Berginski, M. E. | bioRxiv Science

bioRxiv2018

Coral: Clear and customizable visualization of human kinome data

Protein kinases represent one ofthe largest gene families in eukaryotes and play roles in a wide range of cell signaling processes and human diseases, making them attractive targets for drug development. The human kinome is extensively featured inhigh-throughput studiesgenerating genomic, proteomic, and kinase profiling data. Current tools for visualizing kinase data in the context of the human kinome superfamily are limited to encoding data through the addition of nodes to a low-resolution image of the kinome tree. We present Coral, a user-friendly interactive webapplication for visualizing both quantitative and qualitative data. Unlike previous tools, Coral can encode data in three features (node color, node size, and branchcolor), allowsthreemodesofkinomevisualization (the traditional kinome tree as well as radial and dynamic-force networks) and generates high-resolution scalable vector graphic files suitable for publication without the need for refinement in graphic editing software. Due to its user-friendly, interactive, and highly customizable design, Coral is broadly applicable to high-throughput studies of the human kinome. The source code and web application are available at github.com/dphansti/Coral. html and phanstiel-lab.med.unc.edu/Coral respectively.

bioinformatics↗

bioRxiv2018

Tunable molecular tension sensors reveal extension-based control of vinculin loading

Molecular tension sensors have contributed to a growing understanding of mechanobiology. However, the limited dynamic range and inability to specify the mechanical sensitivity of these sensors has hindered their widespread use in diverse contexts. Here, we systematically examine the components of tension sensors that can be altered to improve their functionality. Guided by the development of a first principles model describing the mechanical behavior of these sensors, we create a collection of sensors that exhibit predictable sensitivities and significantly improved performance in cellulo. Utilized in the context of vinculin mechanobiology, a trio of these new biosensors with distinct force- and extension- sensitivities reveal that an extension-based control paradigm regulates vinculin loading. To enable the rational design of molecular tension sensors appropriate for diverse applications, we predict the mechanical behavior, in terms of force and extension, of additional 1020 distinct designs.

biophysics↗