Ermondi Giuseppe, Caron Giulia
Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, I 10125 Torino, Italy.
Biochem Pharmacol. 2006 Dec 15;72(12):1633-45. doi: 10.1016/j.bcp.2006.05.022. Epub 2006 Jul 7.
A variety of ligands interact with proteins in many biological processes; shape complementarity, electrostatic forces and hydrophobicity are the main factors governing these interactions. Although this is accepted by the scientific community, confusion about the significance of certain terms (e.g. hydrophobicity, salt bridge) and the difficulty of discussing the balance of acting forces rather than their single contributions, are two of the main problems encountered by researchers working in the field. These difficulties are sometimes enhanced by the unskilled use of informatics tools, which give great help in understanding the topic (especially from the visual standpoint), but only if used critically. After explaining some general chemical concepts, the commentary discusses the main forces governing ligand-protein interactions, focusing on those generating confusion among scientists with different backgrounds. Three examples of ligand-protein interactions are then discussed to illustrate the advantages and drawbacks of some in silico tools, highlighting the main interactions responsible for complex formation. The same examples are used to point out the limits in separating forces that are mandatory for occurrence of a given interaction and additional forces.
在许多生物过程中，多种配体与蛋白质相互作用；形状互补性、静电力和疏水性是支配这些相互作用的主要因素。尽管这已为科学界所接受，但对于某些术语（如疏水性、盐桥）的意义存在困惑，以及难以讨论作用力的平衡而非其单一贡献，是该领域研究人员遇到的两个主要问题。这些困难有时因信息学工具使用不熟练而加剧，这些工具在理解该主题方面有很大帮助（尤其是从视觉角度），但前提是要批判性地使用。在解释了一些一般化学概念后，本评论讨论了支配配体 - 蛋白质相互作用的主要作用力，重点关注那些在不同背景的科学家中产生困惑的作用力。然后讨论了三个配体 - 蛋白质相互作用的例子，以说明一些计算机模拟工具的优缺点，突出负责复合物形成的主要相互作用。同样的例子用于指出在区分给定相互作用发生所必需的力和额外力方面的局限性。
