TY - JOUR T1 - Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network A1 - van Wijk, Sjoerd J. L. A1 - Melquiond, Adrien S. J. A1 - de Vries, Sjoerd J. A1 - Timmers, H. Th. Marc A1 - Bonvin, Alexandre M. J. J. Y1 - 2012/11/01 N2 - Author Summary During their life, proteins undergo various modifications ranging from structural marking or signaling to degradation. One major biochemical process involves ubiquitin, a small and evolutionary conserved protein. This regulatory protein serves as a tag that, when attached to a protein substrate, alters its function, cellular sub-location or commits the labeled protein to destruction in the proteasome. The high specificity of the ubiquitination pathway is achieved through interactions between two large protein families, E2 and E3, that ensure the efficient covalent conjugation of ubiquitin. By comparing two “almost identical” E2 enzymes, we identified a single minute substitution that, operated by a dynamic network of salt-bridges, functions as a subtle switch that controls interaction selectivity toward E3 proteins. Using a combination of bioinformatics and modeling techniques, complemented by mutagenesis and experimental screening of E2-E3 interactions, we unraveled an equilibrium between an “open”, binding-competent and a “closed”, binding-incompetent state. Subtle modifications in this network are sufficient to switch the selectivity profile. These findings should serves as a cautionary tale and raises new challenges for bioinformatics analysis, modeling and experimental engineering of protein-protein interactions. The dynamic nature of the identified regulatory switch suggests that the widely accepted sequence-structure-function paradigm should be extended to sequence-structure-dynamics-function. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 8 IS - 11 UR - https://doi.org/10.1371/journal.pcbi.1002754 SP - e1002754 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1002754 ER -