How sticky are our proteins? Quantifying hydrophobicity of the human proteome.

Summary: Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the solvent. These residues can play an important functional role, e.g. in protein-protein and membrane interactions. Here, we first investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic surface area, the relative hydrophobic surface area and-using our MolPatch method-the largest hydrophobic patch. Secondly, we analyze how difficult it is to predict these measures from sequence: by adapting solvent accessibility predictions from NetSurfP2.0, we obtain well-performing prediction methods for the THSA and RHSA, while predicting LHP is more challenging. Finally, we analyze implications of exposed hydrophobic surfaces: we show that hydrophobic proteins typically have low expression, suggesting cells avoid an overabundance of sticky proteins. Availability and implementation: The data underlying this article are available in GitHub at https://github.com/ibivu/hydrophobic_patches. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Examining geographic accessibility to radiotherapy in Canada and Greenland for indigenous populations: Measuring inequities to inform solutions.

BACKGROUND: A high cancer burden exists among indigenous populations worldwide. Canada and Greenland have similar geographic features that make health service delivery challenging. We sought to describe geographic access to radiotherapy for indigenous populations in both regions. METHODS: We used geospatial analyses to calculate distance and travel-time from indigenous communities in Canada and Greenland to the nearest radiotherapy center. We calculated the proportion of indigenous communities and populations residing within a 1 and 2-hour drive of a radiotherapy center in Canada, and compared the proportion of indigenous versus non-indigenous populations residing within each drive-time area. We calculated the potential distance and travel-time saved if radiotherapy was available in northern Canada (Yellowknife and Iqaluit), and Greenland (Nuuk). RESULTS: Median one-way travel from indigenous communities to nearest radiotherapy center in Canada was 268 km (3 h when considering any transportation mode), and 4111 km (6 h by plane) in Greenland. In Canada, 84% and 68% of indigenous communities were outside a 1 and 2-hour drive from a radiotherapy center, respectively. Only 2% of the total population in Canada resided outside a 2-hour drive from a radiotherapy center. However, indigenous peoples were 336 times more likely to live more than a 2-hour drive away, compared to non-indigenous peoples. Nearly 3 million km and 4000 h of travel could be saved over a 10-year period for patients with newly diagnosed cancers in Canada, and 7 million km and 10,000 h in Greenland, if radiotherapy was available in Yellowknife, Iqaluit and Nuuk. CONCLUSIONS: Geography is an important barrier to accessing radiotherapy for indigenous populations in Canada and Greenland. A significant disparity exists between indigenous and non-indigenous peoples in Canada. Geospatial analyses can help highlight disparities in access to inform radiotherapy service planning.