title: Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain.
abstract: Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD) models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains) in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery.
authors.affiliation: Department of Internal Medicine, Hematology and Oncology Division, University of Michigan, Ann Arbor, Michigan, 48109, United States of America.
authors.forename: Chao-Yie
authors.initials: CY
authors.lastname: Yang
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America.
authors.forename: James
authors.initials: J
authors.lastname: Delproposto
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America.
authors.forename: Krishnapriya
authors.initials: K
authors.lastname: Chinnaswamy
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America.
authors.forename: William Clay
authors.initials: WC
authors.lastname: Brown
authors.affiliation: Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan; and Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Shuying
authors.initials: S
authors.lastname: Wang
authors.affiliation: Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America.|Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States of America.
authors.forename: Jeanne A
authors.initials: JA
authors.lastname: Stuckey
authors.affiliation: Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Xinquan
authors.initials: X
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D016000:Cluster Analysis; D018360:Crystallography, X-Ray; D006801:Humans; D007368:Interferometry; D000072179:Interleukin-1 Receptor-Like 1 Protein; D000067596:Interleukin-33 / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011956:Receptors, Cell Surface / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000302:isolation & purification
chemical_list: C079241:IL1RL1 protein, human; D000072179:Interleukin-1 Receptor-Like 1 Protein; D000067596:Interleukin-33; D011956:Receptors, Cell Surface; D011994:Recombinant Proteins