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Advances in the Atomic-Scale Modeling of Nanosystems and Nanostructured Materials pp 81–98Cite as

Reactive Simulations for Biochemical Processes

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Part of the book series: Lecture Notes in Physics ((LNP,volume 795))

Abstract

After a brief review of the hybrid QM/MM molecular dynamics scheme and its coupling to the metadynamics method, I will show how such a combination of computational tools can be used to study chemical reactions of general biological interest. Specifically, by using such a reactive hybrid paradigm, where the QM driver is a Car–Parrinello Lagrangian dynamics, we have inspected the ATP hydrolysis reaction in the anti-freezing protein known as heat shock cognate protein (Hsc70) and the unconventional propagation of protons across peptide groups in the H-path of the bovine cytochrome c oxidase. While the former represents a fundamental reaction operated by all living beings in a wealth of processes and functions, the second one is involved in cell respiration. For both systems accurate X-ray data are available, yet the actual reaction mechanism escapes experimental probes. The simulations presented here provide the complementary information missing in experiments, offer a direct insight into the reaction mechanisms at a molecular level, and allow to understand which pathways nature can follow to realize these processes fundamental to living organisms.

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Authors and Affiliations

  1. Institut de Physique et Chimie des Matériaux de Strasbourg, 23 rue du Loess, F-67037, Strasbourg, France

    M. Boero

  2. Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan

    M. Boero

  3. CREST–Japan Science and Technology Agency, Honcho 4-1-8, Kawaguchi, Saitama, Japan

    M. Boero

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  1. M. Boero
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Correspondence to M. Boero .

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Editors and Affiliations

  1. CNRS-UMR 7504, Université Strasbourg, rue du Loess 22, Strasbourg CX 2, 67034, France

    Carlo Massobrio

  2. CNRS-UMR 7504, Université Strasbourg, rue du Loess 22, Strasbourg CX 2, 67034, France

    Hervé Bulou

  3. CNRS-UMR 7504, Université Strasbourg, rue du Loess 22, Strasbourg CX 2, 67034, France

    Christine Goyhenex

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Boero, M. (2010). Reactive Simulations for Biochemical Processes. In: Massobrio, C., Bulou, H., Goyhenex, C. (eds) Advances in the Atomic-Scale Modeling of Nanosystems and Nanostructured Materials. Lecture Notes in Physics, vol 795. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04650-6_3

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  • DOI: https://doi.org/10.1007/978-3-642-04650-6_3

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