Here’s our pick of the best PLOS Computational Biology content for February.
The capacity of biological molecular data acquisition is growing faster than our ability to understand the relationships between molecules in a cell. There are multiple databases that store and organize these molecular data, yet emerging fundamental questions about the functions of these molecules in hierarchical cellular networks are poorly addressed. In a Perspective, Boris Kholodenko and colleagues explore recent advances in the development of publically available databases that help us analyze signal integration and processing by reconstructing multilayered networks that specify biological responses in both model organisms and human cells.
Structural pathways are important because they provide insight into signaling mechanisms, help understand the mechanism of disease-related mutations, and assist in drug discovery. Ozbabacan et al. construct the IL-1 structural pathway and map oncogenic mutations and SNPs. They show that modeling of protein-protein interactions on a large scale can provide accurate, structural atom-level detail of signaling pathways in the human cell and help delineate the mechanism through which a mutation leads to disease.
Numerous approaches have been undertaken over the last 50 years in an effort to explain allostery. Chung-Jung Tsai and Ruth Nussinov survey points of view on allostery in a Perspective, synthesizing them via a mathematical model in order to obtain a coherent understanding of the question of how allostery works. They address this question from three standpoints: thermodynamics, free energy landscape of population shift, and structure; all with exactly the same allosteric descriptors.