Journal of Computational Chemistry

Cover image for Vol. 37 Issue 15

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2

    Tatiana Vasilevskaya, Maria G. Khrenova, Alexander V. Nemukhin and Walter Thiel

    Article first published online: 3 MAY 2016 | DOI: 10.1002/jcc.24395

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    A QM/MM study on the mechanism of peptide cleavage catalyzed by the matrix metalloproteinase type 2 (MMP-2) enzyme addresses a number of methodological issues. This includes the dependence of the QM/MM results on the treatment of the water environment, especially around the solvent-exposed active site.

  2. Necessity of high-resolution for coarse-grained modeling of flexible proteins

    Zhiguang Jia and Jianhan Chen

    Article first published online: 29 APR 2016 | DOI: 10.1002/jcc.24391

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    Low spatial resolution in representing either the protein or solvent molecules results in severe deficiencies in accurate modeling of context-dependent protein conformational transitions. High physical resolution at or near the atomistic level is likely necessary for developing flexible protein models with explicit, microscopic solvents, and the coarse-graining needs to focus on exploiting possible simplification in interaction potentials.

  3. Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR)

    Margareta R. A. Blomberg and Per E. M. Siegbahn

    Article first published online: 29 APR 2016 | DOI: 10.1002/jcc.24396

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    Using the example of NO reduction in the cytochrome c dependent enzyme nitric oxide reductase (cNOR) it is shown how a careful combination of computational and experimental data can produce reliable descriptions of entire catalytic cycles. From the energy profile, the reaction mechanism can be determined and basic bioenergetic questions can be answered.

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    Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

    Martin A. Olsson, Pär Söderhjelm and Ulf Ryde

    Article first published online: 27 APR 2016 | DOI: 10.1002/jcc.24375

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    Different methods have been tested to obtain converged ligand-binding energies with quantum mechanical (QM) methods, based on molecular dynamics simulations at the molecular mechanics level. The results indicate that single-step exponential averaging (ssEA) with cumulant expansion (ssEAc) gives more precise results and uses fewer QM calculations than non-Boltzmann Bennett acceptance ratio approaches employing either all data (NBB13) or only two states at each end point (NBB4).

  5. Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

    Travis V. Harris and Robert K. Szilagyi

    Article first published online: 26 APR 2016 | DOI: 10.1002/jcc.24384

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    A set of general rules was developed for constructing computational models that capture covalent and electrostatic interactions from protein environment with significance to the structure of transition-metal prosthetic group. The rules were developed from detailed analyses of the spin density, Coulomb potential, vertical ionization energies was carried out for a [2Fe-2S] cluster. Their transferability was evaluated for the H-cluster of the FeFe-hydrogenase and the [Cu-OTyrCys] catalytic centers of the galactose oxidase.

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