The replication terminator protein (RTP) of Bacillus subtilis is a homodimer that binds to each replication terminus and impedes replication fork movement in only one orientation with respect to the replication origin. The threedimensional structure of the RTP-DNA complex needs to be determined to understand how Replication of the chromosome of Bacillis subtilis is initiated at an unique origin, and under normal conditions the forks progress bidirectionally until converging at six sequencespecific replication termini that are located approximately 1800 from the origin (1-3). The terminus IR1 (Terl) appears to be the most frequently used site for replication fork arrest in vivo (4). Each terminus arrests replication forks in vivo and in vitro in only one orientation with respect to the replication origin (4-6). The replication terminator protein (RTP) specifically binds as two interacting dimers to each terminus (7-9). RTP is functional in vivo (10) and in vitro (5, 6, 11) in the surrogate Gram-negative Escherichia coli system and arrests the replicative helicases DnaB and PriA of E. coli in a polar mode (5, 6, 9, 11).RTP is a homodimeric protein with subunit molecular mass of 14.5 kDa (12, 13). The crystal structure of RTP has been determined at 2.6-A resolution and the structure reveals a disordered N-terminal arm, four a-helices, and three antiparallel (3-strands. The (2-and (3-strands are connected by an extended loop and the two a4-helices of the two monomers form an antiparallel coiled-coil dimerization domain. The overall structure is a winged helix with the (32-and (33-strands and the connecting loop of the two monomers forming the two wings and the al-, a2-, and a3-helices forming the prototypical helices of the winged helix ( Fig. 1 and ref.14). Two interacting dimers of RTP, bound to the overlapping core and the auxiliary sites, are necessary to impede replication forks (9). We have shown that the (33-strands and the tip of the extended loop that connects P2 with (33 are both necessary for dimerdimer interaction (9). Mutational analyses and biochemical studies have shown that the N-terminal arm, the (32-strand, and the a3-helix of RTP are involved in DNA binding (15).Although the structure of the RTP dimer is symmetrical (14), the protein impedes fork movement in an asymmetric mode (5-7, 9). It is reasonable to suspect that the interaction of the protein with DNA might provide the structural basis of the functional polarity. To understand the mechanistic details of replication fork arrest, it will be necessary to determine the structure of the RTP-DNA complex. The minimum functional unit of the replication terminus of B. subtilis consists of four turns of DNA and two interacting dimers of RTP, a structure that is perhaps too large and too flexible to lend itself to cocrystallization. We have therefore resorted to an alternative approach to derive a model of the three-dimensional structure of the DNA-protein complex. The approach consisted of the conversion of RTP into a site-directed chemical...
Uncertainty propagation (UP) methods are of great importance to design optimization under uncertainty. As a well-known and rigorous probabilistic UP approach, the polynomial chaos expansion (PCE) technique has been widely studied and applied. However, there is a lack of comprehensive overviews and studies of the latest advances of the PCE methods, and there is still a large gap between the academic research and engineering application for PCE due to its high computational cost. In this chapter, latest advances of the PCE theory and method are elaborated, in which the newly developed data-driven PCE method that does not depend on the complete information of input probabilistic distribution as the common PCE approaches is introduced and improved. Meanwhile, the least angle regression technique and the trust region scenario are, respectively, extended to reduce the computational cost of data-driven PCE to accommodate it to practical engineering design applications. In addition, comprehensive comparisons are made to explore the relative merits of the most commonly used PCE approaches in the literature to help designers to choose more suitable PCE techniques in probabilistic design optimization.
A new mineral species of the pyrochlore supergroup, hydroxyplumbopyrochlore (IMA2018-145), (Pb1.5,□0.5)Nb2O6(OH), has been discovered in the Jabal Sayid peralkaline granitic complex of the Arabian Shield, Saudi Arabia. It is associated with quartz, microcline, ‘biotite’, rutile, zircon, calcite, rhodochrosite, columbite-(Fe), goethite, thorite, bastnäsite-(Ce), xenotime-(Y), samarskite-(Y), euxenite-(Y), hydropyrochlore and fluornatropyrochlore. Hydroxyplumbopyrochlore usually shows euhedral octahedra, slightly rhombic dodecahedra and cubes or their combination (0.01–0.06 mm). The mineral is pale yellow to pale brown, transparent with white streak, and has adamantine to transparent lustre. It is brittle with conchoidal fracture. No cleavage or parting are observed. It is isotropic and non-fluorescent. The average microhardness is 463.4 kg mm–2. The calculated density is 6.474 g cm–3. Hydroxyplumbopyrochlore belongs to the cubic crystal system and exhibits the space group Fd $\bar{3}$ m with unit-cell parameters a = 10.5456(6) Å, V = 1172.8(2) Å3 and Z = 8. Electron microprobe analysis gave (6-point average composition, wt.%): CaO 0.32, SrO 0.16, FeO 0.17, Ce2O3 0.07, Pr2O3 0.02, PbO 51.69, Nb2O5 40.06, SiO2 0.05, TiO2 1.68, Ta2O5 4.74, H2Ocalc 0.95, total 99.90, yielding the empirical formula (Pb1.34Ca0.03Fe0.01Sr0.01□0.61)Σ2(Nb1.75Ti0.12Ta0.12Si0.01)Σ2O6(OH0.53O0.08□0.39)Σ1, where □ = vacancy. The Raman spectrum of hydroxyplumbopyrochlore contains the characteristic bands of O–H vibrations and no bands for H2O vibrations.
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