Affiliation:
1. Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam , 1081 HV Noord-Holland, The Netherlands
Abstract
Abstract
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.
Funder
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Publisher
Oxford University Press (OUP)
Subject
Cell Biology,Developmental Biology,Embryology,Anatomy
Cited by
7 articles.
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