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Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.  相似文献   
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Alkanes composed of C−C and C−H show a low electric polarization, and therefore, there is only very weak interaction between alkanes and adsorbents. Thus, it is difficult to separate a specific alkane from a mixture of alkanes by adsorption. Here, two activated “channel-like” crystals generated from brominated thiacalix[4]arene propyl ethers, which adopt 1,3-alternate and partial cone conformations, recognize specific alkane vapors depending on alkane-shape and -size, sorting in three-type alkane guests such as linear, branched, and cyclic alkanes. Two activated crystals, which are prepared by removal of solvent upon heating under reduced pressure, incorporate branched and/or cyclic alkane vapors by a unique “gate-opening” mechanism via a crystal transformation in the process. Linear alkane vapors do not trigger gate opening and are not taken up by the activated crystals. The shape and size molecular-recognition properties of the activated crystals promises considerable usefulness for the separation of linear, branched, and cyclic alkanes.  相似文献   
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Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.  相似文献   
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Tanaka  Mirai  Okuno  Takayuki 《Numerical Algorithms》2021,86(3):1285-1302
Numerical Algorithms - The LP-Newton method solves linear programming (LP) problems by repeatedly projecting a current point onto a certain relevant polytope. In this paper, we extend the...  相似文献   
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The accelerator complex at the RIKEN Radioisotope Beam Factory accelerates heavy ions ranging from oxygen to uranium using triple stripping system to provide the beams at required charge. In many cases, the charge strippers cause problems during high-intensity beams accelerator operation. The charge stripper problem has been most significant during uranium beam acceleration because the lifetimes of the conventional carbon foils are extremely short. We conducted extensive R&D on the first stripper and found a solution using a low-Z gas stripper. We also plan to modify a second stripper operating recently with short-lifetime carbon foils. The stripper with better parameters will be needed when the beam intensity is increased by a new injector system for acceleration of uranium beam with higher charge.  相似文献   
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The ability of chloroform solutions of p-diethylaminomethylthiacalix[4]arene 1 to extract platinum from HCl media was tested. As an ion-pair extractant, compound 1 had the highest platinum extraction ability among all the thiacalix[n]arene derivatives tested in this study. Compound 1 was a highly specific extractant for Pt(IV) ions from single-metal solutions and platinum-group metal solutions from automotive catalyst residue. Various conditions such as contact time, pH, concentration of 1, effect of chloride ions, effect of acidity and Pt(IV) concentration were studied. The distribution ratio of platinum ions (D) was calculated. The platinum complex stoichiometry ratio was obtained using slope analysis. The 1–Pt(IV) complex was characterised using X-ray photoelectron spectroscopy, FT-IR and 1H NMR. Finally, the Pt(IV) extraction percentage of compound 1 was compared with that of previously reported thiacalix[n]arene-based extractants.  相似文献   
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We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.  相似文献   
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