Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids

Dear Colleagues,

More than one-third of all known proteins encoded need at least one metal ion to perform their biological function. In line with their importance, and with the potential cytotoxicity of some essential metals, the concentration and distribution of metal ions in the cell are tightly controlled. This control depends upon the combined action of sensing, transport, delivery, storage, detoxification, and efflux machineries. In addition, various metal-containing cofactors require dedicated biosynthetic enzymes for their assembly. Metal ions are also crucial to tune and stabilize the three-dimensional (3D) structure of nucleic acids, and to promote intermolecular interactions.

To understand how the aforementioned processes work, it is necessary to investigate the 3D structure and mobility of the involved macromolecules at the atomic level. Molecular dynamics (MD) simulations complement experimental information and generate new hypotheses on the molecular and cellular functions of metal ions. Among the specific challenges posed by the MD of metal-binding macromolecular systems, a particularly relevant one is the parametrization of the metal site. This is obviously crucial to achieve an accurate interpretation of the data.

In this Special Issue, we wish to cover recent technical advances in MD simulations of metal-binding to proteins and nucleic acids, as well as novel applications to all kinds of metal-dependent systems, by hosting a mix of original research articles and short critical reviews.

Prof. Dr. Antonio Rosato
Guest Editor

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