Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins
By Juyong Lee, Janez Konc, Dusanka Janezic, Bernard R. Brooks. 2017
7 citations recorded by the source corpus.
The global organization of protein binding sites is analyzed by constructing a weighted network of binding sites based on their structural similarities and detecting communities of structurally similar binding sites based on the minimum description length principle. The analysis reveals that there are two central binding site communities that play the roles of the network hubs of smaller peripheral communities. The sizes of communities follow a power-law distribution, which indicates that the binding sites included in larger communities may be older and have been evolutionary structural scaffolds of more recent ones. Structurally similar binding sites in the same community bind to diverse ligands promiscuously and they are also embedded in diverse domain structures. Understanding the general principles of binding site interplay will pave the way for improved drug design and protein design.
Subfields: Materials Chemistry, Molecular Biology
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Citations in the corpus
- BERTology Meets Biology: Interpreting Attention in Protein Language Models (2020, background): “Past work has shown that binding sites can reveal evolutionary relationships among proteins [42] and that particular structural motifs in binding sites are mainly restricted to specific families or superfamilies of proteins [37].”