Atomistic insights into rhodopsin activation from a dynamic model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.     

Protein folding kinetics under force from molecular simulation

Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.     

Steps along the path to dihydrogen activation at [FeFe] hydrogenase structural models: dependence of the core geometry on electrocatalytic proton reduction

Differences in the rate of electrocatalytic proton reduction by Fe2(mu-PPh2)2(CO)6, DP, and the linked phosphido-bridged analogue Fe2(mu,mu-PPh(CH2)3PPh)(CO)6, 3P, suggest that dihydrogen elimination proceeds through a bridging hydride. The reaction path was examined using electrochemical, spectroscopic, and in silico studies where reduction of 3P gives a moderately stable monoanion [Kdisp(3P-) = 13] and a distorted dianion. The monomeric formulation of 3P- is supported by the form of the IR and EPR spectra. EXAFS analysis of solutions of 3P, 3P-, and 3P2- indicates a large increase in the Fe-Fe separation following reduction (from 2.63 to ca. 3.1-3.55 A). DFT calculations of the 3P, 3P-, 3P2- redox series satisfactorily reproduce the IR spectra in the nu(CO) region and the crystallographic (3P) and EXAFS-derived Fe-Fe distances. Digital simulation of the electrocatalytic response for proton reduction indicates a low rate of dihydrogen evolution from the two-electron, two-proton product of 3P (H23P), with more rapid dihydrogen evolution following further reduction of H23P. Because dihydrogen evolution is not observed upon formation of H2DP, dihydrogen evolution at the two-electron-reduced level does not involve protonation of a hydridic Fe-H ligand. The rates of dihydrogen elimination from H2DP, H23P, and H2Fe2(mu,mu-S(CH2)3S)(CO)6 (H23S) are related to the DFT-calculated H-H distances [H23S (1.880 A) < H23P (2.064 A) < H2DP (3.100 A)], and this suggests a common reaction path for the thiolato- and phosphido-bridged diiron carbonyl compounds.     

Binaural interference and auditory grouping

The phenomenon of binaural interference, where binaural judgments of a high-frequency target stimulus are disrupted by the presence of a simultaneous low-frequency interferer, can largely be explained using principles of auditory grouping and segregation. Evidence for this relationship comes from a number of previous studies showing that the manipulation of simultaneous grouping cues such as harmonicity and onset synchrony can influence the strength of the phenomenon. In this study, it is shown that sequential grouping cues can also influence whether binaural interference occurs. Subjects indicated the lateral position of a high-frequency sinusoidally amplitude-modulated (SAM) tone containing an interaural time difference. Perceived lateral positions were reduced by the presence of a simultaneous diotic low-frequency SAM tone, but were largely restored when the interferer was "captured" in a stream of identical tones. A control condition confirmed that the effect was not due to peripheral adaptation. The data lend further support to the idea that binaural interference is affected by processes related to the perceptual organization of auditory information. Modifications to existing grouping-based models are proposed that may help account for binaural interference effects more successfully.     

Dielectric in situ sensor monitoring of phase separation and changes in the state of each phase

Frequency dependent dielectric measurements have been used to monitor and characterize the phase separation process and changes in state of each phase. The measurements are made in situ using a micro planar sensor. They can be made both in the laboratory as well as in an industrial production or use environment. Two examples are presented. The first is monitoring the onset of phase separation, the buildup in Tg and change in composition of each phase during “reactive processing” of a high performance thermoplastic (TP) PPI, thermoset precursors (TS) DGEBA-MCDEA intially homogeneous blend. The second example involves monitoring the stability, onset of phase separation, as a function of temperature on a mineral oil, stearyl alcohol, water, sufactant emulsion used in the cosmetic industry.     

Large scale synthesis of the acetonides of l-glucuronolactone and of l-glucose: easy access to l-sugar chirons

1,2-O-Isopropylidene-α-l-glucurono-3,6-lactone may be synthesized on a 100-200 g scale from cheaply available d-glucoheptonolactone in an overall yield of 94% in four steps via l-glucuronolactone. Subsequent elaboration to l-glucose, diacetone-l-glucose (1,2:5,6-di-O-isopropylidene-α-l-glucofuranose), and monoacetone-l-glucose (1,2-O-isopropylidene-α-l-glucofuranose) allows easy access to a range of l-sugar chirons.     

Structural Determination of a Photochemically Active Diplatinum Molecule by Time‐Resolved EXAFS Spectroscopy

Metallica : A large contraction of the Pt? Pt bond in the triplet excited state of the photoreactive [Pt₂(P₂O₅H₂)₄]^4? ion is determined by time‐resolved X‐ray absorption spectroscopy (see picture). The strengthening of the Pt? Pt interaction is accompanied by a weakening of the ligand coordination bonds, resulting in an elongation of the platinum–ligand bond that is determined for the first time.

     

Stereochemical analysis of ferrocene and the uncertainty of fluorescence XAFS data

Methods for the quantification of statistically valid measures of the uncertainties associated with X‐ray absorption fine structure (XAFS) data obtained from dilute solutions using fluorescence measurements are developed. Experimental data obtained from 10 mM solutions of the organometallic compound ferrocene, Fe(C₅H₅)₂, are analysed within this framework and, following correction for various electronic and geometrical factors, give robust estimates of the standard errors of the individual measurements. The reliability of the refinement statistics of standard current XAFS structure approaches that do not include propagation of experimental uncertainties to assess subtle structural distortions is assessed in terms of refinements obtained for the staggered and eclipsed conformations of the C₅H₅ rings of ferrocene. Standard approaches (XFIT, IFEFFIT) give refinement statistics that appear to show strong, but opposite, preferences for the different conformations. Incorporation of experimental uncertainties into an IFEFFIT‐like analysis yield refinement statistics for the staggered and eclipsed forms of ferrocene which show a far more realistic preference for the eclipsed form which accurately reflects the reliability of the analysis. Moreover, the more strongly founded estimates of the refined parameter uncertainties allow more direct comparison with those obtained by other techniques. These XAFS‐based estimates of the bond distances have accuracies comparable with those obtained using single‐crystal diffraction techniques and are superior in terms of their use in comparisons of experimental and computed structures.     

Ventral and dorsal streams processing visual motion perception (FDG-PET study)

ABSTRACT: BACKGROUND: Earlier functional imaging studies on visually induced self-motion perception (vection) disclosed a bilateral network of activations within primary and secondary visual cortex areas which was combined with signal decreases, i.e., deactivations, in multisensory vestibular cortex areas. This finding led to the concept of a reciprocal inhibitory interaction between the visual and vestibular systems. In order to define areas involved in special aspects of selfmotion perception such as intensity and duration of the perceived circular vection (CV) or the amount of head tilt, correlation analyses of the regional cerebral glucose metabolism, rCGM (measured by fluorodeoxyglucose positron-emission tomography, FDG-PET) and these perceptual covariates were performed in 14 healthy volunteers. For analyses of the visualvestibular interaction, the CV data were compared to a random dot motion stimulation condition (not inducing vection) and a control group at rest (no stimulation at all). RESULTS: Group subtraction analyses showed that the visual-vestibular interaction was modified during CV, i.e., the activations within the cerebellar vermis and parieto-occipital areas were enhanced. The correlation analysis between the rCGM and the intensity of visually induced vection, experienced as body tilt, showed a relationship for areas of the multisensory vestibular cortical network (inferior parietal lobule bilaterally, anterior cingulate gyrus), the medial parieto-occipital cortex, the frontal eye fields and the cerebellar vermis. The "earlier" multisensory vestibular areas like the parieto-insular vestibular cortex and the superior temporal gyrus did not appear in the latter analysis. The duration of perceived vection after stimulus stop was positively correlated with rCGM in medial temporal lobe areas bilaterally, which included the (para-)hippocampus, known to be involved in various aspects of memory processing. The amount of head tilt was found to be positively correlated with the rCGM of bilateral basal ganglia regions responsible for the control of motor function of the head. CONCLUSIONS: Our data gave further insights into subfunctions within the complex cortical network involved in the processing of visual-vestibular interaction during CV. Specific areas of this cortical network could be attributed to the ventral stream ("what" pathway) responsible for the duration after stimulus stop and to the dorsal stream ("where/how" pathway) responsible for intensity aspects.     

Monitoring the Dynamics of Phase Separation in a Polymer Blend by Confocal Imaging and Fluorescence Correlation Spectroscopy

The phase separation of the polymer blend polystyrene/poly(methyl phenyl siloxane) (PS/PMPS) is studied in situ by laser scanning confocal microscopy (LSCM) and by fluorescence correlation spectroscopy (FCS) at macroscopic and microscopic length scales, respectively. It is shown for the first time that FCS when combined with LSCM can provide independent information on the local concentration within the phase‐separated domains as well as the interfacial width.