On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain

The conformation of the blue light utilising flavin domain of the signalling protein AppA in the dark state is a matter of intensive research, both experimental and theoretical, and has not yet unambiguously been determined. Two contradicting X-ray structures of the dark state have been published previously. We aim at resolving this seeming contradiction by exploring conformational pathways between the two X-ray structures using advanced modelling techniques, such as local-elevation searching and sampling, soft-core non-bonded interactions and protocols of successively biasing the sampling of sets of torsional angles which adopt different values in the two alternative X-ray structures. The results suggest a high energetic barrier for a change in the Trp104 side chain from a ‘Trp-in’ to a ‘Trp-out’ conformation or vice versa, and illustrate the complexity to model conformational transitions involving a large number of degrees of freedom.     

Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a Cyanobacterium Synechocystis sp. PCC6803

Slr1694 in Synechocystis sp. PCC6803 is a family of blue-light photoreceptors based on flavin adenine dinucleotide (FAD) called BLUF (sensor of blue light using FAD) proteins, which include AppA from Rhodobacter sphaeroides and PAC from Euglena gracilis. Illumination of dark-state Slr1694 at 15 degrees C reversibly induced a signaling light state characterized by the red shift in the UV-visible spectrum and by the light-induced Fourier transform infrared (FTIR) difference spectrum for structural changes of a bound flavin and apo protein. Illumination at the medium-low temperature (-35 degrees C) led to the red shift in the UV-visible spectrum despite some small difference in the light-induced changes. In contrast, the -35 degrees C illumination resulted in a completely different light-induced FTIR spectrum, in which almost all of the bands were suppressed with the exception of the bands for the change of C4=O bonding of the FAD isoalloxazine ring. The C4=O bands were induced at -35 degrees C with almost the same intensity, but the band frequency for the light state was upshifted by 6 cm(-)(1). The changes in frequency of the light-state C4=O band and in amplitude of other bands showed the same temperature dependence with a half-change temperature at approximately -20 degrees C. It was indicated that the light-induced structural changes of apo protein and FAD were inhibited at low temperature with the exception of the change in hydrogen bonding to the C4=O group. The light-induced formation of the FTIR bands was similarly inhibited by sample dehydration. We discussed the possibility that this constrained light state is a trapped intermediate state in the photocycle of Slr1694.     

Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue light using FAD (BLUF) protein Slr1694 of the cyanobacterium Synechocystis sp. PCC6803

Slr1694 is a BLUF (sensor of blue light using flavin adenine dinucleotide) protein and a putative photoreceptor in the cyanobacterium Synechocystis sp. PCC6803. Illumination of Slr1694 induced a signaling light state concurrent with a red shift in the UV-visible absorption of flavin, and formation of the bands from flavin and apo-protein in the light-minus-dark Fourier transform infrared (FTIR) difference spectrum. Replacement of Tyr8 with phenylalanine abolished these changes. The light state relaxed to the ground dark state, during which the FTIR bands decayed monophasically. These bands were classifiable into three groups according to their decay rates. The C4=O stretching bands of a flavin isoalloxazine ring had the highest decay rate, which corresponded to that of the absorption red shift. The result indicated that the hydrogen bonding at C4=O is responsible for the UV-visible red shift, consistent with the results of density functional calculation. All FTIR bands and the red shift decayed at the same slower rate in deuterated Slr1694. These results indicated that the dark relaxation from the light state is limited by proton transfer. In contrast, a constrained light state formed under dehydrated conditions decayed much more slowly with no deuteration effects. A photocycle mechanism involving the proton transfer was proposed.     

A way to sense light intensity: Multiple-excitation of the BLUF photoreceptor TePixD suppresses conformational change

TePixD, a cyanobacterial sensor of blue light using flavin adenine dinucleotide (FAD) (BLUF) which exists in a decamer form, was found to exhibit photoreaction sensitive to light intensity. While the number of excited molecules increased monotonically as the laser power increased, the number of decamers exhibiting a global conformational change initially increased, and then decreased with the increase of excitation intensity. This unusual power dependence was analyzed based on a Poisson distribution equation, demonstrating that decamers containing more than one excited monomer subunit do not undergo conformational change. Our results suggest that TePixD functions not only as a photosensor, but also by sensing light intensity.     

Oligomeric-State-Dependent Conformational Change of the BLUF Protein TePixD (Tll0078)

The photochemical reaction dynamics of a BLUF (sensors of blue light using FAD) protein, PixD, from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) were studied by pulsed laser-induced transient grating method. After the formation of an intermediate species with a red-shifted absorption spectrum, two new reaction phases reflecting protein conformational changes were discovered; one reaction phase manifested itself as expansion of partial molar volume with a time constant of 40 μs, whereas the other reaction phase represented a change in the diffusion coefficient D [i.e., the diffusion-sensitive conformational change (DSCC)]. D decreased from 4.9 × 10^− 11 to 4.4 × 10^− 11 m² s^− 1 upon the formation of the first intermediate, and subsequently showed a more pronounced decrease to 3.2 × 10^− 11 m² s^− 1 upon formation of the second intermediate. From a global analysis of signals at various grating wavenumbers, the time constant of D-change was determined to be 4 ms. Although the magnitude and rate constant of the faster volume change were independent of protein concentration, the amplitude of the signal that reflects the later DSCC significantly decreased as the protein concentration decreased. This concentration dependence suggests that two species exist in solution: a reactive species exhibiting the DSCC, and a second species that is nonreactive. The fraction of these species was found to be dependent on the concentration. The difference in reactivity was attributed to the different oligomeric states of TePixD (i.e., pentamer and decamer). The equilibrium of these states in the dark was confirmed by size-exclusion chromatography at various concentrations. These results demonstrated that only the decamer state is responsible for the conformational change. The results may suggest that the oligomeric state is functionally important in the signal transduction of this photosensory protein.     

Response of subarctic vegetation to transient climatic change on the Seward Peninsula in north-west Alaska

Understanding the response of terrestrial ecosystems to climatic warming is a challenge because of the complex interactions of climate, disturbance, and recruitment across the landscape. We use a spatially explicit model (ALFRESCO) to simulate the transient response of subarctic vegetation to climatic warming on the Seward Peninsula (80 000 km²) in north‐west Alaska. Model calibration efforts showed that fire ignition was less sensitive than fire spread to regional climate (temperature and precipitation). In the model simulations a warming climate led to slightly more fires and much larger fires and expansion of forest into previously treeless tundra. Vegetation and fire regime continued to change for centuries after cessation of the simulated climate warming. Flammability increased rapidly in direct response to climate warming and more gradually in response to climate‐induced vegetation change. In the simulations warming caused as much as a 228% increase in the total area burned per decade, leading to an increasingly early successional and more homogenous deciduous forest‐dominated landscape. A single transient 40‐y drought led to the development of a novel grassland–steppe ecosystem that persisted indefinitely and caused permanent increases in fires in both the grassland and adjacent vegetation. These simulated changes in vegetation and disturbance dynamics under a warming climate have important implications for regional carbon budgets and biotic feedbacks to regional climate.     

Light-induced conformational change at low temperature in the coordination of heme c-556 in the reaction center of Rhodopseudomonas viridis

Isolated reaction centers of Rhodopseudomonas viridis with the two high-potential hemes reduced were illuminated at 5 K. Difference spectra show a bleaching of the heme c-556 alpha bands and a red shift of the Soret band. These effects are reversed by warming to around 80 K. They are not induced by near infra-red light absorbed by the chlorine pigments of the reaction centers and they are not associated with electron transfer from P to Q_A. It is concluded that, following direct excitation, heme c-556 becomes five-coordinated. We find no evidence of a significant photooxidation of heme c-559 under the same conditions.     

Isolation and characterization of homologues of plant blue-light photoreceptor (cryptochrome) genes from the fern Adiantum capillus-veneris

Many blue-light mediated physiological responses have been studied in the fern Adiantum capillus-veneris. We have isolated genomic clones encoding sequences similar to those encoding blue-light photoreceptors (cryptochromes) in higher plants using the Arabidopsis CRY1 cDNA as a probe, and these positive clones fall into five independent groups. Using RACE procedures, we obtained full-length cDNA sequences for three of these five groups. The deduced amino acid sequences include the photolyase-homologous domain in the N-terminal half, and they also contain a C-terminal extension of about 200 amino acids in length. These structural features indicate that the genes indeed encode Adiantum cryptochromes and represent a small gene family having at least three members. Received: 16 February 1998 / Accepted: 26 April 1998     

Characterization of conformational changes and protein-protein interactions of rod photoreceptor phosphodiesterase (PDE6)

As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory γ-subunit, the prenyl-binding protein (PrBP/δ), and activated transducin. In solution, the PDE6 catalytic dimer (Pαβ) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pγ subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Pαβ was reconstituted with Pγ truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/δ bound to the PDE6 holoenzyme with high affinity (K(D) = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pγ with the catalytic dimer.     

Retinal development in mandarinfish Siniperca chuatsi and morphological analysis of the photoreceptor layer

We describe the process of retinal development in mandarinfish Siniperca chuatsi from larvae to young fish. The developmental characteristics of the retinal structure and related cells were identified. Siniperca chuatsi were found to exhibit an altricial mode of retinal development that required considerable time to be completed after hatching. The retina was classed as a pure cone type during the early developmental stage. In the subsequent developmental stages, however, double cones gradually occupied the majority of the cone cells, while rod cells represented the majority of the photoreceptor cells. The outer segment (OS) of the rod cells were significantly longer compared with other morphological features, the OS of the two kinds of cone cells were significantly elongated and the diameters of the inner segment (IS) and OS of the double cone cells were significantly narrower in the later developmental stages. Combined with the scattered arrangement of cone cells at the different stages, the retina was found to have sacrificed a considerable part of visual acuity in the developmental process. The distribution of cone cells was observed to have gradually become regionalised during development. The findings of the present study also indicated that S. chuatsi have a high photosensitivity under dim light conditions as a result of specialised structures of the OS of photoreceptor cells and an increased number of rod cells. The loose arrangement of the cone mosaic presumably resulted in a poor imaging quality and, to some extent, the regionalisation of the cone-cell distribution compensated for the above shortcomings, which would enhance the ability of S. chuatsi to perceive targets in important directions for effective predation behaviour.     

Dendritic synchrony and transient dynamics in a coupled oscillator model of the dopaminergic neuron

Transient increases in spontaneous firing rate of mesencephalic dopaminergic neurons have been suggested to act as a reward prediction error signal. A mechanism previously proposed involves subthreshold calcium-dependent oscillations in all parts of the neuron. In that mechanism, the natural frequency of oscillation varies with diameter of cell processes, so there is a wide variation of natural frequencies on the cell, but strong voltage coupling enforces a single frequency of oscillation under resting conditions. In previous work, mathematical analysis of a simpler system of oscillators showed that the chain of oscillators could produce transient dynamics in which the frequency of the coupled system increased temporarily, as seen in a biophysical model of the dopaminergic neuron. The transient dynamics was shown to be consequence of a slow drift along an invariant subset of phase space, with rate of drift given by a Lyapunov function. In this paper, we show that the same mathematical structure exists for the full biophysical model, giving physiological meaning to the slow drift and the Lyapunov function, which is shown to describe differences in intracellular calcium concentration in different parts of the cell. The duration of transients was long, being comparable to the time constant of calcium disposition. These results indicate that brief changes in input to the dopaminergic neuron can produce long lasting firing rate transients whose form is determined by intrinsic cell properties.     

Light-induced extracellular calcium and sodium concentration changes in the retina of Calliphora: involvement in the mechanism of light adaptation

Summary Ion-selective microelectrodes inserted into the compound eyes of Calliphora were used to monitor the changes in extracellular concentration of Ca²⁺ and Na⁺ (Ca_o, Na^o) brought about by a 1-min exposure to white light (maximal luminous intensity 0.1 cd/cm²).Using Ringer solution as the reference (Ca²⁺ = 1 mM), the dark concentration of the calcium in the retina was found to be (1.4 ± 0.4) mM (n=12). Stimulation with light reduces Ca_o. At intensities near maximal the Ca_o signal is phasic, reaching a transient minimum about 6 s after light onset and then rising to a nearly stable plateau below the dark level (-3.3% ± 2.6%). Ca_o signals measured in the white-eyed mutant (chalky), which lacks pigment granules, are comparable to those in the wild type.Conclusions: (a) There are no extracellular Ca²⁺ binding sites that regulate light adaptation, such as were postulated by Hochstrate and Hamdorf (1985). (b) Ca²⁺ influx into the photoreceptors seems to be necessary for light adaptation, (c) The pigment granules have no major function in intracellular calcium regulation.The time course of the Na_o signals resembles that of the Ca_o signals. Because the percentage concentration change is small, light-induced extracellular Na⁺-depletion cannot contribute to a reduced response amplitude at light adaptation.Abbreviations Ca _i intracellular Ca²⁺ concentration - Ca _o extracellular Ca²⁺ concentration - Kino extracellular K⁺ concentration - Na _o extracellular Na⁺ concentration     

Proton dissociation dynamics in the aqueous layer of multilamellar phospholipid vesicles

Summary The water layers interspacing between the phospholipid membranes of a multilamellar vesicle are 3–10 water layers across and their width is adjusted by osmotic pressure (Parsegian, V.A., et al., 1986.Methods Enzymol. 127:400–416).In these thin water layers we dissolved pyranine (8 hydroxypyrene 1,3,6 trisulfonate), a compound which, upon photo excitation, ejects it hydroxy proton with time constant of 100 psec. (Gutman, M. 1986.Methods Enzymol. 127:522–538).In the present study we investigated how the width of the aqueous layer, the density of phosphomoieties on the membrane's surface and the activity of water in the layer affect the capacity of protons to diffuse out from the electrostatic cage of the excited anion before it decays to the ground state.Using a combination of steady-state and subnanosecond time-resolved fluorescence measurements we determined the average number of proton excited-anion recombinations before the proton escapes from the Coulomb cage.The probability of recombination in thin water layer is significantly higher than in bulk. The factor contributing most to enhancement of recombination is the diminished water activity of the thin aqueous layer.The time frame for proton escape from an electrostatic trap as big as a membrane-bound protein is 3 orders of magnitude shorter than turnover time of membrane-bound enzymes. Thus the effects of local forces on proton diffusion, at the time scale of physiological processes, is negligible.     

Aspects of photoreceptor structure and phototactic behavior in Platyhelminthes,with particular reference to the symbiotic turbellarian Paravortex

Photoreceptor structure and function in the Platyhelminthes has traditionally been treated separately in the Turbellaria on one hand and the conventional parasitic classes on the other. In this paper, an attempt is made to bring together data from the literature and to highlight deficiencies and areas where a more integrated approach would be beneficial. This is done with particular reference to the endosymbiont genus Paravortex which belongs to the Turbellaria but which functionally has more similarities to the parasitic platyhelminths especially with regard to the host-finding requirement of the larval stages.     

Molecular dynamics simulation of O2 diffusion in polydimethylsiloxane (PDMS) and end-linked PDMS networks

Molecular dynamics simulations are used to compute diffusion coefficients for O₂ molecules in polydimethylsiloxane (PDMS) and end-linked PDMS networks. The PDMS chains and penetrants are modelled using a hybrid interatomic potential which treats the Si and O atoms along the chain backbone explicitly while coarse-graining the methyl side groups and penetrants. In PDMS models with different molecular weights, diffusivity of the O₂ penetrants is found to modestly decrease with an increase in chain length. To match typical experimental conditions, the end-linked PDMS networks are constructed with a PDMS to crosslinking (CL) molecule mass ratio of 5:1 or 10:1, demanding that the number of CL molecules exceeds the number of PDMS chains in each model. Despite end-linking, the presence of non-bonded CL molecules promotes increased O₂ diffusivity in comparison with uncrosslinked PDMS. Temperature dependence is captured using the Williams–Landel–Ferry equation.     

集胞藻PCC6803中S2P同源蛋白Slr0643及Sll0862 金属蛋白酶活性的体外鉴定

【目的】金属蛋白酶S2P在细菌中通过在膜切割转录调控因子、释放δ因子参与胁迫响应是跨膜信号转导的保守机制,但蓝细菌中S2P的功能还未被鉴定,故我们考察集胞藻PCC6803中的S2P同源蛋白Slr0643及Sll0862的金属蛋白酶活性。【方法】以pET-30b(+)为载体,分别构建重组质粒pF0643和pF0862,在大肠杆菌BL21(CE3)中诱导表达并纯化Slr0643及Sll0862蛋白,以β-酪蛋白为底物检测重组蛋白的酶活性。【结果】体外酶活实验显示重组表达的Slr0643及Sll0862蛋白有内切蛋白酶活性,且其活性受金属螯合剂o-phenanthroline的抑制。体外酶活的鉴定结果为进一步研究Slr0643和Sll0862的体内酶活和生物学功能奠定了基础。【结论】集胞藻PCC6803中的S2P同源蛋白Slr0643及Sll0862具有金属蛋白酶活性。     

Targeted molecular dynamics simulation studies of calcium binding and conformational change in the C-terminal half of gelsolin

Gelsolin consists of six related domains (G1-G6) and the C-terminal half (G4-G6) acts as a calcium sensor during the activation of the whole molecule, a process that involves large domain movements. In this study, we used targeted molecular dynamics simulations to elucidate the conformational transitions of G4-G6 at an atomic level. Domains G4 and G6 are initially ruptured, followed by a rotation of G6 by approximately 90 degrees , which is the dominant conformational change. During this period, local conformational changes occur at the G4 and G5 calcium-binding sites, facilitating large changes in interdomain distances. Alterations in the binding affinities of the calcium ions in these three domains appear to be related to local conformational changes at their binding sites. Analysis of the relative stabilities of the G4-G6-bound calcium ions suggests that they bind first to G6, then to G4, and finally to G5.