Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

By G. Kapp, Sen Liu, Amelie Stein, D. T. Wong, Attila Reményi, Brian J. Yeh, James S. Fraser, J. Taunton, Wendell A. Lim, Tanja Kortemme. 2012

86 citations recorded by the source corpus.

Subfields: Molecular Biology

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In Molecular Biology

Citations in the corpus

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity (2015, background): “PDZ domains and their binding peptides [13], a DNase–inhibitor pair [12,14], a small GTPase and its guanine exchange factor [15], and the interaction between a ubiquitin ligase and a ubiquitin-conjugating enzyme [16].”
Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations” (2013, unknown): “Indeed, we have recently had success at modeling conformational changes that propagate away from a designed mutation by iteratively switching between different sampling and scoring strategies during the course of a single simulation (Kapp et al., 2012).”
Achievements and Challenges in Computational Protein Design. (2017, methodology): “In 2012 the Kortemme lab applied CPD to control protein signaling by designing a GTPase/guanine nucleotide exchange factor (GEF) orthogonal (non-cross-reacting) pair [97].”
Improvements to Robotics-Inspired Conformational Sampling in Rosetta (2013, unknown): “also been applied after high-resolution modeling [5,26,27].”
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity Upon Mutation (2017, background): “37 Backrub has also proved e(cid:27)ective in design applications, such as the redesign of protein-protein interfaces 19 and recapitulation of mutations that alter ligand-binding speci(cid:28)city.”
Emerging themes in the computational design of novel enzymes and protein–protein interfaces (2013, background): “…protein binders – that has been corroborated by experimental atomic structures but note that very exciting progress has been made in computational design of altered protein function, such as novel binding speciﬁcities [8,9] and allosteric regulation [10], and refer readers to a recent review [11].”
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, background): “Traditionally protein flexibility in MSD has been modeled by including multiple backbone conformations as input states [9,13,16,32,38].”