Evidence of local conformational fluctuations and changes in bacteriorhodopsin, dependent on lipids, detergents and trimeric structure, as studied by 13C NMR

AbstractWe examined how the local conformation and dynamics of [3-13C]Ala-labeled bacteriorhodopsin (bR) are altered as viewed from 13C NMR spectra when the natural membrane lipids are partly or completely replaced with detergents. It turned out that the major conformational features of bR, the αII-helices, are generally unchanged in the delipidated or solubilized preparations. Upon partial delipidation or detergent solubilization, however, a significant conformational change occurs, ascribed to local conversion of αII→αI-helix (one Ala residue involved), evident from the upfield displacement of the transmembrane helical peak from 16.4 ppm to 14.5 ppm, conformational change (one or two Ala residues) within αII-helices from 16.4 to 16.0 ppm, and acquired flexibility in the loop region (especially at the F–G loop) as manifested from suppressed peak-intensities in cross-polarization magic angle spinning (CP-MAS) NMR spectra. On the other hand, formation of monomers as solubilized by Triton X-100, Triton N-101 and n-dodecylmaltoside is characterized by the presence of a peak at 15.5 ppm and a shifted absorption maximum (550 nm). The size of micelles under the first two conditions was small enough to yield 13C NMR signals observable by a solution NMR spectrometer, although 13C CP-MAS NMR signals were also visible from a fraction of large-sized micelles. We found that the 16.9 ppm peak (three Ala residues involved), visible by CP-MAS NMR, was displaced upfield when Schiff base was removed by solubilization with sodium dodecyl sulfate, consistent with our previous finding of bleaching to yield bacterioopsin

Classification of fish species based on their spatio-temporal dynamics.

<p>(A) Dendrogram of the Hierarchical Agglomerative Clustering and the separation of 6 clusters. (B-D) Clusters represented on the different principal tensors (PTs), with x-axis showing PT1 projections, and y-axis showing (B) PT2, (C) PT3 and (D) PT4 projections.</p

Results of the principal tensor analysis with 4 principal tensors (PT) explaining together 43% of the total variability in the North Sea fish assemblage.

<p>(A) PT1 showed a spatial gradient in species abundance from North to South. (B) PT2 showed the difference in abundance between strongly localized species (either in the North or the South) and species living in the central part of the North Sea. (C) PT3 showed the abundance difference between species in the West and East of the North Sea. (D) PT4 showed a temporal trend in species abundance.</p

Presentation of the data set and its multidimensional nature.

<p>(A) Community data represented as a three-dimensional tensor. Each pixel represents the abundance level (relative to the average abundance of each species in the survey) of the fish species in the North Sea in its 3 dimensions: species, time and space. (B) Map of the study area showing the 7 predefined areas (called roundfish areas) which serve as the spatial scale of our study.</p

Correlation analysis to identify environmental influences on spatio-temporal community patterns.

<p>Correlation analysis to identify environmental influences on spatio-temporal community patterns.</p