The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins

Membrane proteins participate in many fundamental cellular processes. Until recently, an understanding of the function and properties of membrane proteins was hampered by an absence of structural information at the atomic level. A landmark achievement toward understanding the structure of membrane proteins was the crystallization (1) and structure determination (2-5) the photosynthetic reaction center (RC) from the purple bacteria Rhodopseudomonas viridis, followed by that of the RC from Rhodobacter sphaeroides (6-17). The RC is an integral membrane protein-pigment complex, which carries out the initial steps of photosynthesis (reviewed in 18). RCs from the purple bacteria Rps. viridis and Rb. sphaeroides are composed of three membrane-associated protein subunits (designated L, M, and H), and the following cofactors: four bacteriochlorophylls (Bchl or B), two bacteriopheophytins (Bphe or [phi]), two quinones, and a nonheme iron. The cofactors are organized into two symmetrical branches that are approximately related by a twofold rotation axis (2, 8). A central feature of the structural organization of the RC is the presence of 11 hydrophobic [alpha]-helixes, approximately 20-30 residues long, which are believed to represent the membrane-spanning portion of the RC (3, 9). Five membrane-spanning helixes are present in both the L and M subunits, while a single helix is in the H subunit. The folding of the L and M subunits is similar, consistent with significant sequence similarity between the two chains (19-25). The L and M subunits are approximately related by the same twofold rotation axis that relates the two cofactor branches. RCs are the first membrane proteins to be described at atomic resolution; consequently they provide an important model for discussing the folding of membrane proteins. The structure demonstrates that [alpha]-helical structures may be adopted by integral membrane proteins, and provides confirmation of the utility of hydropathy plots in identifying nonpolar membrane-spanning regions from sequence data. An important distinction between the folding environments of water-soluble proteins and membrane proteins is the large difference in water concentration surrounding the proteins. As a result, hydrophobic interactions (26) play very different roles in stabilizing the tertiary structures of these two classes of proteins; this has important structural consequences. There is a striking difference in surface polarity of membrane and water-soluble proteins. However, the characteristic atomic packing and surface area appear quite similar. A computational method is described for defining the position of the RC in the membrane (10). After localization of the RC structure in the membrane, surface residues in contact with the lipid bilayer were identified. As has been found for soluble globular proteins, surface residues are less well conserved in homologous membrane proteins than the buried, interior residues. Methods based on the variability of residues between homologous proteins are described (13); they are useful (a) in defining surface helical regions of membrane and water-soluble proteins and (b) in assigning the side of these helixes that are exposed to the solvent. A unifying view of protein structure suggests that water-soluble proteins may be considered as modified membrane proteins with covalently attached polar groups that solubilize the proteins in aqueous solution

Dynamical supersymmetry of spin particle-magnetic field interaction

We study the super and dynamical symmetries of a fermion in a monopole background. The Hamiltonian also involves an additional spin-orbit coupling term, which is parameterized by the gyromagnetic ratio. We construct the superinvariants associated with the system using a SUSY extension of a previously proposed algorithm, based on Grassmann-valued Killing tensors. Conserved quantities arise for certain definite values of the gyromagnetic factor: $\N=1$ SUSY requires $g=2$; a Kepler-type dynamical symmetry only arises, however, for the anomalous values $g=0$ and $g=4$. The two anomalous systems can be unified into an $\N=2$ SUSY system built by doubling the number of Grassmann variables. The planar system also exhibits an $\N=2$ supersymmetry without Grassmann variable doubling.Comment: 23 page

A CO survey on a sample of Herschel cold clumps

Context. The physical state of cold cloud clumps has a great impact on the process and efficiency of star formation and the masses of the forming stars inside these objects. The sub-millimetre survey of the Planck space observatory and the far-infrared follow-up mapping of the Herschel space telescope provide an unbiased, large sample of these cold objects. Aims. We have observed (CO)-C-12(1-0) and (CO)-C-13(1-0) emission in 35 high-density clumps in 26 Herschel fields sampling different environments in the Galaxy. Here, we aim to derive the physical properties of the objects and estimate their gravitational stability. Methods. The densities and temperatures of the clumps were calculated from both the dust continuum and the molecular line data. Kinematic distances were derived using (CO)-C-13(1-0) line velocities to verify previous distance estimates and the sizes and masses of the objects were calculated by fitting 2D Gaussian functions to their optical depth distribution maps on 250 mu m. The masses and virial masses were estimated assuming an upper and lower limit on the kinetic temperatures and considering uncertainties due to distance limitations. Results. The derived excitation temperatures are between 8.5-19.5 K, and for most clumps between 10 15 K, while the Herschel-derived dust colour temperatures are more uniform, between 12 16 K. The sizes (0.1-3 pc), (CO)-C-13 column densities (0.5-44 x 10(15) cm(-2)) and masses (from less than 0.1 M-circle dot to more than 1500 M-circle dot) of the objects all span broad ranges. We provide new kinematic distance estimates, identify gravitationally bound or unbound structures and discuss their nature. Conclusions. The sample contains objects on a wide scale of temperatures, densities and sizes. Eleven gravitationally unbound clumps were found, many of them smaller than 0.3 pc, but large, parsec-scale clouds with a few hundred solar masses appear as well. Colder clumps have generally high column densities but warmer objects appear at both low and higher column densities. The clump column densities derived from the line and dust observations correlate well, but are heavily affected by uncertainties of the dust properties, varying molecular abundances and optical depth effects.Peer reviewe

Electronic structure and magnetic properties of RT4Al8 (R = Sc, Y, La, Lu; T = Fe, Mn, Cr) compounds. Hydrostatic pressure effects

We present results of theoretical and experimental studies of the electronic structure and magnetic properties of RFe4Al8, RMn4Al8, and RCr4Al8 compounds with nonmagnetic elements R = Sc, Y, La, and Lu. The electron spectrum and field induced magnetic moment, as well as their dependences on the unit cell volume, are calculated for the paramagnetic phase of the RT4Al8 systems. The calculations are supplemented by measurements of the magnetic susceptibility of representative RT4Al8 compounds as a function of temperature and hydrostatic pressure

A Quench Detection and Monitoring System for Superconducting Magnets at Fermilab

A quench detection system was developed for protecting and monitoring the superconducting solenoids for the Muon-to-Electron Conversion Experiment (Mu2e) at Fermilab. The quench system was designed for a high level of dependability and long-term continuous operation. It is based on three tiers: Tier-I, FPGA-based Digital Quench Detection (DQD); Tier-II, Analog Quench Detection (AQD); and Tier-3, the quench controls and data management system. The Tier-I and Tier-II are completely independent and fully redundant systems. The Tier-3 system is based on National Instruments (NI) C-RIO and provides the user interface for quench controls and data management. It is independent from Tiers I & II. The DQD provides both quench detection and quench characterization (monitoring) capability. Both DQD and AQD have built-in high voltage isolation and user programmable gains and attenuations. The DQD and AQD also includes user configured current dependent thresholding and validation times. A 1st article of the three-tier system was fully implemented on the new Fermilab magnet test stand for the HL-LHC Accelerator Up-grade Project (AUP). It successfully provided quench protection and monitoring (QPM) for a cold superconducting bus test in November 2020. The Mu2e quench detection design has since been implemented for production testing of the AUP magnets. A detailed description of the system along with results from the AUP superconducting bus test will be presented

Structure of the Reaction Center from Rhodopseudomonas sphaeroides R-26 and 2.4.1: Protein-Cofactor (Bacteriochlorophyll, Bacteriopheophytin and Carotenoid) Interactions

The three-dimensional structures of the cofactors and protein subunits of the reaction center (RC) from the carotenoidless mutant strain of Rhodobacter sphaeroides R-26 and the wild-type strain 2.4.1 have been determined by x-ray diffraction to resolutions of 2.8 Å and 3.0 Å with R values of 24% and 26%, respectively. The bacteriochlorophyll dimer (D), bacteriochlorophyll monomers (B), and bacteriopheophytin monomers (φ) form two branches, A and B, that are approximately related by a twofold symmetry axis. The cofactors are located in hydrophobic environments formed by the L and M subunits. Differences in the cofactor-protein interactions between the A and B cofactors, as well as between the corresponding cofactors of Rb, sphaeroides and Rhodopseudomonas viridis [Michel, H., Epp, O. & Deisenhofer, J. (1986) EMBO J. 3, 2445-2451], are delineated. The roles of several structural features in the preferential electron transfer along the A branch are discussed. Two bound detergent molecules of beta-octyl glucoside have been located near B_A and B_B. The environment of the carotenoid, C, that is present in RCs from Rb. sphaeroides 2.4.1 consists largely of aromatic residues of the M subunit. A role of B_B in the triplet energy transfer from D to C and the reason for the preferential ease of removal of B_B from the RC is proposed

NEATH – II. N2H+ as a tracer of imminent star formation in quiescent high-density gas

Star formation activity in molecular clouds is often found to be correlated with the amount of material above a column density threshold of ∼1022cm−2 ⁠. Attempts to connect this column density threshold to a volume density above which star formation can occur are limited by the fact that the volume density of gas is difficult to reliably measure from observations. We post-process hydrodynamical simulations of molecular clouds with a time-dependent chemical network, and investigate the connection between commonly observed molecular species and star formation activity. We find that many molecules widely assumed to specifically trace the dense, star-forming component of molecular clouds (e.g. HCN, HCO+, CS) actually also exist in substantial quantities in material only transiently enhanced in density, which will eventually return to a more diffuse state without forming any stars. By contrast, N2H+ only exists in detectable quantities above a volume density of 104cm−3 ⁠, the point at which CO, which reacts destructively with N2H+, begins to deplete out of the gas phase on to grain surfaces. This density threshold for detectable quantities of N2H+ corresponds very closely to the volume density at which gas becomes irreversibly gravitationally bound in the simulations: the material traced by N2H+ never reverts to lower densities, and quiescent regions of molecular clouds with visible N2H+ emission are destined to eventually form stars. The N2H+ line intensity is likely to directly correlate with the star formation rate averaged over time-scales of around a Myr

Supersymmetry and discrete transformations of the Dirac operators in Taub-NUT geometry

It is shown that the N=4 superalgebra of the Dirac theory in Taub-NUT space has different unitary representations related among themselves through unitary U(2) transformations. In particular the SU(2) transformations are generated by the spin-like operators constructed with the help of the same covariantly constant Killing-Yano tensors which generate Dirac-type operators. A parity operator is defined and some explicit transformations which connect the Dirac-type operators among themselves are given. These transformations form a discrete group which is a realization of the quaternion discrete group. The fifth Dirac operator constructed using the non-covariant Killing-Yano tensor of the Taub-NUT space is quite special. This non-standard Dirac operator is connected with the hidden symmetry and is not equivalent to the Dirac-type operators of the standard N=4 supersymmetry.Comment: 14 pages, latex, no figure