How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II
Abstract not provided
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Results for “COMPLEXITY”
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Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.
Wasmuth, Elizabeth V.↗
Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies
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99 GENERAL AND MISCELLANEOUS↗
Ion complexation waves emerge at the curved interfaces of layered minerals
Abstract Visualizing hydrated interfaces is of widespread interest across the physical sciences and is a particularly acute need for layered minerals, whose properties are governed by the structure of the electric double layer (EDL) where mineral and solution meet. Here, we show that cryo electron microscopy and tomography enable direct imaging of the EDL at montmorillonite interfaces in monovalent electrolytes with ångstrom resolution over micron length scales. A learning-based multiple-scattering reconstruction method for cryo electron tomography reveals ions bound asymmetrically on opposite sides of curved, exfoliated layers. We observe conserved ion-density asymmetry across stacks of interacting layers in cryo electron microscopy that is associated with configurations of inner- and outer-sphere ion-water-mineral complexes that we term complexation waves. Coherent X-ray scattering confirms that complexation waves propagate at room-temperature via a competition between ion dehydration and charge interactions that are coupled across opposing sides of a layer, driving dynamic transitions between stacked and aggregated states via layer exfoliation.
36 MATERIALS SCIENCE↗
Kohn–Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex
A theory for the nuclear chemical shifts of molecules in arbitrary spin states is applied to a set of paramagnetic organometallic complexes of 3d metals. Ligand chemical shifts are calculated and analyzed using Kohn–Sham (KS) density functional theory with and without relativistic corrections. The roles of the KS delocalization error, Gaussian-type versus Slater-type basis sets, relativistic effects (scalar and spin–orbit), and zero field splitting (ZFS) are investigated. A strong functional dependence of the chemical shifts is apparent and correlated with the delocalization error. Here, the functional dependence is between one and two orders of magnitude larger than variations of the NMR shifts due the other influences that are investigated. ZFS effects are negligible in the determination of the NMR chemical shifts of the complexes except at very low temperatures. The DFT calculated shifts agree reasonably well with experiment. A 73 ppm difference in the NMR shifts of the two protons in the amide groups of a high-spin Fe(II) macrocycle complex arises from selective O → Fe dative bonding that only involves the transfer of β spin density, along with orbital delocalization throughout the ligand bonding framework which electronically couples the coordinating oxygen lone pair orbitals directly to the amide trans proton.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Influence of bidentate ligand donor types on the formation and stability in 2 + 1 fac-[M I (CO) 3 ] + (M = Re, 99m Tc) complexes
Using a 2 + 1 ligand system for the fac -[M I (CO) 3 ] + (M = Re, 99m Tc) core, the influence of charge and nitrogen donor type were explored to determine labeling efficiency and stability by experimental and computational methods.
Chemistry↗
Arrested disproportionation in trivalent, mononuclear, and non-metallocene complexes of Zr(iii) and Hf(iii)
Reduction of the group 4 transition metal precursors [(PN) 2 MCl 2 ] (M = Zr (1), and Hf (2)); PN– = (N-(2-(diisopropylphosphino)-4-methylphenyl)-2,4,6-trimethylanilide), both readily prepared by transmetallation of 2 LiPN with [MCl 4 (THF) 2 ], with a slight excess of KC 8 , resulted in the isolation of the trivalent complexes [(PN) 2 MCl] (M = Zr (3), and Hf (4)). Complexes 1–4 were all identified by solid-state X-ray diffraction analysis, whereas in the case of 3 and 4 low temperature X-band EPR spectroscopy allowed for the identification of these metal-centered d 1 radicals. Here, a comparison with the isostructural and isoelectronic but more stable [(PN) 2 TiCl] is also presented.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Complexation-assisted reduction: complexes of glutaroimide-dioxime with tetravalent actinides (Np( iv ) and Th( iv ))
Glutaroimide-dioxime forms strong complexes with Np( iv ) and Th( iv ) in aqueous solution and in crystals. The formation of Np( iv ) complexes from initial Np( v ) is interpreted by a complexation-assisted reduction mechanism.
Zhang, Zhicheng↗
Surprisingly big linker-dependence of activity and selectivity in CO 2 reduction by an iridium(I) pincer complex
In this work, we report the quantitative electroreduction of CO 2 to CO by a PNP-pincer iridium(I) complex bearing amino linkers in DMF/water. The activity and selectivity of the reduction greatly depend on the choice of linker within the ligand. The complex 3-N is far superior to the analogues with methylene and oxygen linkers, showing higher activity and better selectivity for CO 2 over proton reduction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Stability of the complex generalized Hartree-Fock equations
For molecules with complex and competing magnetic interactions, it is often the case that the lowest energy Hartree-Fock solution may only be obtained by removing the spin and time-reversal symmetry constraints of the exact non-relativistic Hamiltonian. To do so results in the complex generalized Hartree-Fock (GHF) method. However, with the loss of variational constraints comes the greater possibility of converging to higher energy minima. Here, we report the implementation of stability test of the complex GHF equations, along with an orbital update scheme should an instability be found. We apply the methodology to finding the local minima of several spin-frustrated hydrogen rings, as well as the non-collinear molecular magnet Cr{sub 3}, illustrating the utility of the broken symmetry GHF method and some of its lesser-known nuances.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
The complex mixed Wentzel–Kramers–Brillouin-full-wave approach and its application to the two dimensional mode structure analysis of ion temperature gradient/collisionless trapped electron mode drift waves
The complex mixed Wentzel–Kramers–Brillouin (WKB)-full-wave approach is applied to the 2D mode structure analysis of ion temperature gradient/collisionless trapped electron mode drift waves in tokamak plasmas. The parallel mode structure is calculated with the full-wave approach, while the radial envelope is calculated with the complex WKB method. The tilting of the global mode structure along radius is demonstrated analytically. The effects of the phase and amplitude variation of the radial envelope on the parallel mode structure are included in terms of a complex radial wave vector in the parallel mode equation. It is shown that the radial equilibrium non-uniformity leads to the asymmetry of the parallel mode structure not only in configuration space but also in spectrum space. The mixed approach provides a practical way to analyze the asymmetric component of the global mode structure due to radial equilibrium non-uniformity.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Carbon dioxide is tightly bound in the [Co(Pyridine)(CO{sub 2})]{sup −} anionic complex
The [Co(Pyridine)(CO{sub 2})]{sup −} anionic complex was studied through the combination of photoelectron spectroscopy and density functional theory calculations. This complex was envisioned as a primitive model system for studying CO{sub 2} binding to negatively charged sites in metal organic frameworks. The vertical detachment energy (VDE) measured via the photoelectron spectrum is 2.7 eV. Our calculations imply a structure for [Co(Pyridine)(CO{sub 2})]{sup −} in which a central cobalt atom is bound to pyridine and CO{sub 2} moieties on either sides. This structure was validated by acceptable agreement between the calculated and measured VDE values. Based on our calculations, we found CO{sub 2} to be bound within the anionic complex by 1.4 eV.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycH–YopH chaperone–effector complex
The structure of a SycH–YopH chaperone–effector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycH–YopH complex is reported, determined to 1.9 Å resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called β-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the β-motif. Biochemical studies establish that the β-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides
Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning
Hyp-1, a pathogenesis-related class 10 (PR-10) protein from H. perforatum, was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The asymmetric unit of the tetartohedrally twinned crystal contains 28 copies of the protein arranged in columns with noncrystallographic sevenfold translational symmetry and with additional pseudotetragonal rotational NCS. Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John’s wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target
In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.
59 BASIC BIOLOGICAL SCIENCES↗