Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins
| Autor: | Dong Ji, Jian Zhang, Qiang Fu, Shaoyong Lu, Yingfei Chen, Yuran Qiu, Duan Ni, Yuanhao Wang, Mingyu Li, Xinyi Li, Jun Pu, Yaqin Liu, Chaoyu Lei |
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| Rok vydání: | 2020 |
| Předmět: |
Cell signaling
GTP' Protein-protein interactions Allosteric regulation Biophysics GTPase Biochemistry Protein–protein interaction 03 medical and health sciences 0302 clinical medicine Structural Biology Genetics Phosphorylation ComputingMethodologies_COMPUTERGRAPHICS 030304 developmental biology 0303 health sciences Chemistry Molecular dynamics simulations Drug discovery Computer Science Applications Cell biology 030220 oncology & carcinogenesis Guanine nucleotide exchange factor Signal transduction K-Ras TP248.13-248.65 Research Article Biotechnology |
| Zdroj: | Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 1184-1199 (2021) Computational and Structural Biotechnology Journal |
| ISSN: | 2001-0370 |
| Popis: | Graphical abstract Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 μs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery. |
| Databáze: | OpenAIRE |
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