Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin

The transport of protons across membranes is an important process in cellular bioenergetics. The light-driven proton pump bacteriorhodopsin is the best-characterized protein providing this function. Photon energy is absorbed by the chromophore retinal, covalently bound to Lys 216 via a protonated Schiff base. The light-induced all-trans to 13-cis isomerization of the retinal results in deprotonation of the Schiff base followed by alterations in protonatable groups within bacteriorhodopsin. The changed force field induces changes, even in the tertiary structure, which are necessary for proton pumping. The recent report of a high-resolution X-ray crystal structure for the late M intermediate of a mutant bacteriorhopsin (with Asp 96-->Asn) displays the structure of a proton pathway highly disturbed by the mutation. To observe an unperturbed proton pathway, we determined the structure of the late M intermediate of wild-type bacteriorhodopsin (2.25 A resolution). The cytoplasmic side of our M2 structure shows a water net that allows proton transfer from the proton donor group Asp 96 towards the Schiff base. An enlarged cavity system above Asp 96 is observed, which facilitates the de- and reprotonation of this group by fluctuating water molecules in the last part of the cycle.

Identification of resilin in the leg of cockroach, Periplaneta americana: confirmation by a simple method using pH dependence of UV fluorescence

We have examined the tarsus (foot) and tibial segments of the cockroach leg to identify structures that contain the elastic protein resilin. The presence of resilin was tested using the conventional criteria of fluorescent emission at 420 nm under UV illumination and histological staining of wholemount tissues by toluidine blue. We have also developed a simple method of confirming identification of resilin through changes in its fluorescence that occur with alteration of pH of the surrounding medium. Using a commonly available excitation filter that only passes light at >330 nm, we found that the emission was present at neutral pH but was eliminated at low pH. It then reversibly reappeared when medium of higher pH was restored. This effect is attributable to a known shift in the absorption maximum of amino acids of resilin that occurs in acidic media (from 330 to 285 nm). The accuracy of this method of identification was confirmed by examination of ligaments of the wing hinge, which has previously been shown to contain resilin in a number of insects. Using these techniques, we have identified resilin in association with ligaments at the tibio-tarsal joint and in the articulation between the fourth and fifth tarsal segments of the leg. The anatomical arrangement of these ligaments suggests that they could aid in the generation of leg movements during walking by functioning as elastic antagonists to the actions of leg muscles. The method of identification we have devised could readily be applied to aid in the localization of resilin in other animals.

Purification of multisubunit membrane protein complexes: isolation of chloroplast FoF1-ATP synthase, CFo and CF1 by blue native electrophoresis

The proton-ATP synthase of thylakoid membranes from chloroplasts (CFoF1) is composed of two parts with different structural and functional properties: the membrane-integral, proton-conducting complex CFo and the hydrophilic part, CF1 which catalyze the formation of adenosine-5'-triphosphate (ATP). To date it is difficult to isolate functional CFoF1 from thylakoids in high purity and yield. Blue native polyacrylamide gel electrophoresis (BN-PAGE) was therefore successfully employed to isolate CFoF1 in a one-step procedure from thylakoid membranes. Using a cathode buffer with low Coomassie Blue G-250 (CBG) concentration (0.002%), CFoF1 remains intact and can be obtained in high purity from solubilized, prepurified ATP synthase. Using BN-PAGE and a cathode buffer with 0.02% CBG, the ATP synthase bifurcates, and we were able to isolate both parts, CFo and CF1, separately. CFoF1, CFo, and CF1, respectively, were electroeluted nearly quantitatively electroeluted from the gel. BN-PAGE is a generally applicable method for the isolation and characterization of multisubunit membrane protein complexes in their native structure. However, the combination of neutral detergents and the negatively charged dye CBG seems to mimic properties of mild ionic detergents. This effect can lead to dissociation of labile subunits and subcomplexes, especially when delipidated membrane protein complexes are applied to BN-PAGE. By variation of the initial electrophoresis conditions, i.e., dye concentration in the cathode buffer, amount of lipid and detergent, BN-PAGE can be used for the isolation of either intact complexes or of subcomplexes.

Dye removal, catalytic activity and 2D crystallization of chloroplast H(+)-ATP synthase purified by blue native electrophoresis

The proton-ATP synthase of thylakoid membranes from spinach chloroplasts (CF(O)F(1)) and its subcomplexes CF(O) and CF(1) were isolated by blue native electrophoresis (BN-PAGE) [Neff, D. and Dencher, N.A. (1999) Biochem. Biophys. Res. Commun. 259, 569-575] and subsequently electroeluted from the gel. A method was developed to remove most of the dye Coomassie G-250 (CBG) using gel filtration, a prerequisite for many biophysical investigations. The dye was removed from the electroeluted CF(O)F(1), CF(O) or CF(1) and exchanged with the detergent CHAPS. ATP hydrolysis activity of CF(1) and ATP synthesis activity of reconstituted CF(O)F(1) were determined before and after dye removal. The secondary structure of CF(O) was studied by CD spectroscopy in the presence and the absence of the dye. CBG neither abolishes the catalytic activity of the isolated CF(O)F(1) and CF(1) nor affects the subunit composition and the high alpha-helical content of CF(O). In crystallization attempts, 2D arrays of CF(O)F(1) and of CF(O) before and after dye removal were obtained. In the aggregates of CF(O), circular structures with a mean diameter of 6.7 nm were observed. Our results indicate that the combination of BN-PAGE and dye removal by gel filtration is a suitable approach to obtain catalytically active protein complexes for further functional and structural characterization.

Three-dimensional graphic reconstruction of the insect exoskeleton through confocal imaging of endogenous fluorescence

The exoskeleton of the cockroach leg was imaged via confocal microscopy to generate digital graphic reconstructions of its three-dimensional structure. The cuticle is autofluorescent and can be visualized without staining, but is maximally imaged in aldehyde-fixed preparations viewed under krypton-argon laser illumination (yellow green (568 nm) excitation, commonly used in confocal microscopes). Images of the entire trochanteral segment of the leg were constructed as montages from optical sections taken as overlapping series that were coincident in the z-axis. Reconstructions of the exoskeleton from these images showed that strain sensing mechanoreceptors are located in association with buttresses and thickenings that form a consistent internal architecture in both juvenile and adult animals. Accuracy of reconstructions was gauged by embedding specimens in Spurr's resin and histologically sectioning them perpendicular to the optical plane of section (z-axis). Comparison of plastic sections with two-dimensional images generated by "resectioning" the software model showed that reconstructed exoskeleton had a high level of accuracy. Imaging of older and larger animals was limited by the sclerotization and increased thickness of the cuticle. Surface extraction algorithms were used to generate vector graphic files in CAD format for export to software used in engineering and design. Among other potential uses, these models have been studied by Finite Element Analysis to examine the distribution of mechanical strains in the exoskeleton that occur during posture and locomotion. The advantages and limitations of the techniques are discussed. These methods may be used in studying the exoskeleton and the anatomy of cuticular mechanoreceptors of other arthropods to similar advantage.

Leptin stimulates gonadotropin releasing hormone release from cultured intact hemihypothalami and enzymatically dispersed neurons

Leptin is a peptide released by adipocytes that has profound effects on central regulation of body metabolism. The present study represents an investigation into leptin effects on hypothalamic control of reproductive function, specifically on GnRH release. Adult male rats (gonadectomized or sham-operated) were used as donors of hypothalamic tissue that was used as intact hemihypothalami or as enzymatically dispersed hemihypothalami in a perifusion culture system. Continuous samples were collected at 10-min intervals for 8 to 10 hr and were assayed to measure temporal changes in GnRH release in response to various doses of leptin infused into the perifusion chambers. Leptin at the highest dose (10(-8) M) resulted in consistent and significant stimulation of GnRH release. There were no effects of treatment for surgical preparation (gonadectomy versus sham) or tissue preparation (intact versus dispersed hemihypothalami). The results of this study support the hypothesis that leptin plays a direct stimulatory role in the regulation of GnRH release. This study describes an important step in our understanding of the mechanism that connects changes in basal metabolism with reproductive function. These results indicate an intact interneuronal network is unnecessary for these leptin effects, but does not exclude a role for interneuronal networks in this regulatory pathway.

Chloroplast F0F1 ATP Synthase Imaged by Atomic Force Microscopy

The F0F1 ATP synthase of chloroplasts was imaged using atomic force microscopy (AFM) in contact mode under physiological conditions. Chloroplast (CF0F1) ATP synthases were reconstituted into liposomes. Liposomes were adsorbed on a mica surface where they spread and formed lipid bilayers containing CF0F1 ATP synthases which could be imaged. From these reconstituted CF0F1 ATP synthases, the CF1 part could be removed either by application of a chemical denaturant or less efficiently by mechanical stripping with the AFM tip. Embedded in the lipid bilayer were seen ring-like structures with a central dimple with outer diameters of 20 +/- 3 nm (chemical denaturant) and ca. 7 nm (mechanical stripping), respectively. Ring-like structures were also observed in a protein-free lipid bilayer. These had diameters of 30 +/- 5 nm and could be clearly distinguished from the structures observed after mechanical stripping. Hence, the ring-like structures observed after mechanical stripping might represent the intrinsic membrane domain CF0 or the oligomer of its subunit III. In addition, isolated CF1 adsorbed directly onto the mica surface was imaged. In accordance with the size known from electron microscopy, a diameter of 13 +/- 4 nm was measured.

Measurements of _{Λ}^{3}H and _{Λ}^{4}H Lifetimes and Yields in Au+Au Collisions in the High Baryon Density Region

We report precision measurements of hypernuclei _{Λ}^{3}H and _{Λ}^{4}H lifetimes obtained from Au+Au collisions at sqrt[s_{NN}]=3.0  GeV and 7.2 GeV collected by the STAR experiment at the Relativistic Heavy Ion Collider, and the first measurement of _{Λ}^{3}H and _{Λ}^{4}H midrapidity yields in Au+Au collisions at sqrt[s_{NN}]=3.0  GeV. _{Λ}^{3}H and _{Λ}^{4}H, being the two simplest bound states composed of hyperons and nucleons, are cornerstones in the field of hypernuclear physics. Their lifetimes are measured to be 221±15(stat)±19(syst)  ps for _{Λ}^{3}H and 218±6(stat)±13(syst)  ps for _{Λ}^{4}H. The p_{T}-integrated yields of _{Λ}^{3}H and _{Λ}^{4}H are presented in different centrality and rapidity intervals. It is observed that the shape of the rapidity distribution of _{Λ}^{4}H is different for 0%-10% and 10%-50% centrality collisions. Thermal model calculations, using the canonical ensemble for strangeness, describes the _{Λ}^{3}H yield well, while underestimating the _{Λ}^{4}H yield. Transport models, combining baryonic mean-field and coalescence (jam) or utilizing dynamical cluster formation via baryonic interactions (phqmd) for light nuclei and hypernuclei production, approximately describe the measured _{Λ}^{3}H and _{Λ}^{4}H yields. Our measurements provide means to precisely assess our understanding of the fundamental baryonic interactions with strange quarks, which can impact our understanding of more complicated systems involving hyperons, such as the interior of neutron stars or exotic hypernuclei.

Measurement of e^{+}e^{-} Momentum and Angular Distributions from Linearly Polarized Photon Collisions

The Breit-Wheeler process which produces matter and antimatter from photon collisions is experimentally investigated through the observation of 6085 exclusive electron-positron pairs in ultraperipheral Au+Au collisions at sqrt[s_{NN}]=200  GeV. The measurements reveal a large fourth-order angular modulation of cos4Δϕ=(16.8±2.5)% and smooth invariant mass distribution absent of vector mesons (ϕ, ω, and ρ) at the experimental limit of ≤0.2% of the observed yields. The differential cross section as a function of e^{+}e^{-} pair transverse momentum P_{⊥} peaks at low value with sqrt[⟨P_{⊥}^{2}⟩]=38.1±0.9  MeV and displays a significant centrality dependence. These features are consistent with QED calculations for the collision of linearly polarized photons quantized from the extremely strong electromagnetic fields generated by the highly charged Au nuclei at ultrarelativistic speed. The experimental results have implications for vacuum birefringence and for mapping the magnetic field which is important for emergent QCD phenomena.

Nonmonotonic Energy Dependence of Net-Proton Number Fluctuations

Nonmonotonic variation with collision energy (sqrt[s_{NN}]) of the moments of the net-baryon number distribution in heavy-ion collisions, related to the correlation length and the susceptibilities of the system, is suggested as a signature for the quantum chromodynamics critical point. We report the first evidence of a nonmonotonic variation in the kurtosis times variance of the net-proton number (proxy for net-baryon number) distribution as a function of sqrt[s_{NN}] with 3.1  σ significance for head-on (central) gold-on-gold (Au+Au) collisions measured solenoidal tracker at Relativistic Heavy Ion Collider. Data in noncentral Au+Au collisions and models of heavy-ion collisions without a critical point show a monotonic variation as a function of sqrt[s_{NN}].

Silicate glass alteration enhanced by iron: origin and long-term implications

Silicate glasses are used as containment matrices for deep geological disposal of nuclear waste arising from spent fuel reprocessing. Understanding the dissolution mechanisms of glasses in contact with iron, an element present in large amounts in the immediate environment (overpack, claystone, etc.) would be a major breakthrough toward predicting radionuclide release in the geosphere after disposal. Two different reacted glass-iron interfaces-a short-term nuclear system and a long-term archeological system-were examined using a multiscale and multianalytical approach including, for the first time on samples of this type, STXM under synchrotron radiation. Comparisons revealed remarkable similarities between the two systems and shed light on Fe-Si interactions, including migration of iron within a porous gel layer and precipitation of Fe-silicates that locally increase short-term glass alteration and are sustainable over the long-term.

Measurements of Proton High-Order Cumulants in sqrt[s_{NN}]=3 GeV Au+Au Collisions and Implications for the QCD Critical Point

We report cumulants of the proton multiplicity distribution from dedicated fixed-target Au+Au collisions at sqrt[s_{NN}]=3.0  GeV, measured by the STAR experiment in the kinematic acceptance of rapidity (y) and transverse momentum (p_{T}) within -0.5<y<0 and 0.4<p_{T}<2.0  GeV/c. In the most central 0%-5% collisions, a proton cumulant ratio is measured to be C_{4}/C_{2}=-0.85±0.09 (stat)±0.82 (syst), which is 2σ below the Poisson baseline with respect to both the statistical and systematic uncertainties. The hadronic transport UrQMD model reproduces our C_{4}/C_{2} in the measured acceptance. Compared to higher energy results and the transport model calculations, the suppression in C_{4}/C_{2} is consistent with fluctuations driven by baryon number conservation and indicates an energy regime dominated by hadronic interactions. These data imply that the QCD critical region, if created in heavy-ion collisions, could only exist at energies higher than 3 GeV.

First Measurement of Λ_{c} Baryon Production in Au+Au Collisions at sqrt[s_{NN}]=200 GeV

We report on the first measurement of the charmed baryon Λ_{c}^{±} production at midrapidity (|y|<1) in Au+Au collisions at sqrt[s_{NN}]=200  GeV collected by the STAR experiment at the Relativistic Heavy Ion Collider. The Λ_{c}/D^{0} [denoting (Λ_{c}^{+}+Λ_{c}^{-})/(D^{0}+D[over ¯]^{0})] yield ratio is measured to be 1.08±0.16  (stat)±0.26  (sys) in the 0%-20% most central Au+Au collisions for the transverse momentum (p_{T}) range 3<p_{T}<6  GeV/c. This is significantly larger than the pythia model calculations for p+p collisions. The measured Λ_{c}/D^{0} ratio, as a function of p_{T} and collision centrality, is comparable to the baryon-to-meson ratios for light and strange hadrons in Au+Au collisions. Model calculations including coalescence hadronization for charmed baryon and meson formation reproduce the features of our measured Λ_{c}/D^{0} ratio.

Global Polarization of Ξ and Ω Hyperons in Au+Au Collisions at sqrt[s_{NN}]=200 GeV

Global polarization of Ξ and Ω hyperons has been measured for the first time in Au+Au collisions at sqrt[s_{NN}]=200  GeV. The measurements of the Ξ^{-} and Ξ[over ¯]^{+} hyperon polarization have been performed by two independent methods, via analysis of the angular distribution of the daughter particles in the parity violating weak decay Ξ→Λ+π, as well as by measuring the polarization of the daughter Λ hyperon, polarized via polarization transfer from its parent. The polarization, obtained by combining the results from the two methods and averaged over Ξ^{-} and Ξ[over ¯]^{+}, is measured to be ⟨P_{Ξ}⟩=0.47±0.10(stat)±0.23(syst)% for the collision centrality 20%-80%. The ⟨P_{Ξ}⟩ is found to be slightly larger than the inclusive Λ polarization and in reasonable agreement with a multiphase transport model. The ⟨P_{Ξ}⟩ is found to follow the centrality dependence of the vorticity predicted in the model, increasing toward more peripheral collisions. The global polarization of Ω, ⟨P_{Ω}⟩=1.11±0.87(stat)±1.97(syst)% was obtained by measuring the polarization of daughter Λ in the decay Ω→Λ+K, assuming the polarization transfer factor C_{ΩΛ}=1.

Measurement of the Sixth-Order Cumulant of Net-Proton Multiplicity Distributions in Au+Au Collisions at sqrt[s_{NN}]=27, 54.4, and 200 GeV at RHIC

According to first-principle lattice QCD calculations, the transition from quark-gluon plasma to hadronic matter is a smooth crossover in the region μ_{B}≤T_{c}. In this range the ratio, C_{6}/C_{2}, of net-baryon distributions are predicted to be negative. In this Letter, we report the first measurement of the midrapidity net-proton C_{6}/C_{2} from 27, 54.4, and 200 GeV Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC). The dependence on collision centrality and kinematic acceptance in (p_{T}, y) are analyzed. While for 27 and 54.4 GeV collisions the C_{6}/C_{2} values are close to zero within uncertainties, it is observed that for 200 GeV collisions, the C_{6}/C_{2} ratio becomes progressively negative from peripheral to central collisions. Transport model calculations without critical dynamics predict mostly positive values except for the most central collisions within uncertainties. These observations seem to favor a smooth crossover in the high-energy nuclear collisions at top RHIC energy.

Beam Energy Dependence of Triton Production and Yield Ratio (N_{t}×N_{p}/N_{d}^{2}) in Au+Au Collisions at RHIC

We report the triton (t) production in midrapidity (|y|<0.5) Au+Au collisions at sqrt[s_{NN}]=7.7-200  GeV measured by the STAR experiment from the first phase of the beam energy scan at the Relativistic Heavy Ion Collider. The nuclear compound yield ratio (N_{t}×N_{p}/N_{d}^{2}), which is predicted to be sensitive to the fluctuation of local neutron density, is observed to decrease monotonically with increasing charged-particle multiplicity (dN_{ch}/dη) and follows a scaling behavior. The dN_{ch}/dη dependence of the yield ratio is compared to calculations from coalescence and thermal models. Enhancements in the yield ratios relative to the coalescence baseline are observed in the 0%-10% most central collisions at 19.6 and 27 GeV, with a significance of 2.3σ and 3.4σ, respectively, giving a combined significance of 4.1σ. The enhancements are not observed in peripheral collisions or model calculations without critical fluctuation, and decreases with a smaller p_{T} acceptance. The physics implications of these results on the QCD phase structure and the production mechanism of light nuclei in heavy-ion collisions are discussed.

Search for the Chiral Magnetic Effect via Charge-Dependent Azimuthal Correlations Relative to Spectator and Participant Planes in Au+Au Collisions at sqrt[s_{NN}]=200 GeV

The chiral magnetic effect (CME) refers to charge separation along a strong magnetic field due to imbalanced chirality of quarks in local parity and charge-parity violating domains in quantum chromodynamics. The experimental measurement of the charge separation is made difficult by the presence of a major background from elliptic azimuthal anisotropy. This background and the CME signal have different sensitivities to the spectator and participant planes, and could thus be determined by measurements with respect to these planes. We report such measurements in Au+Au collisions at a nucleon-nucleon center-of-mass energy of 200 GeV at the Relativistic Heavy-Ion Collider. It is found that the charge separation, with the flow background removed, is consistent with zero in peripheral (large impact parameter) collisions. Some indication of finite CME signals is seen in midcentral (intermediate impact parameter) collisions. Significant residual background effects may, however, still be present.

Evidence for Nonlinear Gluon Effects in QCD and Their Mass Number Dependence at STAR

The STAR Collaboration reports measurements of back-to-back azimuthal correlations of di-π^{0}s produced at forward pseudorapidities (2.6<η<4.0) in p+p, p+Al, and p+Au collisions at a center-of-mass energy of 200 GeV. We observe a clear suppression of the correlated yields of back-to-back π^{0} pairs in p+Al and p+Au collisions compared to the p+p data. The observed suppression of back-to-back pairs as a function of transverse momentum suggests nonlinear gluon dynamics arising at high parton densities. The larger suppression found in p+Au relative to p+Al collisions exhibits a dependence of the saturation scale Q_{s}^{2} on the mass number A. A linear scaling of the suppression with A^{1/3} is observed with a slope of -0.09±0.01.

Probing the Gluonic Structure of the Deuteron with J/ψ Photoproduction in d+Au Ultraperipheral Collisions

Understanding gluon density distributions and how they are modified in nuclei are among the most important goals in nuclear physics. In recent years, diffractive vector meson production measured in ultraperipheral collisions (UPCs) at heavy-ion colliders has provided a new tool for probing the gluon density. In this Letter, we report the first measurement of J/ψ photoproduction off the deuteron in UPCs at the center-of-mass energy sqrt[s_{NN}]=200  GeV in d+Au collisions. The differential cross section as a function of momentum transfer -t is measured. In addition, data with a neutron tagged in the deuteron-going zero-degree calorimeter is investigated for the first time, which is found to be consistent with the expectation of incoherent diffractive scattering at low momentum transfer. Theoretical predictions based on the color glass condensate saturation model and the leading twist approximation nuclear shadowing model are compared with the data quantitatively. A better agreement with the saturation model has been observed. With the current measurement, the results are found to be directly sensitive to the gluon density distribution of the deuteron and the deuteron breakup process, which provides insights into the nuclear gluonic structure.

Observation of D_{s}^{±}/D^{0} Enhancement in Au+Au Collisions at sqrt[s_{NN}]=200 GeV

We report on the first measurement of charm-strange meson D_{s}^{±} production at midrapidity in Au+Au collisions at sqrt[s_{NN}]=200  GeV from the STAR experiment. The yield ratio between strange (D_{s}^{±}) and nonstrange (D^{0}) open-charm mesons is presented and compared to model calculations. A significant enhancement, relative to a pythia simulation of p+p collisions, is observed in the D_{s}^{±}/D^{0} yield ratio in Au+Au collisions over a large range of collision centralities. Model calculations incorporating abundant strange-quark production in the quark-gluon plasma and coalescence hadronization qualitatively reproduce the data. The transverse-momentum integrated yield ratio of D_{s}^{±}/D^{0} at midrapidity is consistent with a prediction from a statistical hadronization model with the parameters constrained by the yields of light and strange hadrons measured at the same collision energy. These results suggest that the coalescence of charm quarks with strange quarks in the quark-gluon plasma plays an important role in D_{s}^{±}-meson production in heavy-ion collisions.

Imaging shapes of atomic nuclei in high-energy nuclear collisions

Atomic nuclei are self-organized, many-body quantum systems bound by strong nuclear forces within femtometre-scale space. These complex systems manifest a variety of shapes1-3, traditionally explored using non-invasive spectroscopic techniques at low energies4,5. However, at these energies, their instantaneous shapes are obscured by long-timescale quantum fluctuations, making direct observation challenging. Here we introduce the collective-flow-assisted nuclear shape-imaging method, which images the nuclear global shape by colliding them at ultrarelativistic speeds and analysing the collective response of outgoing debris. This technique captures a collision-specific snapshot of the spatial matter distribution within the nuclei, which, through the hydrodynamic expansion, imprints patterns on the particle momentum distribution observed in detectors6,7. We benchmark this method in collisions of ground-state uranium-238 nuclei, known for their elongated, axial-symmetric shape. Our findings show a large deformation with a slight deviation from axial symmetry in the nuclear ground state, aligning broadly with previous low-energy experiments. This approach offers a new method for imaging nuclear shapes, enhances our understanding of the initial conditions in high-energy collisions and addresses the important issue of nuclear structure evolution across energy scales.

Erratum: Measurement of the Sixth-Order Cumulant of Net-Proton Multiplicity Distributions in Au+Au Collisions at sqrt[s_{NN}]=27, 54.4, and 200 GeV at RHIC [Phys. Rev. Lett. 127, 262301 (2021)]

This corrects the article DOI: 10.1103/PhysRevLett.127.262301.