biostudies-literatureUnknown121(10)Deng YKementerian Pendidikan MalaysiaNational Research Foundation SingaporeMinistry of Education - SingaporeBiological functions of proteins rely on their specific interactions with binding partners. Many proteins contain multiple domains, which can bind to their targets that often have more than one binding site, resulting in multivalent interactions. While it has been shown that multivalent interactions play a crucial role in modulating binding affinity and specificity, other potential effects of multivalent interactions are less explored. Here, we developed a broadly applicable transfer-matrix formalism and used it to investigate the binding of two-domain ligands to targets with multiple binding sites. We show that 1) ligands with two specific binding domains can drastically boost both the binding affinity and specificity and downshift the working concentration range, compared with single-domBiophysical journal1868-1880https://www.ebi.ac.uk/biostudies/studies/S-EPMC9199096biostudies-literatureModulating binding affinity, specificity, and configurations by multivalent interactions.PMC9199096Yan JEfremov AKDeng YfalseModulating binding affinity, specificity, and configurations by multivalent interactions.Biological functions of proteins rely on their specific interactions with binding partners. Many proteins contain multiple domains, which can bind to their targets that often have more than one binding site, resulting in multivalent interactions. While it has been shown that multivalent interactions play a crucial role in modulating binding affinity and specificity, other potential effects of multivalent interactions are less explored. Here, we developed a broadly applicable transfer-matrix formalism and used it to investigate the binding of two-domain ligands to targets with multiple binding sites. We show that 1) ligands with two specific binding domains can drastically boost both the binding affinity and specificity and downshift the working concentration range, compared with single-dom2022-01-01T00:00:00Z2022 May2025-04-04T08:58:29.458Z2025-04-04T08:58:29.458ZS-EPMC91990963545082710.1016/j.bpj.2022.04.017