Theoretical Study of Endohedral Fullerenes M@C60 (M = Li,Na, or K) in Periodic Boundary Conditions

Journal of Experimental and Theoretical Physics - Density functional calculations in periodic boundary conditions (PBCs) were performed to investigate the structural and electronic properties of...     

Test of Hybrid Metric-Palatini f(R)-Gravity in Binary Pulsars

Journal of Experimental and Theoretical Physics - We developed the parameterized post-Keplerian formalism for hybrid metric-Palatini f(R)-gravity. We obtained analytical expressions in the general...     

Influence of an External Electric Field on the Charge and Field Distributions in a Metal Tip

Journal of Experimental and Theoretical Physics - The electric field and charge distributions in a nanosized truncated metal cone in a strong electric field have been found. The geometry of the...     

Vorticity and Particle Polarization in Relativistic Heavy-Ion Collisions

Physics of Atomic Nuclei - We review studies of vortical motion and the resulting global polarization of $$\Lambda$$ and $$\bar{\Lambda}$$ hyperons in heavy-ion collisions, in particular, within...     

Analytic Continuation of Scattering Data,Asymptotic Normalization Coefficients,and Astrophysics

Physics of Atomic Nuclei - The formalism of asymptotic normalization coefficients and methods for determining them from experimental nuclear data are discussed. A new method is proposed that uses...     

Form Factor of Proton Predicted Using the Data of ppbar Elastic Scattering at $$\boldsymbol{\sqrt{s}=1.96}$$ eV

Physics of Atomic Nuclei - Based on the behavior of elastic scattering of proton and anti-proton at $$\sqrt{s}=1.96$$ TeV for squared four-momentum transfer $$0.26<{-}t<1.2($$ GeV...     

Dynamic Destruction as Analogs of Critical Phenomena in Metal Samples with Various Geometries within a Wide Ranges of Amplitude–Time Characteristics of External Action

Physics of Atomic Nuclei - The quantitative characteristics of the products of dispersion and the cascade of dissipative structures arising in metals under shock-wave loading are determined. The...     

Boiling Water Reactor with a Combined Moderator for Utilization of Reactor Grade Plutonium

Physics of Atomic Nuclei - The article presents the concept of a channel-type reactor with a combined cooled moderator. The moderator consists of ceramic beryllium oxide and a liquid...     

Multiscale cumulative residual distribution entropy and its applications on heart rate time series

Nonlinear Dynamics - Distribution entropy has been proved to reveal stability for short time series and to distinguish different classes of series by complexity. However, there still exists some...     

Structural impact of GTP binding on downstream KRAS signaling

Oncogenic RAS proteins, involved in ∼30% of human tumors, are molecular switches of various signal transduction pathways. Here we apply a new protocol for the NMR study of KRAS in its (inactive) GDP- and (activated) GTP-bound form, allowing a comprehensive analysis of the backbone dynamics of its WT-, G12C- and G12D variants. We found that Tyr32 shows opposite mobility with respect to the backbone of its surroundings: it is more flexible in the GDP-bound form while more rigid in GTP-complexes (especially in WT- and G12D-GTP). Using the G12C/Y32F double mutant, we showed that the presence of the hydroxyl group of Tyr32 has a marked effect on the G12C-KRAS-GTP system as well. Molecular dynamics simulations indicate that Tyr32 is linked to the γ-phosphate of GTP in the activated states – an arrangement shown, using QM/MM calculations, to support catalysis. Anchoring Tyr32 to the γ-phosphate contributes to the capture of the catalytic waters participating in the intrinsic hydrolysis of GTP and supports a simultaneous triple proton transfer step (catalytic water → assisting water → Tyr32 → O1G of the γ-phosphate) leading to straightforward product formation. The coupled flip of negatively charged residues of switch I toward the inside of the effector binding pocket potentiates ligand recognition, while positioning of Thr35 to enter the coordination sphere of the Mg²⁺ widens the pocket. Position 12 mutations do not disturb the capture of Tyr32 by the γ-phosphate, but (partially) displace Gln61, which opens up the catalytic pocket and destabilizes catalytic water molecules thus impairing intrinsic hydrolysis.

Nucleotide exchange to the physiological, activated, GTP-bound form of KRAS results in the anchoring of Tyr32 within the active site.