School of Life Sciences, Technical University of Munich, Freising, Germany.
Comput Biol Chem. 2022 Feb;96:107621. doi: 10.1016/j.compbiolchem.2022.107621. Epub 2022 Jan 4.
Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two.
从定量物理化学的角度研究生命过程是生物工程和生物技术的巨大优势。如果已知其化学成分和热力学性质，定量物理化学方法几乎可以应用于所有生物体，包括病毒。本文提出了一种基于原子计数的确定病毒元素组成的新方法。原子计数法需要了解遗传序列、蛋白质序列和蛋白质拷贝数。本文还提出了一种针对各种病毒（DNA 或 RNA、有包膜或无包膜）的元素组成的程序算法。除了核酸、衣壳蛋白、脂质双层和碳水化合物外，该方法还包括膜蛋白和刺突蛋白。将原子计数法与现有的分子组成和几何方法在 5 种不同形态的病毒以及实验确定的脊髓灰质炎病毒组成上进行了比较。在大多数情况下，原子计数法更准确。这三种方法是互补的，因为它们需要不同类型的输入信息。此外，由于这三种方法基于不同的假设，因此可以比较一种模型的结果与其他两种模型的结果。
