A simple pipeline for creating cover quality images of post-translational modifications to molecular structures in rare disease

Mo Rahman, Onno Faber, Pascale Marill, Otavio Good

View presentation:2022-10-16T19:40:00ZGMT-0600Change your timezone on the schedule page
2022-10-16T19:40:00Z
Exemplar figure, described by caption below
Three-step pipeline begins with parsing tab-delimited file of modified residues and type for three proteins important in rare diseases. UNIX Bash is used for its adaptability, as files with modifications loci may be different across projects. In step two modification data and AlphaFold predictions are loaded in Dalton a novel molecular viewer. Here we are able to edit the structure and add atoms or residues, within a real-time rendered environment. The last step loads the 3D model into rendering software of user choice, iIn the final image we see TGFB1 implicated in Camurati-Engelmann disease, with its pathogenic modifications.

The live footage of the talk, including the Q&A, can be viewed on the session page, Bio+MedVis: Challenges.

Abstract

Changes to molecular structure can have a large impact on biological function and are the basis for many diseases. Structural modifications to proteins, while not changes to the amino acid sequence, can alter their function and have been implicated in rare diseases. Visualizing these modifications on a 3D model helps understand how the characteristics of a molecule are affected. We present a simple pipeline to create high-quality rendered images of post-translational protein modifications. Data provided by CompOmics group at VIB and Ghent University in Ghent, Belgium is parsed using standard UNIX commands, then added to AlphaFold predicted structures using a newly developed viewer Dalton, and finally rendered to an image. Well-designed and simple to make visualizations demystify rare diseases and mechanisms of post-translational structural modifications, making it easier to conduct further research in these fields.