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- W3129848319 abstract "Ligands are known to modulate protein mechanics, yet a thorough understanding of principles governing protein-ligand mechanics remains elusive. In this study, we explore the effect of ligand binding site on mechanical stability of structurally homologous ubiquitin family proteins, namely ubiquitin and small ubiquitin related modifier 1 (SUMO1). Ubiquitin and SUMO1 share a common β-grasp fold and can withstand high unfolding forces due to their β-clamp geometry. Both ubiquitin and SUMO1 offer unique platform to probe the role of ligand binding site relative to the β-clamp. We compare ubiquitin/CUE2-1 complex, where ligand binds directly to the β-clamp with previously studied SUMO1/S12 complex, where ligand binds far from the β-clamp. Using single molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we find CUE2-1 does not modulate mechanical stability of ubiquitin. Our SMD simulations on SUMO1/S12 complex corroborate previously reported enhancement in mechanical stability of SUMO1 on ligand binding. We demonstrate the observed differences in the ligand modulation arise due to differences in binding site and binding mode of the two complexes. Our simulations reveal that the transition state structure of SUMO1 gets perturbed on binding with S12. In contrast, the binding of CUE-2 has minimal structural impact of ubiquitin. Thus our study demonstrates that a direct interaction with the β-clamp does not necessarily modulate the mechanical stability of proteins, an observation in contrast with previous studies. Instead ligand binding far from the β-clamp can reinforce the mechanical stability of the proteins. Our study highlights the importance of ligand binding site in modulating mechanical stability of ubiquitin family proteins." @default.
- W3129848319 created "2021-03-01" @default.
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- W3129848319 date "2021-02-01" @default.
- W3129848319 modified "2023-09-30" @default.
- W3129848319 title "Role of Ligand Binding Site in Modulating Mechanical Properties of Ubiquitin Family Proteins" @default.
- W3129848319 doi "https://doi.org/10.1016/j.bpj.2020.11.2232" @default.
- W3129848319 hasPublicationYear "2021" @default.
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