Method of counting atoms to determine the elemental composition of viruses and its applications in biothermodynamics and environmental sciences

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Comput Biol Chem. January 4, 2022; 96: 107621. doi: 10.1016 / j.compbiolchem.2022.107621. Online ahead of print.

ABSTRACT

The quantitative physico-chemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physico-chemical approach can be applied to virtually all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this article, a new method is suggested to determine the elemental composition of viruses, based on counting atoms. The method of counting atoms requires knowledge of the genetic sequence, protein sequences and protein copy numbers. An algorithm has been suggested for a program which finds the basic composition of various viruses (DNA or RNA, enveloped or not). With the exception of nucleic acid, capsid proteins, lipid bilayer, and carbohydrates, this method includes membrane proteins as well as spike proteins. The method of counting atoms was compared to the molecular composition and to the existing geometric methods on 5 viruses of different morphology, as well as to the experimentally determined composition of the poliovirus. The method of counting atoms has been found to be more accurate in most cases. The three methods were found to be complementary, as they require different types of input information. In addition, since the 3 methods are based on different assumptions, the results of one model can be compared to those of the other two.

PMID: 34998080 | DOI: 10.1016 / j.compbiolchem.2022.107621

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