TY - JOUR
T1 - Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations
AU - Makepeace, Karl A.T.
AU - Brodie, Nicholas I.
AU - Popov, Konstantin I.
AU - Gudavicius, Geoff
AU - Nelson, Christopher J.
AU - Petrotchenko, Evgeniy V.
AU - Dokholyan, Nikolay V.
AU - Borchers, Christoph H.
N1 - Funding Information:
The University of Victoria-Genome British Columbia Proteomics Centre is grateful to Genome Canada and Genome British Columbia for financial support through the (project Genomics Innovation Network (codes 204PRO for operations and 214PRO for technology development) and the Genomics Technology Platform (264PRO). CHB is also grateful for support from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Leading Edge Endowment Fund ( University of Victoria ), and for support from the Segal McGill Chair in Molecular Oncology at McGill University (Montreal, Quebec, Canada). CHB is also grateful for support from the Warren Y. Soper Charitable Trust and the Alvin Segal Family Foundation to the Jewish General Hospital (Montreal, Quebec, Canada). NVD also acknowledges support from NIH grants R01GM114015 and R01GM123247 . Appendix A
Publisher Copyright:
© 2019 The Authors
PY - 2020/1/16
Y1 - 2020/1/16
N2 - For disordered proteins, ligand binding can be a critical event that changes their structural dynamics. The ability to characterize such changes would facilitate the development of drugs designed to stabilize disordered proteins, whose mis-folding is important for a number of pathologies, including neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular dynamics (MD) simulations to characterize the structural changes in disordered proteins that result from ligand binding. We show here that both an ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P, are disordered, yet exhibit structures that are distinct from chemically denatured unfolded states in solution, and that they undergo transitions to a more structured state upon ligand binding. These systems may serve as models for the characterization of ligand-induced disorder-to-order transitions in proteins using structural proteomics approaches. Significance: In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular-dynamics simulations to characterize the structural changes in disordered proteins that result from ligand binding. The protein-ligand systems studied here (the ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P) may serve as models for understanding ligand-induced disorder-to-order transitions in proteins. Additionally, the structural proteomic techniques demonstrated here are shown to be effective tools for the characterization of disorder-to-order transitions and can be used to facilitate study of other systems in which this class of structural transition can be used for modulating major pathological features of disease, such as the abnormal protein aggregation that occurs with Parkinson's disease and Alzheimer's disease.
AB - For disordered proteins, ligand binding can be a critical event that changes their structural dynamics. The ability to characterize such changes would facilitate the development of drugs designed to stabilize disordered proteins, whose mis-folding is important for a number of pathologies, including neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular dynamics (MD) simulations to characterize the structural changes in disordered proteins that result from ligand binding. We show here that both an ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P, are disordered, yet exhibit structures that are distinct from chemically denatured unfolded states in solution, and that they undergo transitions to a more structured state upon ligand binding. These systems may serve as models for the characterization of ligand-induced disorder-to-order transitions in proteins using structural proteomics approaches. Significance: In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular-dynamics simulations to characterize the structural changes in disordered proteins that result from ligand binding. The protein-ligand systems studied here (the ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P) may serve as models for understanding ligand-induced disorder-to-order transitions in proteins. Additionally, the structural proteomic techniques demonstrated here are shown to be effective tools for the characterization of disorder-to-order transitions and can be used to facilitate study of other systems in which this class of structural transition can be used for modulating major pathological features of disease, such as the abnormal protein aggregation that occurs with Parkinson's disease and Alzheimer's disease.
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U2 - 10.1016/j.jprot.2019.103544
DO - 10.1016/j.jprot.2019.103544
M3 - Article
C2 - 31683063
AN - SCOPUS:85074468126
SN - 1874-3919
VL - 211
JO - Journal of Proteomics
JF - Journal of Proteomics
M1 - 103544
ER -