Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement

KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states. Both dimerize through an α4–α5 interface, but the relative orientation of the protomers and their contacts differ substantially. Dimerization of KRAS-GTP, stabilized by electrostatic interactions between R135 and E168, favors an orientation on the membrane that promotes accessibility of the effector-binding site. Remarkably, “cross”-dimerization between GTP- and GDP-bound KRAS molecules is unfavorable. These models provide a platform to elucidate the structural basis of RAF activation by RAS and to develop inhibitors that can disrupt the KRAS dimerization. The methodology is applicable to many other farnesylated small GTPases.     

The Self-Association of the KRAS4b Protein is Altered by Lipid-Bilayer Composition and Electrostatics

KRAS is a peripheral membrane protein that regulates multiple signaling pathways, and is mutated in ≈30 % of cancers. Transient self-association of KRAS is essential for activation of the downstream effector RAF and oncogenicity. The presence of anionic phosphatidylserine (PS) lipids in the membrane was shown to promote KRAS self-assembly, however, the structural mechanisms remain elusive. Here, we employed nanodisc bilayers of defined lipid compositions, and probed the impact of PS concentration on KRAS self-association. Paramagnetic NMR experiments demonstrated the existence of two transient dimer conformations involving alternate electrostatic contacts between R135 and either D153 or E168 on the “α4/5-α4/5” interface, and revealed that lipid composition and salt modulate their dynamic equilibrium. These dimer interfaces were validated by charge-reversal mutants. This plasticity demonstrates how the dynamic KRAS dimerization interface responds to the environment, and likely extends to the assembly of other signaling complexes on the membrane.     

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N‐terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC‐helix and charged residues upstream of the NtA motif. Additionally, we show that the R‐spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure‐based mechanism for the auto‐transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization‐related drug resistance.     

Molecular dynamics simulations of the Hras‐GTP complex and the Hras‐GDP complex

We study the structures of the Hras‐GTP complex and the Hras‐GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras‐GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg²⁺. Our simulations show that the averaged structure differences between the Hras‐GTP complex and Hras‐GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α2 ‐ helix of Hras‐GDP is shorter than the α2 ‐ helix of Hras‐GTP. The averaged number of water molecules in the first hydration sphere in Hras‐GDP complex is larger than that in Hras‐GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras‐GTP and in Hras‐GDP. In Hras‐GDP complex, β‐phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras‐GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc.     

Oncogenic KRAS G12D mutation promotes dimerization through a second,phosphatidylserine–dependent interface: a model for KRAS oligomerization

KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric ‘α–α’ dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric ‘α–β’ interface. The ‘α–β’ association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary ‘α–α’ interface releases β interfaces from the membrane promoting formation of the secondary ‘α–β’ interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β–β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins.

Studies of membrane-dependent dimerization of KRAS on nanodiscs using paramagnetic NMR titrations and mutagenesis revealed a novel asymmetric ‘α–β’ interface that provides a potential mechanism for the enhanced assembly of KRAS–G12D nanoclusters.     

Extending the Lifetime of Native GTP‐Bound Ras for Site‐Resolved NMR Measurements: Quantifying the Allosteric Dynamics

Characterization of native GTP‐bound Ras is important for an appreciation of its cellular signaling and for the design of inhibitors, which however has been depressed by its intrinsic instability. Herein, an effective approach for extending the lifetime of Ras?GTP samples by exploiting the active role of Son of Sevenless (Sos) is demonstrated that sustains the activated state of Ras. This approach, combined with a postprocessing method that suppresses residual Ras?GDP signals, is applied to the site‐resolved NMR measurement of the allosteric dynamics of Ras?GTP. The observed network of concerted motions well covers the recently identified allosteric inhibitor‐binding pockets, but the motions are more confined than those of Ras?GppNHp, advocating the use of native GTP for development of allosteric inhibitors. The Sos‐based approach is anticipated to generally facilitate experiments on active Ras when native GTP is preferred.     

Cell‐Permeant and Photocleavable Chemical Inducer of Dimerization

Chemical inducers of dimerization (CIDs) have been developed to orchestrate protein dimerization and translocation. Here we present a novel photocleavable HaloTag‐ and SNAP‐tag‐reactive CID (MeNV‐HaXS) with excellent selectivity and intracellular reactivity. Excitation at 360 nm cleaves the methyl‐6‐nitroveratryl core of MeNV‐HaXS. MeNV‐HaXS covalently links HaloTag‐ and SNAP‐tag fusion proteins, and enables targeting of selected membranes and intracellular organelles. MeNV‐HaXS‐mediated translocation has been validated for plasma membrane, late endosomes, lysosomes, Golgi, mitochondria, and the actin cytoskeleton. Photocleavage of MeNV‐HaXS liberates target proteins and provides access to optical manipulation of protein relocation with high spatiotemporal and subcellular precision. MeNV‐HaXS supports kinetic studies of protein dynamics and the manipulation of subcellular enzyme activities, which is exemplified for Golgi‐targeted cargo and the assessment of nuclear import kinetics.     

A Usual G‐Protein‐Coupled Receptor in Unusual Membranes

G‐protein‐coupled receptors (GPCRs) are the largest family of membrane‐bound receptors and constitute about 50 % of all known drug targets. They offer great potential for membrane protein nanotechnologies. We report here a charge‐interaction‐directed reconstitution mechanism that induces spontaneous insertion of bovine rhodopsin, the eukaryotic GPCR, into both lipid‐ and polymer‐based artificial membranes. We reveal a new allosteric mode of rhodopsin activation incurred by the non‐biological membranes: the cationic membrane drives a transition from the inactive MI to the activated MII state in the absence of high [H⁺] or negative spontaneous curvature. We attribute this activation to the attractive charge interaction between the membrane surface and the deprotonated Glu134 residue of the rhodopsin‐conserved ERY sequence motif that helps break the cytoplasmic “ionic lock”. This study unveils a novel design concept of non‐biological membranes to reconstitute and harness GPCR functions in synthetic systems.     

Extraordinary transport behavior of gases in isothermally annealed poly(4‐methyl‐1‐pentene) membranes

Poly(4‐methyl‐1‐pentene) (PMP) membranes were modified through isothermal annealing to investigate the change of their crystalline structure and rigid and mobile amorphous fractions (RAF and MAF), assuming a three‐phase model, affected the gas transport behavior. The crystalline structure was characterized by wide‐angle X‐ray diffraction (WAXD) and small‐angle X‐ray scattering (SAXS) techniques, and the free volume properties were analyzed by positron annihilation lifetime spectroscopy. Compared with the pristine membrane, the annealed membranes show higher crystallinity; the crystals undergo partial structural change from form III to form I. The lamellar crystal thickness, rigid amorphous fraction thickness, and long period in the lamellar stacks increase with crystallinity. The annealed PMP membranes exhibit higher permeability due to the increase in larger size free volumes in MAF and higher selectivity due to the increase in smaller size free volumes in RAF, respectively. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2368–2376     

Thermal dimerization kinetics of 3‐(p‐bromo‐phenyl)‐pyridazinium benzoyl methylid in solutions

3‐(p‐Bromo‐phenyl)‐pyridazinium‐benzoyl methylid (BPPBM) participates in solution at 3 + 3 dipolar thermal dimerization that can be spectrally monitored by the extinction in its visible intramolecular charge transfer (ICT) band. The attenuation of ICT band intensity shows the decrease of the BPPBM concentration with the increasing of dimer concentration. The complex kinetics of light‐assisted dimerization process was studied taking into account that the thermodynamic equilibrium is reached after more than 24 h. On the basis of general order of reaction theory, we found that the dimerization reaction must be described as a multistep mechanism. The rate constants of the dimerization reactions in ethanol (k = 0.00897 s^?1) and benzene (k = 0.00774 s^?1) solutions were correlated with the BPPBM and dimer structural features established by using the HyperChem 5.02 simulation program package. A kinetic mechanism of 3 + 3 dipolar thermal dimerization for the studied ylid is proposed. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 230–239, 2008     

Reversible Dimerization of Phosphine‐Stabilized Silylenes by Silylene Insertion into SiII–H and SiII–Cl σ‐Bonds at Room Temperature

Contrary to the classical silylene dimerization leading to a disilene structure, phosphine stabilized hydro‐ and chloro‐silylenes ( 2 a , b ) undergo an unique dimerization via silylene insertion into Si? X σ‐bonds (X=H, Cl), which is reversible at room temperature. DFT calculations indicate that the insertion reaction proceeds in one step in a concerted manner.     

Measuring and simulating morphology gradients in injection‐molded talc‐reinforced isotactic polypropylene

Injection molded polymer parts are known to exhibit structural gradients of crystallinity, crystallite phases and crystallite orientations. The structural variations depend on the geometry, the material properties, and the processing conditions, and affect the mechanical properties of the molded part. We explore the use of raster‐scanning small‐ and wide‐angle X‐ray scattering (SAXS, WAXS) for mapping the microstructure in dogbone specimens of an isotactic polypropylene (PP) homopolymer and a talc‐reinforced isotactic PP compound. The specimens were injection molded with different mold temperatures and injection speeds, and the mapping approach revealed systematic structural heterogeneities and asymmetries. Accompanying numerical simulations of the injection molding process yielded predictions of the flow pattern, including the shear rate distribution and the resulting orientation of the flake‐shaped talc particles. We found a clear correspondence between the experimentally observed data and the simulations, in particular regarding the asymmetry of the orientation distributions relative to the center of the dogbone cross section, caused by asymmetric flow through the entrance of the mold. Furthermore, the shear rate distribution correlated with the occurrence of α‐ and β‐phases. Subtle differences in the crystallized structures along the long axis of the dogbones suggest an explanation to the observation that the specimens studied always tended to break at the same position in tensile tests. The results clearly demonstrate the potential of mapping experiments which combine lateral resolution on macroscopic length scales with the molecular‐scale resolution from scattering. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 1157–1167     

Lewis‐Pair‐Mediated Selective Dimerization and Polymerization of Lignocellulose‐Based β‐Angelica Lactone into Biofuel and Acrylic Bioplastic

This contribution reports an unprecedentedly efficient dimerization and the first successful polymerization of lignocellulose‐based β‐angelica lactone (β‐AL) by utilizing a selective Lewis pair (LP) catalytic system, thereby establishing a versatile bio‐refinery platform wherein two products, including a dimer for high‐quality gasoline‐like biofuel (C₈–C₉ branched alkanes, yield=87 %) and a heat‐ and solvent‐resistant acrylic bioplastic (M_n up to 26.0 kg mol^?1), can be synthesized from one feedstock by one catalytic system. The underlying reason for exquisite selectivity of the LP catalytic system toward dimerization and polymerization was explored mechanistically.     

Simulating GTP:Mg and GDP:Mg with a simple force field: A structural and thermodynamic analysis

Di‐ and tri‐phosphate nucleotides are essential cofactors for many proteins, usually in an Mg²⁺‐bound form. Proteins like GTPases often detect the difference between NDP and NTP and respond by changing conformations. To study such complexes, simple, fixed charge force fields have been used, which allow long simulations and precise free energy calculations. The preference for NTP or NDP binding depends on many factors, including ligand structure and Mg²⁺ coordination and the changes they undergo upon binding. Here, we use a simple force field to examine two Mg²⁺ coordination modes for the unbound GDP and GTP: direct, or “Inner Sphere” (IS) coordination by one or more phosphate oxygens and indirect, “Outer Sphere” (OS) coordination involving one or more bridging waters. We compare GTP: and GDP:Mg binding with OS and IS coordination; combining the results with experimental data then indicates that GTP prefers the latter. We also examine different kinds of IS coordination and their sensitivity to a key force field parameter: the optimal Mg:oxygen van der Waals distance R_min. Increasing R_min improves the Mg:oxygen distances, the GTP: and GDP:Mg binding affinities, and the fraction of GTP:Mg with β + γ phosphate coordination, but does not improve or change the GTP/GDP affinity difference, which remains much larger than experiment. It has no effect on the free energy of GDP binding to a GTPase. © 2012 Wiley Periodicals, Inc.     

Synthesis and biological evaluations of mono‐ and bis‐ferrocene uracil derivatives

Mono‐ ( 3a – 3e and 4a – 4e ) and bis‐ferrocene ( 5a – 5e and 6a – 6e ) conjugated 5‐substituted uracil derivatives that are bridged by 1,2,3‐triazole linker were synthesized. The impact of ferrocene unit and spacer between ferrocene and triazole on radical scavenging potency was observed. Bis‐ferrocenyl uracil derivatives exhibited better antiproliferative activities than their mono‐ferrocenyl analogs. Bis‐ferrocenyl methyl‐ ( 5b ) and halogen‐substituted ( 5e , 6c , and 6d ) uracil derivatives showed pronounced and selective cytostatic activities on colon adenocarcinoma (CaCo‐2) and Burkitt lymphoma (Raji) cells, with higher potency and selectivity than the reference drug 5‐fluorouracil. Generation of reactive oxygen species (ROS) in CaCo‐2 and Raji cells when treated with compounds 5b , 5e , and 6d was observed. Bis‐ferrocenyl 5‐chlorouracil 6c induced significant disruption in mitochondrial membrane potential that is accompanied by activation of apoptosis in CaCo‐2, Raji, and acute lymphoblastic leukemia (CCRF‐CEM) cells, while 6d caused mitochondrial dysfunction and apoptosis induction in CaCo‐2 and Raji cells. Potent antiproliferative activity of 6c and 6d could be associated with mitochondrial membrane potential disruption accompanied by apoptosis induction. Our findings highlighted 6c and 6d with potent and selective antiproliferative activity on CaCo‐2, Raji, and CCRF‐CEM cells that may be associated with targeting cancer cell mitochondria, as a molecular target.     

Effect of thermal history on the free volume properties of semi‐crystalline poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) membranes by positron annihilation lifetime spectroscopy

Free volume properties of a series of poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) (PHBV) membranes, which were produced by various nonisothermal crystallization processes (rapid‐, step‐, and slow‐cooling processes), were investigated using positron annihilation lifetime (PAL) spectroscopy over a temperature range of 25–90 °C. From the annihilation lifetime parameters, the temperature dependence of free volume size, amount, size distribution, and fractional free volume and thermal expansion properties of free volume were discussed. A model which assumed that amorphous phase was subdivided into mobile and rigid amorphous fractions (MAF and RAF) in the semicrystalline polymer was considered to interpret the temperature dependence of those free volume properties. Morphological observation of the semicrystalline polymer by small‐angle X‐ray scattering (SAXS) indicated that the rapid‐cooled (cold‐crystallized) membranes showed a much thinner thickness of the repeating lamellar/amorphous layers and most likely higher amount of RAF, which restrained the chain motion, than the step‐ and slow‐cooled (melt‐crystallized) membranes. The difference of free volume properties among various PHBV membranes was created according to the crystalline structure of the polymer from different thermal history. The polymer crystallized with slower cooling rate induced higher crystallinity and resulted in less free volume amount and lower fractional free volume. In addition, the thermal expansion coefficients of free volume size were affected by the crystallization rate of PHBV polymer. Larger distribution of the free volume size of melt‐crystallized membranes was observed as a result of the bimodal distribution of the lamellar periodicity and less amount of RAF than that of the cold‐crystallized membranes. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 855–865, 2009     

Two‐ and Three‐Component Reactions Leading to New Enamines Derived from 2,3‐Dicyanobut‐2‐enoates

The three‐component reactions of 1‐azabicyclo[1.1.0]butanes 1 , dicyanofumarates (E)‐ 5 , and MeOH or morpholine yielded azetidine enamines 8 and 9 with the cis‐orientation of the ester groups at the C?C bond ((E)‐configuration; Schemes 3 and 4). The structures of 8a and 9d were confirmed by X‐ray crystallography. The formation of the products is explained via the nucleophilic addition of 1 onto (E)‐ 5 , leading to a zwitterion of type 7 (Scheme 2), which is subsequently trapped by MeOH or morpholine ( 10a ), followed by elimination of HCN. Similarly, two‐component reactions between secondary amines 10a – 10c and (E)‐ 5 gave products 12 with an (E)‐enamine structure and (Z)‐oriented ester groups. On the other hand, two‐component reactions involving primary amines 10d – 10f or NH₃ led to the formation of the corresponding (Z)‐enamines, in which the (E)‐orientation of ester groups was established.     

Efficient Trapping of 1,2‐Cyclohexadienes with 1,3‐Dipoles

1,2‐Cyclohexadienes are transient intermediates that undergo rapid dimerization and intermolecular trapping with activated olefins and heteroatomic nucleophiles. Fluoride‐mediated desilylative elimination of readily accessible 6‐silylcyclohexene‐1‐triflates allows the mild, chemoselective, and functional‐group tolerant generation of cyclic allene intermediates, which undergo efficient trapping reactions with stable 1,3‐dipoles. The reactions proceed with high levels of both regio‐ and diastereoselectivity. The reaction of cyclic allenes with azides is accompanied by the facile loss of dinitrogen, resulting in the formation of tetrahydroindoles or polycylic aziridines depending on the azide employed.     

Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors

Journal of Computer-Aided Molecular Design - KRAS has long been referred to as an ‘undruggable’ target due to its high affinity for its cognate ligands (GDP and GTP) and its lack of...     

Rhodium‐Catalyzed Cross‐Cyclotrimerization and Dimerization of Allenes with Alkynes

It has been established that a cationic rhodium(I)/binap complex catalyzes the cross‐cyclotrimerization of two molecules of a monosubstituted allene with one molecule of a functionalized alkyne to give 3,6‐dialkylidenecyclohex‐1‐enes. In contrast, the reactions involving di‐ or trisubstituted allenes and/or unfunctionalized alkynes afforded cross‐dimerization products, substituted dendralenes, through β‐hydrogen elimination from the corresponding rhodacycles.