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Atomic structures of ternary Yb–Cd–Mg icosahedral quasicrystals and a 1/1 approximant

ABSTRACT: A systematic study of the structures of ternary icosahedral Yb–Cd–Mg quasicrystals with different Mg contents has been carried out by single-crystal X-ray diffraction; occupational and positional disorder in the resulting structures was compared with that in a Yb–Cd–Mg 1/1 approximant. Atomic structures of ternary icosahedral (i) Yb–Cd–Mg quasicrystals (QCs) with five different Mg contents up to 46.4?at.% and a corresponding 1/1 approximant (AP), which has a composition of Yb13.3Cd70.3Mg16.5, have been analysed by single-crystal X-ray diffraction. The structures of the iQCs were found to be isostructural to the parent i-YbCd5.7, which consists of a so-called Tsai-type rhombic triacontahedron (RTH) cluster and double Friauf polyhedron, and that of the 1/1 AP was found to be isostructural to YbCd6, which is described by a body-centred packing of the same type of RTH cluster. In the iQCs, it was found that there are three types of Cd/Mg occupation, namely, Cd preferential site, Mg preferential site and Cd/Mg mixed site, and the occupation probabilities of Mg atoms at the Mg preferential site show a saturation behaviour around the Mg content of 20?at.%. This selective Mg occupation is identified as a cause of the non-linear increase in the icosahedral lattice constant with increasing Mg content. The 1/1 AP has a similar selective Mg occupation to that of the iQCs in terms of the shell structures of the Tsai-type RTH cluster. In both iQCs and the 1/1 AP, the Mg preferential sites have a smaller number of Yb atoms among their coordination numbers. Moreover, short-range order (s.r.o.) diffuse scattering was observed on the diffraction patterns of the iQCs at the positions corresponding to a face-centred-type (F-type) icosahedral superlattice. The F-type s.r.o. was found to result from the Mg substitution.

SUBMITTER: Yamada T

PROVIDER: S-EPMC5744414 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Project description:Targeted protein degradation (TPD) has emerged as a powerful approach for removing (rather than inhibiting) proteins implicated in diseases. A key step in TPD is the formation of an induced proximity complex where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI and initiating the proteasomal degradation process. Here, we address three critical aspects of the TPD process using atomistic simulations: 1) formation of the ternary complex induced by a degrader molecule, 2) conformational heterogeneity of the ternary complex, and 3) degradation efficiency via the full Cullin Ring Ligase (CRL) macromolecular assembly. We combine experimental biophysical data---in this case hydrogen-deuterium exchange mass spectrometry (HDX-MS, which measures the solvent exposure of protein residues)---with molecular dynamics (MD) simulations aided by enhanced sampling techniques to accurately predict ternary complex structures at atomic resolution. We demonstrate improved efficiency, accuracy, and reliability in the ternary structure predictions of the bromodomain of the cancer target SMARCA2 with the E3 ligase VHL mediated by three different degrader molecules. The simulations accurately reproduce X-ray crystal structures -- including a new structure that we determined in this work (PDB ID: 7S4E) -- with root mean square deviations (RMSD) of 1.1 to 1.6 \r{A}. The simulations also reveal a structural ensemble of low-energy conformations of the ternary complex. Snapshots from these simulations are used as seeds for additional simulations, where we perform 7.1 milliseconds of aggregate simulation time using Folding@home. The detailed free energy surface captures the crystal structure conformation within a low-energy basin and is consistent with solution-phase experimental data (HDX-MS and SAXS). Finally, we graft a structural ensemble of the ternary complexes onto the full CRL and perform enhanced sampling simulations, which suggest that differences in degradation efficiency may be related to the proximity distribution of lysine residues on the POI relative to the E2-loaded ubiquitin. Several of the predicted ubiquitinated lysine residues have been validated through a ubiquitin mapping proteomics experiment. DOI 10.1038/s41467-022-33575-4

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Atomic structures of ternary Yb–Cd–Mg icosahedral quasicrystals and a 1/1 approximant

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