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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.

Background To establish a decision model based on two- (2D) and three-dimensional (3D) eye data of patients with ptosis for developing personalized surgery plans. Methods Data of this retrospective, case-control study was collected from March 2019 to June 2019 at the Department of Ophthalmology, Shanghai Ninth People’s Hospital, and then the patients were followed up for 3 months. One hundred fifty-two complete feature eyes from 100 voluntary patients with ptosis and satisfactory surgical results were selected, with 48 eyes excluded due to any severe condition or improper collection and shooting angle. Three experimental schemes were set as follows: use 2D distance alone, use 3D distance alone, and use two distances at the same time. The five most common evaluation indicators used in the binary classification problem to test the decision model were accuracy (ACC), precision, recall, F1-score, and area under the curve (AUC). Results For diagnostic discrimination, recall of “3D”, “2D” and “Both” schemes were 0.875, 0.875 and 0.938 respectively. And precision of the three schemes were 0.8333, 0.7778 and 1.0000 for the surgical procedure classification. Values of “Both” scheme that combined 2D and 3D data were the highest in two classifications. Conclusions In this study, 3D eye data are introduced into clinical practice to construct a decision model for ptosis surgery. Our decision model presents exceptional prediction effect, especially when 2D and 3D data employed jointly.