The paper investigates the influence of accretion heating and turbulent heat conduction on the equilibrium of protoplanetary disks, extending the 2D axisymmetric passive disk model of Flock. The ...model includes dust sublimation and radiative transfer with the flux-limited diffusion approximation, and predicts the density and temperature profiles as well as the dust-to-gas ratio of the disk. It is shown that the accretion heating can have a large impact: for accretion rates above 5 10−8 M yr−1 a zone forms behind the silicate condensation front with sufficiently high temperature to sublimate the dust and form a gaseous cavity. Assuming a Prandtl number ∼0.7, it is furthermore shown that the turbulent heat conduction cannot be neglected in the evaluation of the temperature profile. While the inner rim position is not affected by viscous heating, the dead zone edge shifts radially outward for higher accretion rates.
The L to M reaction of the bacteriorhodopsin photocycle includes the crucial proton transfer from the retinal Schiff base to Asp85. In spite of the importance of the L state in deciding central ...issues of the transport mechanism in this pump, the serious disagreements among the three published crystallographic structures of L have remained unresolved. Here, we report on the X-ray diffraction structure of the L state, to 1.53–1.73 Å resolutions, from replicate data sets collected from six independent crystals. Unlike earlier studies, the partial occupancy refinement uses diffraction intensities from the same crystals before and after the illumination to produce the trapped L state. The high reproducibility of inter-atomic distances, and bond angles and torsions of the retinal, lends credibility to the structural model. The photoisomerized 13-
cis retinal in L is twisted at the C
13
=
C
14 and C
15
=
NZ double-bonds, and the Schiff base does not lose its connection to Wat402 and, therefore, to the proton acceptor Asp85. The protonation of Asp85 by the Schiff base in the L→M reaction is likely to occur, therefore,
via Wat402. It is evident from the structure of the L state that various conformational changes involving hydrogen-bonding residues and bound water molecules begin to propagate from the retinal to the protein at this stage already, and in both extracellular and cytoplasmic directions. Their rationales in the transport can be deduced from the way their amplitudes increase in the intermediates that follow L in the reaction cycle, and from the proton transfer reactions with which they are associated.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
An M intermediate of wild-type bacteriorhodopsin and an N intermediate of the V49A mutant were accumulated in photostationary states at pH 5.6 and 295 K, and their crystal structures determined to ...1.52
Å and 1.62
Å resolution, respectively. They appear to be M
1 and N′ in the sequence, M
1↔M
2↔M′
2↔N↔N′→O→BR, where M
1, M
2, and M′
2 contain an unprotonated retinal Schiff base before and after a reorientation switch and after proton release to the extracellular surface, while N and N′ contain a reprotonated Schiff base, before and after reprotonation of Asp96 from the cytoplasmic surface. In M
1, we detect a cluster of three hydrogen-bonded water molecules at Asp96, not present in the BR state. In M
2, whose structure we reported earlier, one of these water molecules intercalates between Asp96 and Thr46. In N′, the cluster is transformed into a single-file hydrogen-bonded chain of four water molecules that connects Asp96 to the Schiff base. We find a network of three water molecules near residue 219 in the crystal structure of the non-illuminated F219L mutant, where the residue replacement creates a cavity. This suggests that the hydration of the cytoplasmic region we observe in N′ might have occurred spontaneously, beginning at an existing water molecule as nucleus, in the cavities from residue rearrangements in the photocycle.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the ...haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Crystal structures of the Asp$^{96}$ to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined ...to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp$^{85}$ and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis, 15-anti and an extensive rearrangement of the three-dimensional network of hydrogenbonded residues and bound water that accounts for the changed pK$_a$ values (where K$_a$ is the acid constant) of the Schiff base and Asp$^{85}$. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Context.
Multiple mechanisms are known to give rise to turbulence in protoplanetary disks, which facilitates the accretion onto the central star. Small dust particles that are well coupled to the gas ...undergo diffusion due to this turbulent motion.
Aims.
This paper investigates the influence of turbulence-induced dust diffusion on the equilibrium of protoplanetary disks.
Methods.
The model accounts for dust sublimation, radiative transfer with the flux-limited diffusion approximation, and dust diffusion. It predicts the density and temperature profiles as well as the dust-to-gas ratio of the disk.
Results.
It is shown that dust diffusion can have a large impact: Assuming the dust survives for 10
4
s or longer before it can be evaporated, this leads the dust diffusion to widen the inner disk considerably. This effect is generated through a feedback mechanism as the diffusion length is much shorter than the disk width. With increasing dust diffusion, the inclination of the inner rim toward the stellar radiation becomes steeper until it is almost vertical. The temperature range of evaporation and condensation, which is linked to the dust composition, has no influence on this effect.
Conclusions.
For realistic parameters, dust diffusion cannot be neglected when determining the equilibrium of the disk. Stronger turbulence inside the disk induces more dust diffusion. Therefore, the dust density grows more gradually over a greater distance and less radiation reaches the disk surface. The new equilibrium shape of the disk is more inclined toward the star. This effect is universal and independent of the specific dust composition.
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FMFMET, NUK, UL, UM, UPUK
In order to understand how isomerization of the retinal drives unidirectional transmembrane ion transport in bacteriorhodopsin, we determined the atomic structures of the BR state and M ...photointermediate of the E204Q mutant, to 1.7 and 1.8 Å resolution, respectively. Comparison of this M, in which proton release to the extracellular surface is blocked, with the previously determined M in the D96N mutant indicates that the changes in the extracellular region are initiated by changes in the electrostatic interactions of the retinal Schiff base with Asp85 and Asp212, but those on the cytoplasmic side originate from steric conflict of the 13-methyl retinal group with Trp182 and distortion of the π-bulge of helix G. The structural changes suggest that protonation of Asp85 initiates a cascade of atomic displacements in the extracellular region that cause release of a proton to the surface. The progressive relaxation of the strained 13-cis retinal chain with deprotonated Schiff base, in turn, initiates atomic displacements in the cytoplasmic region that cause the intercalation of a hydrogen-bonded water molecule between Thr46 and Asp96. This accounts for the lowering of the pKa of Asp96, which then reprotonates the Schiff base via a newly formed chain of water molecules that is extending toward the Schiff base.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The paper investigates the influence of accretion heating and turbulent heat conduction on the equilibrium of protoplanetary disks, extending the 2D axis-symmetric passive disk model of Flock (Flock ...et al. 2016, ApJ 827, 144). The model includes dust sublimation and radiative transfer with the flux-limited diffusion approximation, and predicts the density and temperature profiles as well as the dust to gas ratio of the disk. It is shown that the accretion heating can have a large impact: For accretion rates above 5*10^(-8) M_solar /yr a zone forms behind the silicate condensation front with sufficiently high temperature to sublimate the dust and form a gaseous cavity. Assuming a Prandtl number ~ 0.7, it is furthermore shown that the turbulent heat conduction cannot be neglected in the evaluation of the temperature profile. While the inner rim position is not affected by viscous heating, the dead zone edge shifts radially outward for higher accretion rates.
Context. Multiple mechanisms are known to give rise to turbulence in protoplanetary disks, which facilitates the accretion onto the central star. Small dust particles that are well coupled to the gas ...undergo diffusion due to this turbulent motion. Aims. This paper investigates the influence of turbulence induced dust diffusion on the equilibrium of protoplanetary disks. Methods. The model accounts for dust sublimation, radiative transfer with the flux-limited diffusion approximation and dust diffusion. It predicts the density and temperature profiles as well as the dust-to-gas ratio of the disk. Results. It is shown that dust diffusion can have a large impact: assuming the dust survives for 104 seconds or longer before it can be evaporated, leads the dust diffusion to widen the inner disk considerably. The latter effect is generated through a feedback mechanism as the diffusion length is much smaller than the disk width. With increasing dust diffusion, the inclination of the inner rim towards the stellar radiation becomes steeper until it is almost vertical. The temperature range of evaporation and condensation, which is linked to the dust composition, has no influence on this effect. Conclusions. For realistic parameters dust diffusion can not be neglected when determining the equilibrium of the disk. Stronger turbulence inside the disk induces more dust diffusion. Therefore, the dust density grows more gradually over a greater distance and less radiation reaches the disk surface. The new equilibrium shape of the disk is more inclined towards the star. This effect is universal and independent of the specific dust composition.
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