{"title":"阐明生物网络中结合统计与香农信息之间的联系","authors":"Kinshuk Banerjee, Biswajit Das","doi":"10.1063/5.0226904","DOIUrl":null,"url":null,"abstract":"<p><p>The response of a biological network to ligand binding is of crucial importance for regulatory control in various cellular biophysical processes that is achieved with information transmission through the different ligand-bound states of such networks. In this work, we address a vital issue regarding the link between the information content of such network states and the experimentally measurable binding statistics. Several fundamental networks of cooperative ligand binding, with the bound states being adjacent in time only and in both space and time, are considered for this purpose using the chemical master equation approach. To express the binding characteristics in the language of information, a quantity denoted as differential information index is employed based on the Shannon information. The index, determined for the whole network, follows a linear relationship with (logarithmic) ligand concentration with a slope equal to the size of the system. On the other hand, the variation of Shannon information associated with the individual network states and the logarithmic sensitivity of its slope are shown to have generic forms related to the average binding number and variance, respectively, the latter yielding the Hill slope, the phenomenological measure of cooperativity. Furthermore, the variation of Shannon information entropy, the average of Shannon information, is also shown to be related to the average binding.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1000,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Elucidating the link between binding statistics and Shannon information in biological networks.\",\"authors\":\"Kinshuk Banerjee, Biswajit Das\",\"doi\":\"10.1063/5.0226904\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The response of a biological network to ligand binding is of crucial importance for regulatory control in various cellular biophysical processes that is achieved with information transmission through the different ligand-bound states of such networks. In this work, we address a vital issue regarding the link between the information content of such network states and the experimentally measurable binding statistics. Several fundamental networks of cooperative ligand binding, with the bound states being adjacent in time only and in both space and time, are considered for this purpose using the chemical master equation approach. To express the binding characteristics in the language of information, a quantity denoted as differential information index is employed based on the Shannon information. The index, determined for the whole network, follows a linear relationship with (logarithmic) ligand concentration with a slope equal to the size of the system. On the other hand, the variation of Shannon information associated with the individual network states and the logarithmic sensitivity of its slope are shown to have generic forms related to the average binding number and variance, respectively, the latter yielding the Hill slope, the phenomenological measure of cooperativity. Furthermore, the variation of Shannon information entropy, the average of Shannon information, is also shown to be related to the average binding.</p>\",\"PeriodicalId\":15313,\"journal\":{\"name\":\"Journal of Chemical Physics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2024-09-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Physics\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1063/5.0226904\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, PHYSICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Physics","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1063/5.0226904","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
Elucidating the link between binding statistics and Shannon information in biological networks.
The response of a biological network to ligand binding is of crucial importance for regulatory control in various cellular biophysical processes that is achieved with information transmission through the different ligand-bound states of such networks. In this work, we address a vital issue regarding the link between the information content of such network states and the experimentally measurable binding statistics. Several fundamental networks of cooperative ligand binding, with the bound states being adjacent in time only and in both space and time, are considered for this purpose using the chemical master equation approach. To express the binding characteristics in the language of information, a quantity denoted as differential information index is employed based on the Shannon information. The index, determined for the whole network, follows a linear relationship with (logarithmic) ligand concentration with a slope equal to the size of the system. On the other hand, the variation of Shannon information associated with the individual network states and the logarithmic sensitivity of its slope are shown to have generic forms related to the average binding number and variance, respectively, the latter yielding the Hill slope, the phenomenological measure of cooperativity. Furthermore, the variation of Shannon information entropy, the average of Shannon information, is also shown to be related to the average binding.
期刊介绍:
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
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