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Journal articleHeal WP, Wright MH, Thinon E, et al., 2012,
Journal articleHeal WP, Tate EW, 2012,
Journal articleFurse S, Brooks NJ, Seddon AM, et al., 2012,
Journal articleBradshaw RT, Aronica PGA, Tate EW, et al., 2012,
Journal articleTate EW, Goss RJM, 2011,
Journal articleDelmotte A, Tate EW, Yaliraki SN, et al., 2011,
Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin-myosin light chain interaction, PHYSICAL BIOLOGY, Vol: 8, ISSN: 1478-3975
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.
Journal articlede la Riva L, Willing SE, Tate EW, et al., 2011,
Journal articleSerwa R, Tate EW, 2011,
Activity-based protein profiling (ABPP) is emerging as a game-changing tool for drug discovery, target validation, and basic biology. In this issue, Chang et al. (2011) report the ABPP-facilitated discovery of JW480, a highly selective potent and orally bioavailable inhibitor of monoalkylglycerol ether hydrolase KIAA1363 that dramatically impairs in vivo growth of human prostate cancer cell lines.
Journal articleHeal WP, Dang TH, Tate EW, 2011,
The development and application of chemical technologies enabling direct analysis of enzyme activity in living systems has undergone explosive growth in recent years. Activity-based protein profiling (ABPP) is a key constituent of this broad field, and is among the most powerful and mature chemical proteomic technologies. This tutorial review introduces the essential features of ABPP and the design and application of activity-based probes (ABPs) from drug target elucidation and in vivo visualisation of enzyme activity to comprehensive profiling of the catalytic content of living systems, and the discovery of new biological pathways.
Journal articleHeal WP, Jovanovic B, Bessin S, et al., 2011,
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