The Experts below are selected from a list of 162 Experts worldwide ranked by ideXlab platform
Pradeep L Ramachandran - One of the best experts on this subject based on the ideXlab platform.
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the short lived Signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes
Journal of the American Chemical Society, 2011Co-Authors: Pradeep L Ramachandran, Janet E Lovett, Patrick Carl, Marco Cammarata, Yang Ouk Jung, Hyotcherl Ihee, Christiane R Timmel, Jasper J Van ThorAbstract:The Signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient Signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump–probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the Signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 A upon illumination. The SAXS/WAXS Difference Signal for the Signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformat...
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the short lived Signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes
Journal of the American Chemical Society, 2011Co-Authors: Pradeep L Ramachandran, Janet E Lovett, Patrick Carl, Marco Cammarata, Yang Ouk Jung, Hyotcherl Ihee, Christiane R Timmel, Jae Hyuk Lee, Jasper J Van ThorAbstract:The Signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient Signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the Signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 A upon illumination. The SAXS/WAXS Difference Signal for the Signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations.
Andre W Visser - One of the best experts on this subject based on the ideXlab platform.
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hydrodynamic Signal perception in the copepod acartia tonsa
Marine Ecology Progress Series, 1999Co-Authors: Thomas Kiørboe, Enric Saiz, Andre W VisserAbstract:Copepods may remotely detect predators from the velocity gradients these generate in the ambient water. Each of the different components and characteristics of a velocity gradient (acceleration, vorticity, longitudinal and shear deformation) can cause a velocity Difference between the copepod and the ambient water and may, therefore, be perceived by mechanoreceptory setae. We hypothesised that the threshold value for escape response to a particular component depends solely on the magnitude of the velocity Difference (= Signal strength) it generates. In experiments we isolated the different components and noted the minimum intensities to which the copepod Acartia tonsa responded. As hypothesised, threshold Signal strengths due to longitudinal and shear deformation were similar, ∼0.015 cm s -1 , and were invariant with developmental stage. The latter implies that the threshold deformation rate for response scales inversely with size, i.e. that large stages respond to lower fluid deformation rates than small stages and, hence, may detect predators at longer distances. Signals due to vorticity and acceleration did not elicit escape responses, even though their magnitude exceeded threshold Signal strength due to deformation. We suggest that A. tonsa cannot distinguish such Signals from those due to their own behaviour (sinking, swimming, passive reorientation due to gravity) because they cause a similar spatial distributions of the Signal across the body. Reinterpretation of data from the literature revealed that threshold Signal strength due to deformation varies by ca 2 orders of magnitude between copepods and exceeds the neurophysiological response threshold by more than a factor of 10. In contrast, threshold deformation rates vary much less, ∼ 0.5 to 5 s -1 . Model calculations suggest that such threshold deformation rates are just sufficient to allow efficient predator detection while at the same time just below maximum turbulent deformation rates, thus preventing inordinate escapes.
Jasper J Van Thor - One of the best experts on this subject based on the ideXlab platform.
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the short lived Signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes
Journal of the American Chemical Society, 2011Co-Authors: Pradeep L Ramachandran, Janet E Lovett, Patrick Carl, Marco Cammarata, Yang Ouk Jung, Hyotcherl Ihee, Christiane R Timmel, Jasper J Van ThorAbstract:The Signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient Signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump–probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the Signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 A upon illumination. The SAXS/WAXS Difference Signal for the Signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformat...
Peter Fuhr - One of the best experts on this subject based on the ideXlab platform.
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reproducibility of functional connectivity and graph measures based on the phase lag index pli and weighted phase lag index wpli derived from high resolution eeg
PLOS ONE, 2014Co-Authors: Martin Hardmeier, Florian Hatz, H Bousleiman, Christian Schindler, Cornelis J Stam, Peter FuhrAbstract:Functional connectivity (FC) and graph measures provide powerful means to analyze complex networks. The current study determines the inter-subject-variability using the coefficient of variation (CoV) and long-term test-retest-reliability (TRT) using the intra-class correlation coefficient (ICC) in 44 healthy subjects with 35 having a follow-up at years 1 and 2. FC was estimated from 256-channel-EEG by the phase-lag-index (PLI) and weighted PLI (wPLI) during an eyes-closed resting state condition. PLI quantifies the asymmetry of the distribution of instantaneous phase Differences of two time-series and signifies, whether a consistent non-zero phase lag exists. WPLI extends the PLI by additionally accounting for the magnitude of the phase Difference. Signal-space global and regional PLI/wPLI and weighted first-order graph measures, i.e. normalized clustering coefficient (gamma), normalized average path length (lambda), and the small-world-index (SWI) were calculated for theta-, alpha1-, alpha2- and beta-frequency bands. Inter-subject variability of global PLI was low to moderate over frequency bands (0.12
Jasper J Van Thor - One of the best experts on this subject based on the ideXlab platform.
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the short lived Signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes
Journal of the American Chemical Society, 2011Co-Authors: Pradeep L Ramachandran, Janet E Lovett, Patrick Carl, Marco Cammarata, Yang Ouk Jung, Hyotcherl Ihee, Christiane R Timmel, Jae Hyuk Lee, Jasper J Van ThorAbstract:The Signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient Signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the Signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 A upon illumination. The SAXS/WAXS Difference Signal for the Signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations.