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  • 1
    Electronic Resource
    Electronic Resource
    Binding of flexible ligands to proteins: Valproic acid and its interaction with cytochrome P450cam (1993)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 48 (1993), S. 161-180 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A combined theoretical and experimental study of the binding and interaction of valproic acid (VPA) with the bacterial cytochrome P450cam enzyme and the determination of regio- and stereoselective hydroxylation product distribution was performed. From the experiments, C4—;OH VPA was found to be the predominant hydroxylation product with a small amount of C5—OH VPA formed. The experimental stereoselectivity of hydroxylation was 2R4S 〉 ∼ 2S4R 〉 2R4R 〉 ∼ 2S4S and 2S5 〉 ∼ 2R5. The overall goals of the theoretical study were twofold: (1) to characterize as completely as possible, using energy optimization and molecular dynamics simulations, the interactions of flexible ligands with their target proteins, and (2) to determine the extent to which these results could be used to develop criteria to predict or explain the experimentally observed regio- and stereoselectivity of hydroxylation of the flexible ligands. Among the useful insights into the behavior of flexible ligands upon binding to their traget proteins obtained are (1) a large change in conformation occurs for many conformers of VPA upon binding to P450cam, (2) low- energy conformers of VPA do not necessarily lead to optimum interactions with the target protein, and (3) the most favorable mode of interaction of this flexible ligand with the protein binding site has been identified and found to be a result of strong electrostatic interactions between VPA and both Tyr96 and Asp297. For the study of the hydroxylated VPA products, the challenging aspect of this problem was to determine criteria for weighing the contribution of each of the possible protein-ligand complexes. To this end, various possibilities were examined and compared with the experimental results. No single complex was found to reproduce the observed experimental regio- and stereoselectivity. This result indicates that more than one bioactive form of VPA contributes to its oxidation. Results most consistent with experiment are obtained by using the interaction energy of the protein-ligand complex as a criterion for including its contribution to product formation. Although there are remaining disparities between predicted and observed product distributions, the combined theoretical and experimental effort has led to insights into the modes of interaction of this flexible ligand that lead to its observed product specificity. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560480718
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular-orbital studies of the mechanism of xanthine oxidase-catalyzed oxidation of purines, especially 2-chloropurineSupported by the Robert A. Welch Foundation (Grant No. D-182) of Houston, Texas, and by the Texas Technological College (No. 191-4753). (1967)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 1 (1967), S. 699-719 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Les réactions de la 2-chloropurine et d'autre bases, catalysées par la xanthine oxidase, ont été étudiées avec des méthodes différentes basées sur l'idée des orbitales molécularies, telles que HMO, ω-SCF—HMO, et PPP. Ces études not démontré l'importance des indices de réactivité électronique pour comprendre les réactions d'enzymes. De plus il paraît possible de prédire la spécificité de l'enzyme d'une analyse systématique de la différence entre les sites de réactions prédits et observés dans des substrats avec des substituants 2- et 8-oxy.Les concepts de densité d'obritale de frontière, de superdélocalisabilité et d'énergie de localisation se sont avérés tres utiles. Les Méthodes différentes ont donné en général dees résultats consistants.
    Abstract: Ein genauses Studium der durch Xanthine-Oxidas katalysierten Reaktionen von 2-Chloropurin und anderen Basen mittels verschiedenen MO-Methoden, wie HMO, ω-SCF—HMO, PPP, zeigt dass die Enzymreaktionen in der Sprache von elektronischen Reaktivitätsindizes beschrieben werden können. Es scheint möglich das Enzymspezifizität von einer systematischen Analysis der Verschiedenheit zwischen theoretisch berechnbeten und observierten Reaktionslagen in Substraten Mit 2- und 8-oxy Substituenten vorherzusagen.De Regriffe der Grenzorbitaldichte, des Superdelokalisabilitäts und der Lokalisierungsenergie sind sich sehyr nützlich rewiesen. Verschiedence MO-Methoden gaben im allgemeinen übereinstimmende Resultate.
    Notes: A detailed study to the xanthine oxidase-catalyzed reactions of 2-chloropurine and other substrate bases with various molecular-orbital techniques such as HMO, ω-SCF—HMO, and ppp semiempirical SCF—LCAO—MO has shown that the enzyme reactions can be understood in terms of electronic reactivity indices. Furthermore, it appeared possible to suggest the enzyme specificity from a systematic analysis of discrepancy between mo theoretically predicted and observed reaction sites in substrates with 2- and 8-oxy substituents. In other words, the discrepancy does not necessarily indicate the failure of the MO melthodes for such substrates, but it is possible to utilize the result in correlating with binding specificity of the ES complex. This has been done specifically for 2-chloropurine.Among several electronic reacxtivity indices, frontier orbital density, superdelocalizability, and localization energy have been proved to be very useful. Diferent MO methods gave, in general, consistent results.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560010519
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  • 3
    Electronic Resource
    Electronic Resource
    Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 346-350 
    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: Atomic partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110309
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  • 4
    Electronic Resource
    Electronic Resource
    Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1483-1506 
    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: Density functional theory is tested on a large ensemble of model compounds containing a wide variety of functional groups to understand better its ability to reproduce experimental molecular geometries, relative conformational energies, and dipole moments. We find that gradient-corrected density functional methods with triple-ζ plus polarization basis sets reproduce geometries well. Most bonds tend to be approximately 0.015 Å longer than the experimental results. Bond angles are very well reproduced and most often fall within a degree of experiment. Torsions are, on average, within 4 degrees of the experimental values. For relative conformational energies, comparisons with Hartree-Fock calculations and correlated conventional ab initio methods indicate that gradient-corrected density functionals easily surpass the Hartree-Fock approximation and give results which are nearly as accurate as MP2 calculations. For the 35 comparisons of conformational energies for which experimental data was available, the root mean square (rms) deviation for gradient-corrected functionals was approximately 0.5 kcal mol-1. Without gradient corrections, the rms deviation is 0.8 kcal mol-1, which is even less accurate than the Hartree-Fock calculations. Calculations with extended basis sets and with gradient corrections incorporated into the self-consistent procedure generate dipole moments with an rms deviation of 5%. Dipole moments from local density functional calculations, with more modest basis sets, can be scaled down to achieve roughly the same accuracy. In this study, all density functional geometries were generated by local density functional self-consistent calculations with gradient corrections added in a perturbative fashion. Such an approach generates results that are almost identical to the self-consistent gradient-corrected calculations, which require significantly more computer time. Timings on scalar and vector architectures indicate that, for moderately sized systems, our density functional implementation requires only slightly less computer resources than established Hartree-Fock programs. However, our density functional calculations scale much better and are significantly faster than their MP2 counterparts, whose results they approach. © 1995 John Wiley & Sons, Inc.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540161206
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  • 5
    Electronic Resource
    Electronic Resource
    Simulations of internal rotation potential energies for substituted ethanes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 743-753 
    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: Two approaches to the simulation of internal rotation potential energies in substituted ethanes are formulated for general applications. Called the vicinal Fourier coefficient and vicinal pair energy methods, they differ only in form. The latter procedure has the advantage of yielding energy terms that represent pairwise interactions between vicinal substitutents. As numerical examples, the potential energies of ethane and five of its simple methyl and chloro derivatives are employed to simulate the corresponding energies of two higher derivatives of the series. The initial energy data were calculated by the molecular mechanics method (MM2) with geometry optimizations and the ab initio MO procedure (STO-3G) with standard geometries. Results indicate that simulated energies are reasonably accurate for the flexible-rotor model (MM2) and extremely accurate for the rigid-rotor model (STO-3G). Deviations appear to be systematic and may be rationalized on the basis of molecular structure.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110607
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  • 6
    Electronic Resource
    Electronic Resource
    Control of mouse myoblast commitment to terminal differentiation by mitogens (1980)
    New York, N.Y. : Wiley-Blackwell
    Journal of Supramolecular Structure 14 (1980), S. 483-498 
    Details
    ISSN: 0091-7419
    Keywords: myoblast differentiation ; muscle cell culture ; mitogens ; growth factors ; myoblast cell lines ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Regulation of the transition of mouse myoblasts from proliferation to terminal differentiation was studied with clonal density cultures of a permanent clonal myoblast cell line. In medium lacking mitogenic activity, mouse myoblasts withdraw from the cell cycle, elaborate muscle-specific gene products, and fuse to form multinucleated myotubes. Addition of a purified mitogen, fibroblast growth factor, to mitogen-depleted medium stimulates continued proliferation and prevents terminal differentiation. When mitogens are removed for increasing durations and then refed, mouse myoblasts irreversibly commit to terminal differentiation: after 2-4 h in the absence of mitogens, myoblasts withdraw from the cell cycle, elaborate muscle-specific gene products, and fuse in the presence of mitogens that have been fed back. Population kinetics of commitment determined with 3H-thymidine labeling and autoradiography suggest the following cell-cycle model for mouse myoblast commitment: (1) if mitogens are present in the extracellular environment of myoblasts in G1 of the cell cycle, the cells enter S and continue through another cell cycle; (2) if mitogens have been absent for 2 or more hours, cells in G1 do not enter S; the cells commit to differentiate, permanently withdraw from the cell cycle (will not enter S if mitogens are refed), and they subsequently elaborate acetylcholine receptors and fuse (even if mitogens are refed); (3) cells in other phases of the cell cycle continue to transit the cell cycle in the absence of mitogens until reaching the next G1. The commitment kinetics and experiments with mitotically synchronized cells suggest that the commitment “decision” is made during G1. Present results do not, however, exclude commitment of some cells in other phases of the cell cycle.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jss.400140407
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  • 7
    Electronic Resource
    Electronic Resource
    Human placental cell surface antigens: Expression by cultured cells of diverse phenotypic origin (1979)
    New York, N.Y. : Wiley-Blackwell
    Journal of Supramolecular Structure 11 (1979), S. 503-515 
    Details
    ISSN: 0091-7419
    Keywords: glycoproteins ; two-dimensional electrophoresis ; differentiation ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The present work examined the expression of cell surface glycoprotein antigens in cultured human cell lines. The set of glycoproteins studied was defined by their immunoreactivity with antiserum developed to Triton-solubilized extracts of placental brush border membranes. Studies were performed using cell lines of trophoblastic (BeWo, JEG-3) and nontrophoblastic (Chang liver cells) origin, as well as diploid fibroblast cell lines (WI-38, GM-38).Antiplacental brush border antiserum reacts with at least 19 distinct antigens present in placental membrane preparations, each of which can be resolved and identified in two-dimensional electrophoresis. The subunit molecular weight and isoelectric point for all components were defined by their positions in the two-dimensional matrix. Thirteen of these could be detected among the five cell lines examined by lactoperoxidase-catalyzed cell surface iodination. One of these 13 antigens has been identified as the placental isoenzyme of alkaline phosphatase (PAP). The expression of this component is limited to choriocarcinonia cells and Chang liver cells and it is not present in diploid fibroblasts. Under normal circumstances expression of PAP is unique to the differentiated placenta but has been frequently demonstrated in both trophoblastic and nontrophoblastic neoplasms.Two other antigens are variably expressed among the different cell types examined in the present study and their presence or absence was independent of the trophoblastic, epithelial nontrophoblastic, or fibroblastic origin of the cells.Ten surface antigens were expressed in all five cell lines. Six of these had previously been found common to membranes from three adult differentiated tissues, including liver and kidney, as well as placenta (Wada et al, J Supramol Struc 10(3):287-305, 1979). The presence of this set of antigens in cultured cells as well extends the possibility that these are ubiquitously expressed on human cell surfaces. Two other antigens observed in all cultured cells had been found in both placental and either kidney or liver membranes and may represent common functions shared by many tissues which are also necessary for growth in vitro. The two remaining placental antigens seen in all cultured cells have previously been shown to be absent in adult tissues. Their presence in cultured cells but not in the membranes of resting differentiated tissues may signify the expression of glycoproteins characteristic of trophoblasts in all cells adapted to growth in culture.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jss.400110409
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  • 8
    Electronic Resource
    Electronic Resource
    Regulation of glucose carriers in chick fibroblasts (1977)
    New York, N.Y. : Wiley-Blackwell
    Journal of Supramolecular Structure 7 (1977), S. 499-513 
    Details
    ISSN: 0091-7419
    Keywords: glucose ; carrier ; regulation ; transport ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The derepression of glucose transport initiated by removing glucose from the incubation medium requires both protein and RNA synthesis. The synthesis and accumulation of putative mRNA for the carrier protein(s) can be demonstrated by inhibiting protein synthesis with cycloheximide (2 μg/ml). Release from inhibition with simulataneous addition of actionmycin D (1-5 μg/ml) results in a burst of carrier synthesis that achieves virtually maximal derepression in 4-6 h. An external energy source provided by a “nonrepressive” sugar (D-fructose, D-xylose) or by pyruvate is required to accomplish carrier synthesis. Previous failure to demonstrate mRNA accumulation was due to the depletion of energy in the starved cells. Glucose acts as a repressor at a posttranscriptional step, probably at the level of turnover of formed carrier.The protection of formed carrier in the absence of glucose and by inhibitors of protein synthesis even in the presence of glucose has encouraged conjecture that a protease is activated by a metabolic product of glucose that is analogous to a co-repressor. The glucose metabolite either activates the protease by direct interaction with it or alters the conformation of the carrier to expose a critical region to protease attack. Indeed the regulation of carrier density in the membrane of chick fibroblasts may be achieved entirely by carrier inactivation, the rate of which is a function of glucose concentration in the culture medium.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jss.400070319
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  • 9
    Electronic Resource
    Electronic Resource
    Activation of cyclic AMP-dependent protein kinase and stimulation of protein phosphorylation in response to adenosine in C-1300 murine neuroblastoma (1979)
    New York, N.Y. : Wiley-Blackwell
    Journal of Supramolecular Structure 10 (1979), S. 125-135 
    Details
    ISSN: 0091-7419
    Keywords: protein phosphorylation ; cAMP-dependent protein kinases ; adenosine on cyclic AMP ; C1300 neuroblastoma ; Life Sciences ; Molecular Cell Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: DEAE-cellulose chromatography of the 20,000g supernatant fraction of homogenates of C-1300 murine neuroblastoma (clone N2a) yields one major and two minor peaks of cyclic AMP-dependent protein kinase activity. Assessment of the endogenous activation state of the enzyme(s) reveals that the enzyme is fully activated by the treatment of whole cells with adenosine (10 μM) in the presence of the phosphodiesterase inhibitor Ro 20 1724 (0.7 mM). This treatment produces a large elevation in the cyclic AMP content of the cells. The treatment of whole cells with adenosine alone (1-100 μM) or Ro 20 1724 alone (0.1-0.7 mM) produces minimal elevations in cyclic AMP but nevertheless causes significant activations of cyclic AMP-dependent protein kinase. The autophosphorylation of whole homogenates of treated and untreated cells was studied using [γ-32P] ATP, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Treatments which activate cyclic AMP-dependent protein kinase selectively stimulate the incorporation of 32P into several proteins. This stimulation is most prominent in the 15,000-dalton protein band. The addition of cyclic AMP to phosphorylation reactions containing homogenate of untreated cells stimulates the phosphorylation of the same protein bands. These results indicate that adenosine may have regulatory functions through its effect on the cyclic AMP: cyclic AMP-dependent protein kinase system.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jss.400100203
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