title: Intrinsic Disorder in Transmembrane Proteins: Roles in Signaling and Topology Prediction.
abstract: Intrinsically disordered regions (IDRs) are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP) are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies. We found that 50% of transmembrane proteins have at least one IDR of 30 amino acids or more. Interestingly, these domains preferentially localize to the cytoplasmic side especially of multi-pass transmembrane proteins, suggesting that disorder prediction could increase the confidence of topology prediction algorithms. This was supported by the successful prediction of the topology of the uncharacterized multi-pass transmembrane protein TMEM117, as confirmed experimentally. Pathway analysis indicated that IDPs are enriched in cell projection and axons and appear to play an important role in cell adhesion, signaling and ion binding. In addition, we found that IDP are enriched in phosphorylation sites, a crucial post translational modification in signal transduction, when compared to fully ordered proteins and to be implicated in more protein-protein interaction events. Accordingly, IDPs were highly enriched in short protein binding regions called Molecular Recognition Features (MoRFs). Altogether our analyses strongly support the notion that the transmembrane IDPs act as hubs in cellular signal events.
authors.affiliation: Faculty of life science, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Bürgi
authors.affiliation: Department of Cell Biology, Microbiology, and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL, 33620, United States of America.
authors.forename: Bin
authors.initials: B
authors.lastname: Xue
authors.affiliation: Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33647, United States of America.|Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.|Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Kingdom of Saudi Arabia.
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Uversky
authors.affiliation: Faculty of life science, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: F Gisou
authors.identifier: http://orcid.org/0000-0002-8522-274X
authors.initials: FG
authors.lastname: van der Goot
mesh_terms: D000465:Algorithms; D002448:Cell Adhesion / Q000235:genetics / Q000502:physiology; D019295:Computational Biology; D005455:Fluorescent Antibody Technique; D006367:HeLa Cells; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry*; D010766:Phosphorylation; D010957:Plasmids / Q000235:genetics; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D054875:Ubiquitination
chemical_list: D008565:Membrane Proteins