Bikiel Damián E, Boechi Leonardo, Capece Luciana, Crespo Alejandro, De Biase Pablo M, Di Lella Santiago, González Lebrero Mariano C, Martí Marcelo A, Nadra Alejandro D, Perissinotti Laura L, Scherlis Damián A, Estrin Darío A
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, Argentina.
Phys Chem Chem Phys. 2006 Dec 28;8(48):5611-28. doi: 10.1039/b611741b. Epub 2006 Oct 11.
Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.
血红素蛋白存在于所有生物体内，执行着各种各样的任务，从电子传递、有机化合物的氧化到小分子的传感与运输。在这项工作中，我们回顾了经典和量子力学原子模拟工具在血红素蛋白化学中几个相关问题研究中的应用：（i）使用经典分子动力学模拟研究构象分析、配体迁移和溶剂化效应；（ii）使用量子力学（QM）方法探索活性位点的电子结构和自旋态能量学；（iii）通过量子力学-分子力学（QM-MM）混合技术研究血红素蛋白与小配体的相互作用；（iv）最后，通过量子和经典工具的结合来解决化学反应性和催化问题。
