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WIREs Comput Mol Sci
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The description of electronic processes inside proteins from Car–Parrinello molecular dynamics: chemical transformations

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Abstract Used in the past mainly to solve problems in the field of physics, ab initio (Car–Parrinello) molecular dynamics (CPMD) is taking its place in the study of problems in chemistry and biochemistry. In particular, with regard to electronic processes in the interior of proteins that are either too subtle or too rapid to be studied by conventional structural biology tools, and too complex landscapes that cannot be resolved with either standard quantum chemical or traditional force‐field methods. The availability of faster and more powerful supercomputers has facilitated the usage of CPMD, whereas the development of methods to investigate complex landscapes (such as metadynamics) has opened significantly the range of biological problems that can be afforded. Here, we overview the progress in this field from the first studies of biological systems in the late 90s, with some illustrative examples in the area of enzymatic reactions. This article is categorized under: Molecular and Statistical Mechanics > Molecular Interactions

Atomic rearrangement and free energy surface (FES) corresponding to the glycosyl transfer reaction in trehalose‐6‐phosphate synthase (OtsA). Hydrogen atoms have been omitted for clarity, except the one being transferred from the sugar acceptor to the UDP phosphate group. Bonds being broken/formed are represented by a dotted black line (configurations 1, 3, and 4), whereas the crucial donor … acceptor hydrogen bond is represented by a dotted red line. (Reproduced from Ref 65. Copyright 2011, John Wiley & Sons, Ltd.)

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Proposed ‘front‐face’ mechanism for glycosyl transfer with retention of configuration. Some authors refer to it as a SNi‐like type of reaction. The species in parenthesis is expected to be a transient intermediate.112

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The glycosidic bond (red) is formed via the transfer of a monosaccharide (green) from a donor molecule (monosaccharide activated by a cofactor, gray) to an acceptor (blue). The acceptor might sit in the same face of the sugar that was previously occupied by the cofactor (retention of configuration) or in the opposite one (inversion of configuration).

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Computed mechanism of Cpd I reduction in catalase. The two pathways (A and B) are indicated by red and blue arrows, respectively. (Reproduced with permission from Refs 62 (Copyright 2009, American Chemical Society) and 111 (Copyright 2012, Elsevier).)

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Main reaction scheme of the catalytic cycle of catalase enzymes.

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Computed complex of the 1,3–1,4‐β‐glucanase enzyme with a 1,3–1,4‐β‐glucan tetrasaccharide. The saccharide ring located at the active site was predicted to be distorted in a skew‐boat conformation. (Reproduced with permission from Ref 103. Copyright 2010, Informa, PLC.)

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Free energy profiles for the main catalytic step in the DNA repair enzyme MutY, which is represented by the elongation of the N9·C1′ bond length. The bond length is constrained at various distances, and the averaged force on the constraint is integrated over the change in reaction coordinate to obtain the free energy. At a glycosidic bond length of 1.9 Å, a spontaneous, concerted proton transfer occurs from E43 to N7, mediated by a bridging water molecule. The proton exchanges reversibly between N7, wat1, and E43 within a range of glycosidic bond distances (1.9–2.3 Å), indicated by the orange circle. (Reproduced with permission from Ref 73. Copyright 2012, American Chemical Society.)

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