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  • 1
    Electronic Resource
    Electronic Resource
    A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation (1995)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 4363-4366 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00120a018
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  • 2
    Electronic Resource
    Electronic Resource
    Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 3483-3492 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new practical approach to studying enzyme reactions by combining ab initio QM/MM calculations with free energy perturbation is presented. An efficient iterative optimization procedure has been developed to determine optimized structures and minimum energy paths for a system with thousands of atoms on the ab initio QM/MM potential: the small QM sub-system is optimized using a quasi-Newton minimizer in redundant internal coordinates with ab initio QM/MM calculations, while the large MM sub-system is minimized by the truncated Newton method in Cartesian coordinates with only molecular mechanical calculations. The above two optimization procedures are performed iteratively until they converge. With the determined minimum energy paths, free energy perturbation calculations are carried out to determine the change in free energy along the reaction coordinate. Critical to the success of the iterative optimization procedure and the free energy calculations is the smooth connection between the QM and MM regions provided by a recently proposed pseudobond QM/MM approach [J. Chem. Phys. 110, 46 (1999)]. The methods have been demonstrated by studying the initial proton transfer step in the reaction catalyzed by the enzyme triosephosphate isomerase (TIM). © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480503
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  • 3
    Electronic Resource
    Electronic Resource
    A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: Solvation effects on the conformational equilibrium of dimethoxyethane (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 1722-1730 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Solvent effects on the conformational equilibria of dimethoxyethane (DME, CH3–O–CH2–CH2–O–CH3) have been studied using molecular dynamics simulation with a combined molecular mechanical and semiempirical quantum mechanical potential energy function. The potential of mean force around the central O–C–C–O dihedral angle of DME in water was determined using umbrella sampling, with the DME molecule treated by the modified intermediate neglect of diatomic differential overlap (MNDO) method and water molecules described using the extended simple point charge model. This potential of mean force shows the same bias as the gas phase potential energy surface calculated by MNDO: the heights of the barriers are underestimated and the stability of the gauche conformation with respect to the trans conformation is overestimated. However, the calculated stabilization of the gauche state by solvation is in good agreement with experimental results, suggesting a quite reasonable description of this system by the combined potential energy function. The solute–water atom pair distributions and the averaged percentage of solute–water hydrogen bonding does not change much when the central dihedral angle changes, but in the gauche conformation one water hydrogen can be hydrogen bonded with the two solute oxygen atoms simultaneously. The interactions between DME and its explicit water environment favor the gauche over the trans conformation much more than predicted by the reaction field model, although the overall relative stabilities predicted by the latter model are not so biased due to compensation of errors. The trans conformation of the outer C–O–C–C dihedral angles is most favored during the simulations, which is qualitatively different from the reaction field prediction that the trans–gauche+–gauche− would be the most stable conformer in solution. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468699
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  • 4
    Electronic Resource
    Electronic Resource
    IFN-γ mediates CD4 + T-cell loss and impairs secondary antitumor responses after successful initial immunotherapy (2007)
    [s.l.] : Nature Publishing Group
    Nature medicine 13 (2007), S. 354-360 
    Details
    ISSN: 1546-170X
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Protective cell-mediated immune responses in cancer are critically dependent on T-helper type 1 (TH1) cytokines such as interferon-γ (IFN-γ). We have previously shown that the combination of CD40 stimulation and interleukin-2 (IL-2) leads to synergistic antitumor responses in several ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nm1554
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  • 5
    Electronic Resource
    Electronic Resource
    Interleukin-13 sensitivity and receptor phenotypes of human glial cell lines: non-neoplastic glia and low-grade astrocytoma differ from malignant glioma (2000)
    Springer
    Cancer immunology immunotherapy 49 (2000), S. 319-324 
    Details
    ISSN: 1432-0851
    Keywords: Key words Interleukin 13 ; Astrocytoma ; Receptors ; Astrocytes ; STAT6
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Many of the actions and receptor components of interleukin-13 (IL-13), a pleiotrophic cytokine with immunotherapeutic potential, are shared with IL-4. Because human low-grade astrocytoma cells express IL-4 receptors and their growth is arrested by IL-4, we speculated that IL-13 sensitivity and receptor expression might also be present. The purpose of the current study was to investigate IL-13 receptor components and sensitivity in a series of glial cell lines derived from adult human non-neoplastic cerebral cortex, low-grade astrocytoma, anaplastic astrocytoma, and glioblastoma multiforme. Unlike peripheral blood lymphocytes (PBL), glial cells did not express IL-2 receptor γ chain. IL-13 receptor α-1 (IL-13Rα1), however, was present in 11/13 glial lines and PBL. Deficient cell lines were all glioblastoma-derived. All anaplastic astrocytoma and glioblastoma but not other glial lines or PBL expressed IL-13 receptor α-2 (IL-13Rα2). In non-neoplastic glia, low-grade, and anaplastic astrocytoma, IL-13 decreased DNA synthesis, an effect reversible with antibody to IL-4Rα. Results indicate that low-grade astrocytoma cells resemble non-neoplastic glia in terms of IL-13 sensitivity and IL-4Rα/IL-13Rα1 receptor profile but alterations occur with malignant progression. Glioblastoma cells were uniformly insensitive to IL-13 and, unlike other glia, failed to phosphorylate STAT6 after IL-13 challenge. Data suggest that IL-13 and analysis of IL-13 receptors may have clinical application in glial tumors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002620000110
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  • 6
    Electronic Resource
    Electronic Resource
    Molecular Dynamics with a Quantum-Chemical Potential: Solvent Effects on an SN2 Reaction at Nitrogen (1996)
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 2 (1996), S. 191-195 
    Details
    ISSN: 0947-6539
    Keywords: computer simulations ; molecular dynamics ; nucleophilic substitutions ; quantum chemistry ; solvent effects ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvent effects on an SN2 reaction at nitrogen (Cl- + NH2Cl → ClNH2 + Cl-) in dimethyl ether solution were studied by means of molecular dynamics simulation with a combined quantum-chemical and molecular-mechanical potential. The energetics and geometrical parameters of the reaction in the gas phase, calculated by means of the semiempirical model PM3(the quantum chemical part of the combined potential), were compared with ab initio calculations up to the 6-311 + G* */MP2 and 6-311 + G(2 d,p)/MP2 levels of theory. Compared with the gas phase potential energy surface, the free energy profile of the reaction in dimethyl ether solution shows that the solvent makes the ion-dipole complex well shallower by approximately 6.4 kcal mol-1 and raises the height of the effective barrier from the complex to the transition state by about 2.2 kcal mol-1. The overall transition barrier between the separated reactants and the products is raised from 6.4 kcal mol-1 to 15.0 kcal mol-1 upon solvation. The radial distribution functions between solvent-solute atom pairs at different stages of the reaction course were compared. Results show that better solvation of the charge-localised separated reactants is responsible for the increase in the barrier height. Polarisation of the solute by its surroundings is also discussed.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chem.19960020211
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  • 7
    Electronic Resource
    Electronic Resource
    Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1311-1318 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential7 was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151112
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  • 8
    Electronic Resource
    Electronic Resource
    The reaction pathway of the isomerization of d-xylose catalyzed by the enzyme d-xylose isomerase: A theoretical study (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 545-555 
    Details
    ISSN: 0887-3585
    Keywords: semi-empirical ; PM3 method ; quantum mechanics ; molecular mechanics ; reaction pathway ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Different pathways of the metal-induced isomerization of D-xylose to D-xylulose are investigated and compared in detail using energy minimization and molecular dynamics simulation. Two theoretical models are constructed for the reaction: in vacuum and in the enzyme D-xylose isomerase. The vacuum model is constructed based on the X-ray structure of the active site of D-xylose isomerase. It contains the atoms directly involved in the reaction and is studied using a semi-empirical molecular orbital method (PM3). The model in the enzyme includes the effects of the enzyme environment on the reaction using a combined quantum mechanical and molecular mechanical potential. For both models, the structures of the reactants, products, and intermediate complexes along the isomerization pathway are optimized. The effects of the position of the “catalytic Mg2+ ion” on the energies of the reactions are studied. The results indicate: 1) in vacuum, the isomerization reaction is favored when the catalytic metal cation is at site A, which is remote from the substrate; 2) in the enzyme, the catalytic metal cation, starting from site A, moves and stays at site B, which is close to the substrate; analysis of the charge redistribution of the active site during the catalytic process shows that the metal ion acts as a Lewis acid to polarize the substrate and catalyze the hydride shift; these results are consistent with previous experimental observations; and 3) Lys183 plays an important role in the isomerization reaction. The ε-NH3+ group of its side chain can provide a proton to the carboxide ion of the substrate to form a hydroxyl group after the hydride shift step. This role of Lys183 has not been suggested before. Based on our calculations, we believe that this is a reasonable mechanism and consistent with site-directed mutation experiments. © 1997 Wiley-Liss Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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