand binding site is accurate. This shows that the proposed dynamic homology modelling approach can be used to create reasonable models for the understanding of structure and dynamics of other rhodopsin-like GPCRs.

Temperature-dependent phase behavior and the crystal-forming nucleation process of ethyl 4-fluoro-2,3-dihydroxystearate monolayers.

The phase behavior of enantiomeric compounds as well as mixtures of enantiopure and racemic diastereomers of ethyl 4-fluoro-2,3-dihydroxystearates has been investigated using surface pressure-area isotherms and Brewster angle microscopy (BAM). All mixtures exhibit a small plateau region within the surface pressure-area isotherm at 20 degrees C, whereas the enantiopure compound shows an isotherm behavior similar to that of fatty acids. Corresponding to the film balance measurements, the BAM images demonstrate different shapes of the domains within the coexistence region of the liquid-condensed/liquid-expanded phase. The domain structures of the monolayers were visualized after Langmuir-Blodgett transfer on mica sheets by scanning force microscopy (SFM). From the SFM images it becomes obvious that small crystallites are formed for all investigated compounds; however, their molecular assembly is diverse for different enantiomers. Variations in the phase behavior can be correlated with interactions between the polar molecular moieties and the subphase and altered intermolecular interactions. Molecular modeling calculations were applied to elucidate the structural organization of these intermolecular interactions. Ab initio calculations of the minima conformers of (S,S,R)- and (S,S,S)-ethyl 4-fluoro-2,3-dihydroxystearates have been performed to predict with the HARDPACK program the two-dimensional lattice structure based on the P1 space group. These calculations showed that intermolecular hydrogen bridges are crucial for the interactions within and between the molecules.