Bertini Luca, Bruschi Maurizio, Cosentino Ugo, Greco Claudio, Moro Giorgio, Zampella Giuseppe, De Gioia Luca
Department of Environmental Science, University of Milano-Bicocca, Milan, Italy.
Methods Mol Biol. 2014;1122:207-68. doi: 10.1007/978-1-62703-794-5_14.
It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.
众所周知，过渡金属离子常常与蛋白质结合，赋予其非常特定的功能特性。事实上，金属蛋白在诸如H2、O2和N2等小分子的运输和活化以及其他一些生化过程中发挥着关键的生物学作用。然而，尽管蛋白质活性位点中过渡金属的存在使得生物化学过程非常丰富，但由于过渡金属的存在，金属蛋白结构-活性关系的实验揭示通常很困难，过渡金属本质上具有非常多样且往往难以捉摸的化学性质。因此，计算方法正成为表征金属蛋白的非常流行的工具。特别是，由于CPU的持续技术发展，计算能力变得越来越便宜，适用于研究金属蛋白的计算工具越来越容易获得，因此在分子生物学和生物化学实验室中也更常用。在这里，我们介绍基于量子力学的主要程序和计算方法，这些方法通常用于研究金属蛋白和相关生物启发化合物的结构、电子和反应性质，特别关注正确研究此类生物分子系统时通常必须解决的实际和技术方面。
