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At least 829 records · Page 46

Many roads to the seam: How conformational flexibility drives nonadiabatic relaxation in a prototypical tetrapyrrolic chromophore

Large and structurally flexible chromophores pose challenges for in silico modeling of photodeactivation due to the many vibrational modes that can funnel the system toward energy degeneracy. In this work, we examine how the multiple degrees of freedom in biliverdin, a prototypical tetrapyrrolic chromophore, cooperate to drive access to the S 1 /S 0 intersection seam in vacuo. We begin by mapping the ground-state potential energy surface to identify representative biliverdin conformers relevant to photoexcitation. We then use a CASSCF-based framework to map the excited-state landscape and characterize the intersection seam, identifying distinct conical-intersection types. Finally, we employ ab initio multiple spawning to resolve the dynamical pathways by which the system accesses these regions. DFT potential-energy and free-energy mappings indicate that, although several conformers are relevant, the “locked-helix” ZsZsZs conformer predominates in the ground state. The intersection seam comprises numerous geometrically distinct regions characterized by varying degrees and combinations of dihedral torsion, pyramidalization, and bond-length alternation. Yet only select regions lie within energetic reach, and moderate barriers separate them from the S 1 minimum. Nonadiabatic dynamics combined with multivariate analyses show that, despite extensive mode coupling during deactivation that guides the system toward multiple regions of the seam, a single dihedral torsion, together with bond-length alternation, predominantly drives energy degeneracy. This work offers new insight into biliverdin’s intrinsic photochemical response and underscores a general feature of flexible chromophores: many modes may participate during photorelaxation, but only a limited subset ultimately dictates seam accessibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of the possibility of designing more compact DF lasers driven by combustion of preheated fuels

We report a theoretical calculation of the processes proceeding in the combustor of combustion-driven cw DF/HF chemical lasers with different mixtures of fuels preheated to high temperatures. Calculation results demonstrate a great effect of the preheating temperature on the yield of F atoms and strongest deactivator, on the primary dilution ratio Ψp and on the estimated specific power. When fuels are preheated to about 1300 K, the specific power is improved by about 74.2 %, and the total mass of the fuel is reduced by about 43 %, which makes it possible to realise a more compact and efficient design of combustion-driven cw DF/HF chemical lasers at elevated combustor pressures. Fuel preheating can facilitate the development of chemical lasers and high-power lasers based not only on airborne and space-borne platforms, but also on mobile ground-based platforms. (active media)

42 ENGINEERING↗

Tandem catalysis for the production of alkyl lactates from ketohexoses at moderate temperatures

Significance Retro-aldol reactions of biomass-derived monosaccharides enable the production of a number of industrially relevant, renewable platform chemicals (e.g., C 2 –C 4 α-hydroxy carboxylic acids, acrylic acid, and esters thereof; and ethylene and propylene glycol). Here, we show a set of retro-aldol catalysts that can perform these reactions at significantly lower temperatures (∼100 °C) than previously reported, and demonstrate that these catalysts enable the key retro-aldol step when used in combination with a 1,2-hydride shift catalyst to create a reaction cascade that converts ketohexoses to lactic acid. The use of moderate temperatures enables numerous desirable features such as lower pressure and significantly less catalyst deactivation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oscillatory redox behavior in oxides: Cyclic surface reconstruction and reactivity modulation via the Mars–van Krevelen mechanism

The breaking of translational symmetry at oxide surfaces gives rise to coordinatively unsaturated cations/anions and surface restructuring—key factors that govern surface reactivity. Using direct in situ environmental transmission electron microscopy (TEM) observations along with atomistic modeling, we report oscillatory redox behavior in CuO under H 2 , where cyclic surface reconstruction and reactivity modulation occur via the Mars–van Krevelen (MvK) mechanism. We observe self-switching between oxygen-rich and oxygen-deficient surface reconstructions, alternately activating and deactivating the surface for H 2 O formation. During periods of chemical inactivity, the oxygen-deficient surface undergoes slow reoxidation via lattice oxygen diffusing from subsurface and bulk reservoirs, restoring the active oxygen-rich surface termination. The inherent disparity in chemical activity among undercoordinated surface ions, along with sluggish subsurface-to-surface oxygen replenishment, drives this oscillatory redox cycle, modulating H2-induced loss of lattice oxygen at the surface and its delayed replenishment from the subsurface. This creates spatiotemporally separated redox steps at the oxide surface. The phenomena and atomistic insights presented here have significant implications for manipulating the surface reactivity of oxides by tuning the separation of these redox steps.

36 MATERIALS SCIENCE↗

Circumventing thermodynamic limitations in converting carbon dioxide into carbon nanotubes via tandem catalysis

Carbon nanotubes (CNTs) are important materials for electronics and structural composites, but their production still relies on hydrocarbon-based chemical vapor deposition, an energy-intensive and fossil-dependent process, limited by rapid catalyst deactivation. Using CO2 as a carbon feedstock offers a sustainable route for CNT synthesis, yet direct CO2 conversion to CNTs is thermodynamically unfavorable and existing CO2-to-carbon pathways mainly yield amorphous or weakly graphitized solids. Here, we demonstrate a tandem electrochemical–thermochemical (EC-TC) strategy that overcomes these limitations. CO2 is first electrochemically reduced to a tunable mixture of C2H4 and CO, which is directly fed into a thermochemical reactor and converted into CNTs with controllable morphology and high CNT-to-metal mass ratios (~200) over NiFe catalysts at 750 °C. In situ synchrotron-based characterization and density functional theory calculations reveal that CO dissociation and C2H4 decomposition on NiFe alloys cooperatively promote CNT nucleation and sustained growth. This EC-TC strategy establishes a modular route for converting CO2 into value-added carbon nanomaterials.

03 NATURAL GAS↗

Advanced spectrometric methods for characterizing bio-oils to enable refineries to reduce fuel carbon intensity during co-processing

A promising approach for supplementing petroleum-derived fuels to support reductions in green-house gas emissions is to convert abundant biomass feedstocks into renewable carbon-rich oils using pyrolysis. However, the resultant bio-oils contain various oxygenated compounds that can impart acidity, chemical and thermal instability, and immiscibility with petroleum derived fuels, necessitating further upgrading to derive fuel blendstocks. Co-processing bio-oils and petroleum-derived liquids in existing refineries is a potentially near-term, cost-effective approach for upgrading bio-oils while reducing refinery carbon intensities. However, one cause for hesitation in co-processing bio-oils is limited comprehensive characterization and speciation of the bio-oil components. Advanced analytical techniques are currently under investigation to enable identification of elusive species in bio-oils, enabling researchers to develop strategies to mitigate catalyst deactivation agents and contaminants. This review provides a brief overview of several analytical methods commonly used to analyze bio-oils and their limitations. In addition, advanced techniques currently under development are discussed to further elucidate bio-oil components that may limit its end use. This will help inform the technical and economic feasibility of co-processing bio-oils with petroleum-derived liquids, therefore, improving the overall downstream processes for biofuels blendstock production.

09 BIOMASS FUELS↗

The tarantula toxin GxTx detains K + channel gating charges in their resting conformation

Allosteric ligands modulate protein activity by altering the energy landscape of conformational space in ligand–protein complexes. Here we investigate how ligand binding to a K + channel’s voltage sensor allosterically modulates opening of its K + -conductive pore. The tarantula venom peptide guangxitoxin-1E (GxTx) binds to the voltage sensors of the rat voltage-gated K + (Kv) channel Kv2.1 and acts as a partial inverse agonist. When bound to GxTx, Kv2.1 activates more slowly, deactivates more rapidly, and requires more positive voltage to reach the same K + -conductance as the unbound channel. Further, activation kinetics are more sigmoidal, indicating that multiple conformational changes coupled to opening are modulated. Single-channel current amplitudes reveal that each channel opens to full conductance when GxTx is bound. Inhibition of Kv2.1 channels by GxTx results from decreased open probability due to increased occurrence of long-lived closed states; the time constant of the final pore opening step itself is not impacted by GxTx. When intracellular potential is less than 0 mV, GxTx traps the gating charges on Kv2.1’s voltage sensors in their most intracellular position. Gating charges translocate at positive voltages, however, indicating that GxTx stabilizes the most intracellular conformation of the voltage sensors (their resting conformation). Kinetic modeling suggests a modulatory mechanism: GxTx reduces the probability of voltage sensors activating, giving the pore opening step less frequent opportunities to occur. This mechanism results in K + -conductance activation kinetics that are voltage-dependent, even if pore opening (the rate-limiting step) has no inherent voltage dependence. We conclude that GxTx stabilizes voltage sensors in a resting conformation, and inhibits K + currents by limiting opportunities for the channel pore to open, but has little, if any, direct effect on the microscopic kinetics of pore opening. The impact of GxTx on channel gating suggests that Kv2.1’s pore opening step does not involve movement of its voltage sensors.

Physiology↗

Kinetics and selectivity of methane oxidation on an IrO 2 (110) film

Undercoordinated, bridging O-atoms (O br ) are highly active as H-acceptors in alkane dehydrogenation on IrO 2 (110) surfaces but transform to HO br groups that are inactive toward hydrocarbons. The low C–H activity and high stability of the HO br groups cause the kinetics and product selectivity during CH 4 oxidation on IrO 2 (110) to depend sensitively on the availability of O br atoms prior to the onset of product desorption. From temperature programmed reaction spectroscopy (TPRS) and kinetic simulations, we identified two O br -coverage regimes that distinguish the kinetics and product formation during CH 4 oxidation on IrO 2 (110). Under excess O br conditions, when the initial O br coverage is greater than that needed to oxidize all the CH 4 to CO 2 and HO br groups, complete CH 4 oxidation is dominant and produces CO 2 in a single TPRS peak between 450 and 500 K. However, under O br -limited conditions, nearly all the initial O br atoms are deactivated by conversion to HO br or abstracted after only a fraction of the initially adsorbed CH 4 oxidizes to CO 2 and CO below 500 K. Thereafter, some of the excess CH x groups abstract H and desorb as CH 4 above ~500 K while the remainder oxidize to CO 2 and CO at a rate that is controlled by the rate at which Obr atoms are regenerated from HObr during the formation of CH 4 and H 2 O products. We also show that chemisorbed O-atoms ('on-top O') on IrO 2 (110) enhance CO 2 production below 500 K by efficiently abstracting H from Obr atoms and thereby increasing the coverage of O br atoms available to completely oxidize CH x groups at low temperature. Furthermore, our results provide new insights for understanding factors which govern the kinetics and selectivity during CH 4 oxidation on IrO 2 (110) surfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Maximized lateral inhibition in paired magnetic domain wall racetracks for neuromorphic computing

Lateral inhibition is an important functionality in neuromorphic computing, modeled after the biological neuron behavior that a firing neuron deactivates its neighbors belonging to the same layer and prevents them from firing. In most neuromorphic hardware platforms lateral inhibition is implemented by external circuitry, thereby decreasing the energy efficiency and increasing the area overhead of such systems. Recently, the domain wall—magnetic tunnel junction (DW-MTJ) artificial neuron is demonstrated in modeling to be intrinsically inhibitory. Without peripheral circuitry, lateral inhibition in DW-MTJ neurons results from magnetostatic interaction between neighboring neuron cells. However, the lateral inhibition mechanism in DW-MTJ neurons has not been studied thoroughly, leading to weak inhibition only in very closely-spaced devices. This work approaches these problems by modeling current- and field- driven DW motion in a pair of adjacent DW-MTJ neurons. We maximize the magnitude of lateral inhibition by tuning the magnetic interaction between the neurons. The results are explained by current-driven DW velocity characteristics in response to an external magnetic field and quantified by an analytical model. Dependence of lateral inhibition strength on device parameters is also studied. Finally, lateral inhibition behavior in an array of 1000 DW-MTJ neurons is demonstrated. Our results provide a guideline for the optimization of lateral inhibition implementation in DW-MTJ neurons. Finally, with strong lateral inhibition achieved, a path towards competitive learning algorithms such as the winner-take-all are made possible on such neuromorphic devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Atmospheric pressure plasma treatment of skin: penetration into hair follicles

Sterilization of skin prior to surgery is challenged by the reservoir of bacteria that resides in hair follicles. Atmospheric pressure plasma jets (APPJs) have been proposed as a method to treat and deactivate these bacteria as atmospheric plasmas are able to penetrate into structures and crevices with dimensions similar to those found in hair follicles. In this paper, we discuss results from a computational investigation of an APPJ sustained in helium flowing into ambient air, and incident onto a layered dielectric similar to human skin in which there are idealized hair follicles. We found that, depending on the location of the follicle, the bulk ionization wave (IW) incident onto the skin, or the surface IW on the skin, are able to launch IWs into the follicle. The uniformity of treatment of the follicle depends on the location of the first entry of the plasma into the follicle on the top of the skin. Typically, only one side of the follicle is treated on for a given plasma pulse, with uniform treatment resulting from rastering the plasma jet across the follicle over many pulses. Plasma treatment of the follicle is sensitive to the angle of the follicle with respect to the skin, width of the follicle pocket, conductivity of the dermis and thickness of the underlying subcutaneous fat layer, the latter due to the change in capacitance of the tissue.

60 APPLIED LIFE SCIENCES↗

Hysteresis as a probe of turbulent bifurcation in intrinsic rotation reversals on Alcator C-Mod

Analysis and modeling of a new set of rotation reversal hysteresis experiments unambiguously show that changes in turbulence are responsible for the intrinsic rotation reversal and the linear to saturated ohmic confinement (LOC/SOC) transition on Alcator C-Mod. Plasmas on either side of the reversal exhibit different toroidal rotation profiles and therefore different turbulence characteristics despite profiles of density and temperature that are indistinguishable within measurement uncertainty. The deactivation of subdominant (in linear growth rate and heat transport) ion-temperature gradient and trapped electron mode-like instabilities in a mixedmode state is identified as the only possible change in turbulence within a quasilinear transport approximation across the reversal which is consistent with the measured profiles and the inferred heat and particle fluxes. This indicates an explanation for the LOC/SOC transition that provides a mechanism for hysteresis through the dynamics of subdominant modes and changes in their relative populations, and does not involve a change in most (linearly) unstable ion-scale drift-wave instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Platinum vs transition metal carbide surfaces as catalysts for olefin and alkyne conversion: binding and hydrogenation of ethylidyne

The development of heterogeneous catalysts with activity for the hydrogenation of unsaturated hydrocarbons is of economic importance. Ethylene (C 2 H 4 ) and acetylene (C 2 H 2 ) are probe molecules useful to understand the hydrogenation mechanisms, where the most studied surfaces are Pt(111) and Pd(111), however, they have a limited activity due to the formation and accumulation of ethylidyne (CCH 3 ) species. Therefore, alternative catalysts should be developed to limit and/or avoid the formation of ethylidyne on the surface. Transition metal carbides has been reported as alternative catalysts, with the additional advantage of lower prices. The thermodynamics of ethylidyne binding and its transformations on δ-MoC(001), TiC(001), and β-Mo 2 C(100) surfaces are studied by means of periodic DFT. The results indicate that ethylidyne could be transformed to ethyl and ethane on δ-MoC(001) and TiC(001) surfaces, which are relevant species to the Horiuti-Polanyi mechanism. Therefore, these surfaces could be an alternative to Pt(111) and Pd(111), since ethylidyne could be transformed to other species, avoiding or limiting their deactivation. Conversely, ethylidyne cannot be transformed to vinyl (CHCH 2 ) or ethylene in a Horiuti-Polanyi-like mechanism; then, it is not thermodynamically feasible to use any of the studied surfaces in the selective hydrogenation of acetylene, since ethylidyne accumulation could poison the surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CRISPR/Cas9-based gene activation and base editing in Populus

The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone “717-1B4” (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone “717-1B4” and poplar clone “WV94” (P. deltoides “WV94”), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%–14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone “717-1B4”. Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of Cu Species in Dealuminated Beta Zeolite Studied by Operando Closed-Cell Gas Reaction STEM

Direct conversion of ethanol to C3+ olefins is an attractive pathway to produce sustainable aviation fuels [1]. We recently reported a copper-containing catalyst supported on dealuminated (DeAl) beta zeolite that is capable of catalyzing cascade ethanol to olefins reactions with high olefins selectivity (88% C3+ olefin selectivity at 100% ethanol conversion). However, one of the deactivation mechanisms of the catalyst is copper sintering [2]. It was found that copper agglomerates can be redispersed through a simple oxidative treatment. To better understand the kinetics and process conditions conducive to redispersion, we studied the atmosphere and temperature dependent Cu species in Cu/DeAl-Beta catalyst under conditions matching those of the working catalyst.

beta zeolite↗

CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors

Abstract Tools for synthetically controlling gene expression are a cornerstone of genetic engineering. CRISPRi and CRISPRa technologies have been applied extensively for programmable modulation of gene transcription, but there are few such tools for targeted modulation of protein translation rates. Here, we employ CRISPR-Cas13 as a programmable activator of translation. We develop a novel variant of the catalytically-deactivated Cas13d enzyme dCasRx by fusing it to translation initiation factor IF3. We demonstrate dCasRx-IF3’s ability to enhance expression 21.3-fold above dCasRx when both are targeted to the start of the 5′ untranslated region of mRNA encoding red fluorescent protein in Escherichia coli. Activation of translation is location-dependent, and we show dCasRx-IF3 represses translation when targeted to the ribosomal binding site, rather than enhancing it. We provide evidence that dCasRx-IF3 targeting enhances mRNA stability relative to dCasRx, providing mechanistic insights into how this new tool functions to enhance gene expression. We also demonstrate targeted upregulation of native LacZ 2.6-fold, showing dCasRx-IF3’s ability to enhance expression of endogenous genes. dCasRx-IF3 requires no additional host modification to influence gene expression. This work outlines a novel approach, CRISPR-RNAa, for post-transcriptional control of translation to activate gene expression.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Insight into Allosteric Inhibition of Mycobacterium tuberculosis Tryptophan Synthase

The rise of antibiotic‐resistant pathogens requires redirecting drug discovery effort toward new cellular targets to provide new treatment options. Such alternative, yet unexplored opportunities exist in central metabolism, where many enzymes are only conditionally essential and thus their successful exploitation requires understanding of metabolic fluxes and pathway regulations under certain environmental conditions. In Mycobacterium tuberculosis , tryptophan biosynthesis represents one such promising pathway that could be targeted. In Mtb, the multistep L‐Trp synthesis involves several enzymes: TrpEG, TrpD, TrpC and TrpAB, which is validated as conditionally essential in vivo . The whole‐cell screening of a diversity‐oriented synthetic library identified a novel bactericidal azetidine derivative, BRD4592, that specifically inhibits TrpAB (tryptophan synthase). TrpAB is a heterotetrameric, PLP‐dependent complex catalyzing two last reactions in L‐Trp synthesis: the conversion of indole‐3‐glycerol phosphate to indole and glyceraldehyde 3‐phosphate (TrpA) followed by indole and L‐Ser condensation to yield L‐Trp (TrpB). During the catalytic cycle, indole is transferred from the TrpA to TrpB active site through 25 Å hydrophobic channel to react with the L‐Ser‐PLP adduct. The enzymatic activities and substrate channeling are coordinated by complex allosteric communication between the subunits. This regulation involves cycling between various conformational states, with both subunits adopting either an open (inactive) or closed (active) state. Detailed kinetic, biophysical and structural evidence reveals that BRD4592 is an allosteric, mixed‐type inhibitor, which binds specifically to a novel site within the intersubunit channel, at the TrpA‐TrpB interface. The molecule promotes closed, active state of the TrpB subunit and increases enzyme affinity for the L‐Ser substrate. BRD4592 acts on three levels: it limits flexibility of the interface potentially disrupting mutual activation of the subunits, prevents indole translocation, and increases product inhibition providing means to successfully inhibit both, TrpA and TrpB reactions. Our results indicate that allosteric binders may represent an effective tool to deactivate central metabolism enzymes, which often are allosterically regulated and might be predisposed for this type of inhibition. Support or Funding Information This work was supported by the Broad Institute Tuberculosis donor group, the Pershing Square Foundation, the Bill & Melinda Gates Foundation under grant OPP1032518, the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contracts HHSN272200700058C and HHSN272201200026C and the U. S. Department of Energy, Office of Biological and Environmental Research, under contract DE‐AC02‐06CH11357. For this work, University of Chicago is a subgrantee of Structural Genomics Consortium under a Bill & Melinda Gates Foundation grant for the Structure‐Guided Drug Discovery Coalition.

Michalska, Karolina↗

Comparison of heavy-ion transport simulations: Collision integral with pions and Δ resonances in a box

Simulations by transport codes are indispensable for extracting valuable physical information from heavy-ion collisions. Pion observables such as the π - /π + yield ratio are expected to be sensitive to the symmetry energy at high densities. To evaluate, understand, and reduce the uncertainties in transport-code results originating from different approximations in handling the production of Δ resonances and pions. We compare ten transport codes under controlled conditions for a system confined in a box, with periodic boundary conditions, and initialized with nucleons at saturation density and at a temperature of 60 MeV. The reactions NN↔NΔ and Δ↔Nπ are implemented, but the Pauli blocking and the mean-field potential are deactivated in the present comparison. Thus, these are cascade calculations including pions and Δ resonances. Results are compared to those from the two reference cases of a chemically equilibrated ideal gas mixture and of the rate equation. For the numbers of Δ and π, deviations from the reference values are observed in many codes, and they depend significantly on the size of the time step. These deviations are tied to different ways in ordering the sequence of reactions, such as collisions and decays, that take place in the same time step. Better agreements with the reference values are seen in the reaction rates and the number ratios among the isospin species of Δ and π. Both the reaction rates and the number ratios are, however, affected by the correlations between particle positions, which are absent in the Boltzmann equation, but are induced by the way particle scatterings are treated in many of the transport calculations. The uncertainty in the transport-code predictions of the π - /π + ratio, after letting the existing Δ resonances decay, is found to be within a few percent for the system initialized at n/p=1.5. In conclusion, the uncertainty in the final π - /π + ratio in this simplified case of particles in a box is sufficiently small so that it does not strongly impact constraining the high-density symmetry energy from heavy-ion collisions. Most of the sources of uncertainties have been understood, and individual codes may be further improved in future applications. This investigation will be extended in the future to heavy-ion collisions to ensure the problems identified here remain under control.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras

K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras–GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.

Xu, Shenyuan (ORCID:0000000299031944)↗