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排序方式: 共有163条查询结果,搜索用时 31 毫秒
1.
2.
Seda Keskin 《Molecular simulation》2013,39(1):14-24
Grand canonical Monte Carlo and equilibrium molecular dynamics simulations were used to assess the performance of an rht-type metal–organic framework (MOF), Cu-TDPAT, in adsorption-based and membrane-based separation of CH4/H2, CO2/CH4 and CO2/H2 mixtures. Adsorption isotherms and self-diffusivities of pure gases and binary gas mixtures in Cu-TDPAT were computed using detailed molecular simulations. Several properties of Cu-TDPAT such as adsorption selectivity, working capacity, diffusion selectivity, gas permeability and permeation selectivity were computed and compared with well-known zeolites and MOFs. Results showed that Cu-TDPAT is a very promising adsorbent and membrane material especially for separation of CO2 and it can outperform traditional zeolites and MOFs such as DDR, MFI, CuBTC, IRMOF-1 in adsorption-based CO2/CH4 and CO2/H2 separations. 相似文献
3.
Abstract A set of protein conformations are analyzed by normal mode analysis. An elastic network model is used to obtain fluctuation and cooperativity of residues with low amplitude fluctuations across different species. Slow modes that are associated with the function of proteins have common features among different protein structures. We show that the degree of flexibility of the protein is important for proteins to interact with other proteins and as the species gets more complex its proteins become more flexible. In the complex organism, higher cooperativity arises due to protein structure and connectivity. 相似文献
4.
Semih Engin Arif Can Keskin Tolga Akdemir Dilruba Seyhan 《Zoology in the Middle East.》2013,59(4):368-371
Fourteen species of aphids (Hemiptera: Aphidoidea) are recorded as new to Saudi Arabia. These are: Aphis coreopsidis (Thomas, 1878); Aphis illinoisensis Shimer, 1866; Baizongia pistaceae (Linnaeus, 1767); Capitophorus elaeagni (del Guercio, 1894); Dysaphis plantaginea (Passerini, 1860); Eucarazzia elegans (Ferrari, 1872); Geoica lucifuga (Zehntner, 1897); Hayhurstia atriplicis (Linnaeus, 1761); Macrosiphoniella absinthii (Linnaeus, 1758); Macrosiphoniella sanborni (Gillette, 1908); Smynthurodes betae Westwood, 1849; Uroleucon cichorii (Koch, 1855), and Wahlgreniella nervata (Gillette, 1908). Among these, three species, i.e. A. coreopsidis, A. illinoisensis, and W. nervata are alien species. 相似文献
5.
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of phipsi pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge-based pairwise dependent phipsi energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all-atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native-state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context-dependent phipsi correlations into the chain that would affect the choice of native-state torsional angles. 相似文献
6.
Keskin O 《Journal of biomolecular structure & dynamics》2002,20(3):333-345
Molecular fluctuations of the native conformation of c-AMP dependent protein kinase (cAPK) have been investigated with three different approaches. The first approach is the full atomic normal mode analysis (NMA) with empirical force fields. The second and third approaches are based on a coarse-grained model with a single single-parameter- harmonic potential between close residues in the crystal structure of the molecule without any residue specificity. The second method calculates only the magnitude of fluctuations whereas the third method is developed to find the directionality of the fluctuations which are essential to understand the functional importance of biological molecules. The aim, in this study, is to determine whether using such coarse-grained models are appropriate for elucidating the global dynamic characteristics of large proteins which reduces the size of the system at least by a factor of ten. The mean-square fluctuations of C(alpha) atoms and the residue cross-correlations are obtained by three approaches. These results are then compared to test the results of coarse grained models on the overall collective motions. All three of the approaches show that highly flexible regions correspond to the activation and solvent exposed loops, whereas the conserved residues (especially in substrate binding regions) exhibit almost no flexibility, adding stability to the structure. The anti-correlated motions of the two lobes of the catalytic core provide flexibility to the molecule. High similarities among the results of these methods indicate that the slowest modes governing the most global motions are preserved in the coarse grained models for proteins. This finding may suggest that the general shapes of the structures are representative of their dynamic characteristics and the dominant motions of protein structures are robust at coarse-grained levels. 相似文献
7.
Cells expressing indoleamine 2,3-dioxygenase inhibit T cell responses 总被引:34,自引:0,他引:34
Mellor AL Keskin DB Johnson T Chandler P Munn DH 《Journal of immunology (Baltimore, Md. : 1950)》2002,168(8):3771-3776
Pharmacological inhibition of indoleamine 2,3-dioxygenase (IDO) activity during murine gestation results in fetal allograft rejection and blocks the ability of murine CD8(+) dendritic cells to suppress delayed-type hypersensitivity responses to tumor-associated peptide Ags. These observations suggest that cells expressing IDO inhibit T cell responses in vivo. To directly evaluate the hypothesis that cells expressing IDO inhibit T cell responses, we prepared IDO-transfected cell lines and transgenic mice overexpressing IDO and assessed allogeneic T cell responses in vitro and in vivo. T cells cocultured with IDO-transfected cells did not proliferate but expressed activation markers. The potency of allogeneic T cell responses was reduced significantly when mice were preimmunized with IDO-transfected cells. In addition, adoptive transfer of alloreactive donor T cells yielded reduced numbers of donor T cells when injected into IDO-transgenic recipient mice. These outcomes suggest that genetically enhanced IDO activity inhibited T cell proliferation in vitro and in vivo. Genetic manipulation of IDO activity may be of therapeutic utility in suppressing undesirable T cell responses. 相似文献
8.
The aim of the study was to examine the effects of zinc supplementation on some hematological parameters. Sixty newborn male
broiler chicks were utilized in the study. Zinc (Zn) was added into drinking water at levels of 0, 125, 500, and 1000 mg/kg.
In the study, there was no significant difference between control and Zn-supplemented groups in erythrocyte count, hemoglobin
amount, hematocrit levels, total leukocyte count, and differential leukocyte % levels, but the α-naphthyl acetate esterase
ANAE(+) lymphocyte rate significantly (p<0.05) increased in the 125-ppm Zn-supplemented group compared with the control group. In conclusion, the data obtained may
be beneficial in demonstrating the effects of zinc on, at least, these parameters. 相似文献
9.
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) belongs to a class of catalytic enzymes involved in phosphoryl transfer and is a new target for the development of novel antimicrobial agents. In the present study, the fundamental consideration is to view the overall structure of HPPK as a network of interacting residues and to extract the most cooperative collective motions that define its global dynamics. A coarse-grained model, harmonically constrained according to HPPK's crystal structure is used. Four crystal structures of HPPK (one apo and three holo forms with different nucleotide and pterin analogs) are studied with the goal of providing insights about the function-dynamic correlation and ligand induced conformational changes. The dynamic differences are examined between HPPK's apo- and holo-forms, because they are involved in the catalytic reaction steps. Our results indicate that the palm-like structure of HPPK is nearly rigid, whereas the two flexible loops: L2 (residues 43-53) and L3 (residues 82-92) exhibit the most concerted motions for ligand recognition and presumably, catalysis. These two flexible loops are involved in the recognition of HPPKs nucleotide and pterin ligands, whereas the rigid palm region is associated with binding of these cognate ligands. Six domains of collective motions are identified, comprised of structurally close but not necessarily sequential residues. Two of these domains correspond to the flexible loops (L2 and L3), whereas the remaining domains correspond to the rigid part of the molecule. 相似文献
10.
Keskin DB Marshall B Munn D Mellor AL Gearhart DA 《Cellular & molecular biology letters》2007,12(1):82-102
The activity of indoleamine 2, 3-dioxygenase (IDO; E.C. 1.13.11.42) catalyzes the oxidative cleavage of tryptophan to form
kynurenine. IDO activity consumes superoxide anions; therefore, we postulated that over-expression of IDO might mitigate superoxide-anion
dependent, oxidative modification of cellular proteins in vitro. We prepared and characterized RAW 264.7 macrophages that were stably transfected with either an IDO expression vector or
the control (empty) vector. We detected IDO mRNA, protein, and enzyme activity in the IDO-transfected macrophages, but not
in the macrophages transfected with the empty vector. To generate superoxide anions in situ, we treated the IDO-and control-transfected cultures with xanthine or hypoxanthine, and then used ELISA methods to quantitate
the relative levels of oxidatively modified proteins in total cell lysates. The levels of protein carbonyls were similar in
IDO-transfected and vector-transfected macrophages; however, protein nitration was significantly less in IDO-transfected cells
compared to control transfectants. In addition, steady-state levels of superoxide anions were significantly lower in the IDO-transfected
cultures compared with control transfectants. Our results are consistent with the concept that, besides degrading tryptophan,
IDO activity may protect cells from oxidative damage. 相似文献