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.     

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.     

Nature-inspired dimerization as a strategy to modulate neuropeptide pharmacology exemplified with vasopressin and oxytocin

Vasopressin (VP) and oxytocin (OT) are cyclic neuropeptides that regulate fundamental physiological functions via four G protein-coupled receptors, V_1aR, V_1bR, V₂R, and OTR. Ligand development remains challenging for these receptors due to complex structure–activity relationships. Here, we investigated dimerization as a strategy for developing ligands with novel pharmacology. We regioselectively synthesised and systematically studied parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimer constructs of VP, OT and dVDAVP (1-deamino-4-valine-8-d-arginine-VP). All disulfide-linked dimers, except for the head-to-tail cyclized constructs, retained nanomolar potency despite the structural implications of dimerization. Our results support a single chain interaction for receptor activation. Dimer orientation had little impact on activity, except for the dVDAVP homodimers, where an antagonist to agonist switch was observed at the V_1aR. This study provides novel insights into the structural requirements of VP/OT receptor activation and spotlights dimerization as a strategy to modulate pharmacology, a concept also frequently observed in nature.

Structural and pharmacological study of parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimers of vasopressin and oxytocin. This study spotlights dimerization as a strategy to modulate the pharmacology of neuropeptides.     

The amount of immobilized polymer in PMMA SiO2 nanocomposites determined from calorimetric data

For semicrystalline polymers there is an ongoing debate at what temperature the immobilized or rigid amorphous fraction (RAF) devitrifies (relaxes). The question if the polymer crystals are melting first and simultaneously the RAF devitrifies or the RAF devitrifies first and later on the crystals melt cannot be answered easily on the example of semicrystalline polymers. This is because the crystals, which are the reason for the immobilization of the polymer, often disappear (melt) in the same temperature range as the RAF. For polymer nanocomposites the situation is simpler. Silica nanoparticles do not melt or undergo other phase transitions altering the polymer-nanoparticle interaction in the temperature range where the polymer is thermally stable (does not degrade). The existence of an immobilized fraction in PMMA SiO₂ nanocomposites was shown on the basis of heat capacity measurements at the glass transition of the polymer. The results were verified by enthalpy relaxation experiments below the glass transition. The immobilized layer is about 2 nm thick at low filler content if agglomeration is not dominant. The thickness of the layer is similar to that found in semicrystalline polymers and independent from the shape of the nanoparticles. Nanocomposites therefore offer a unique opportunity to study the devitrification of the immobilized fraction (RAF) without interference of melting of crystals as in semicrystalline polymers. It was found that the interaction between the SiO₂ nanoparticles and the PMMA is so strong that no devitrification occurs before degradation of the polymer. No gradual increase of heat capacity or a broadening of the glass transition was found. The cooperatively rearranging regions (CRR) are either immobilized or mobile. No intermediate states are found. The results obtained for the polymer nanocomposites support the view that the reason for the restricted mobility must disappear before the RAF can devitrify. For semicrystalline polymers this means that rigid crystals must melt before the RAF can relax.     

Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1

Inhibitors of Apoptosis Proteins (IAPs) are conserved E3-ligases that ubiquitylate substrates to prevent apoptosis and activate the NF-kB survival pathway, often deregulated in cancer. IAPs-mediated regulation of NF-kB signaling is based on the formation of protein complexes by their type-I BIR domains. The XIAP-BIR1 domain dimerizes to bind two TAB1 monomers, leading to downstream NF-kB activation. Thus, impairment of XIAP-BIR1 dimerization could represent a novel strategy to hamper cell survival in cancer. To this aim, we previously reported NF023 as a potential inhibitor of XIAP-BIR1 dimerization. Here we present a thorough analysis of NF023 binding to XIAP-BIR1 through biochemical, biophysical and structural data. The results obtained indicate that XIAP-BIR1 dimerization interface is involved in NF023 binding, and that NF023 overall symmetry and the chemical features of its central moiety are essential for an efficient interaction with the protein. Such strategy provides original hints for the development of novel BIR1-specific compounds as pro-apoptotic agents.     

Direct identification of all oncogenic mutants in KRAS exon 1 by cycling temperature capillary electrophoresis

Over the past few decades, advances in genetics and molecular biology have revolutionized our understanding of cancer initiation and progression. Molecular progression models outlining genetic events have been developed for many solid tumors, including colon cancer. Previous reports in the literature have shown a relationship between different KRAS mutations and prognosis and response to medical treatment in colon cancer patients. Furthermore, the presence of a mutated KRAS has been correlated with different clinicopathological variables including age and gender of patients and tumor location. To our knowledge, few institutions screen for KRAS mutations on regular basis in colon cancer patients despite such evidence that knowledge of KRAS exon 1 status is informative. Here, we report on a mutation analysis method adapted to a 96-capillary electrophoresis instrument that allows identification of all 12 oncogenic mutations in KRAS exon 1 under denaturing conditions. To determine the optimal parameters, a series of DNA constructs generated by site-directed mutagenesis was analyzed and the migration times of all mutant peaks were measured. A classification tree was then made based on the differences in migration time between the mutants and an internal standard. A randomized series of 500 samples constructed with mutagenesis as well as 60 blind samples from sporadic colon carcinomas was analyzed to test the method. No wild-type samples were scored as mutants and all mutants were correctly identified. Post polymerase chain reaction (PCR) analysis time of 96 samples was performed within 40 min.     

The mechanism of Raf activation through dimerization

Raf, a threonine/serine kinase in the Raf/MEK/ERK pathway, regulates cell proliferation. Raf''s full activation requires dimerization. Aberrant activation through dimerization is an important therapeutic target. Despite its clinical importance, fundamental questions, such as how the side-to-side dimerization promotes the OFF-to-ON transition of Raf''s kinase domain and how the fully activated ON-state kinase domain is stabilized in the dimer for Raf signaling, remain unanswered. Herein, we decipher an atomic-level mechanism of Raf activation through dimerization, clarifying this enigma. The mechanism reveals that the replacement of intramolecular π–π stacking by intermolecular π–π stacking at the dimer interface releases the structural constraint of the αC-helix, promoting the OFF-to-ON transition. During the transition, the inhibitory hydrophobic interactions were disrupted, making the phosphorylation sites in A-loop approach the HRD motif for cis-autophosphorylation. Once fully activated, the ON-state kinase domain can be stabilized by a newly identified functional N-terminal basic (NtB) motif in the dimer for Raf signaling. This work provides atomic level insight into critical steps in Raf activation and outlines a new venue for drug discovery against Raf dimerization.

We decipher an atomic-level mechanism of Raf activation through dimerization, revealing that the disruption of intramolecular π–π stacking at the dimer interface promotes the OFF-to-ON transition.     

High-Pressure Reaction Profiles and Activation Volumes of 1,3-Cyclohexadiene Dimerizations Computed by the Extreme Pressure-Polarizable Continuum Model (XP-PCM)

Quantum chemical calculations are reported for the thermal dimerizations of 1,3-cyclohexadiene at 1 atm and high pressures up to the GPa range. Computed activation enthalpies of plausible dimerization pathways at 1 atm agree well with the experiment activation energies and the values from previous calculations. High-pressure reaction profiles, computed by the recently developed extreme pressure-polarizable continuum model (XP-PCM), show that the reduction of reaction barrier is more profound in concerted reactions than in stepwise reactions, which is rationalized on the basis of the volume profiles of different mechanisms. A clear shift of the transition state towards the reactant under pressure is revealed for the [6+4]-ene reaction by the calculations. The computed activation volumes by XP-PCM agree excellently with the experimental values, confirming the existence of competing mechanisms in the thermal dimerization of 1,3-cyclohexadiene.     

Theoretical comparison of ketene dimerization in the gas and liquid phase

We present the first theoretical comparison between ketene dimerization in gas phase and ketene dimerization in solution. Density functional theory (DFT) calculations on the ketene dimerization were carried out considering the following product dimers: diketene (d-I), 1,3-cyclobutanedione (d-II), 2,4-dimethylene-1,3-dioxetane (d-III), and 2-methyleneoxetan-3-one (d-IV). All structures were optimized at the PW86x+PBEc/DZP level of theory. Based on these geometries, a total of 58 meta and hybrid functionals were used to evaluate the heat of dimerization. The MPW1K functional was found to fit the experimental data best and subsequently used in the final analyses for all energy calculations. It was found on both kinetic and thermodynamic grounds that only d-I and d-II are formed during ketene dimerization in gas phase and solution. In gas phase, d-I is favored over d-II by 2 kcal/mol. However, the dimerization barrier for d-I is 1 kcal/mol higher than for d-II. Solvation makes dimerization more favorable. On the enthalpic surface this is due to a favorable interaction between the dimer dipole moment and solvent molecules. The dimer is stabilized further on the Gibbs energy surface by an increase of the dimerization entropy in solution compared to gas phase. The species d-I remains the most stable dimer in solution by 1 kcal/mol. Kinetically, the dimerization barriers for the relevant species d-I and d-II are cut in half by solvation, due to both favorable dimer-dipole/solvent interactions (DeltaH++, DeltaG++) and an increase in the activation entropies (DeltaS++). While the dimerization barrier for d-II is lowest for the gas phase and toluene, the barrier for d-I formation becomes lowest for the more polar solvent acetone by 1 kcal/mol as d-I dimerization has the most polar transition state.     

Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

Dimeric structures chlorophyll (a) (Chla) and their mono‐ and dihydrated have been suggested to play an important role in the mechanism of photoreaction center chlorophyll special pairs PSI and PSII. Despite their functional importance, the molecular basis structures for interacting two Chla molecules and the structural stabilization role of H₂O in the formation of hydrated Chla dimer complexes is poorly understood. In this article, the different coordination modes between two interacting Chla molecules and the configurational (orientation and distance) features between the dimer and bound H₂O molecules are characterized by means of super molecule approach the density functional theory DFT. An estimation of the thermodynamic quantities is made for Chla dimerization and hydration processes. The results indicate that structure including ester linkages via H₂O hydrogen bonding is the most favorable conformation for the dihydrated chlorophyll (a) dimer at B3LYP/6‐31G*‐DCP level of calculation. The dispersion interaction is shown to be of great significance for the Chla dimer stabilization. In aqueous nonpolar solvent, the thermodynamics show that Chla has a slightly stronger driving force for full hydration than for dimerization and that hydration of the dimers is rather weakly exergonic. The tetrahydrated dimers having a similar arrangement to that in crystals of ethyl chlorophyllide (a) dihydrate are found to be more stable than the Chla dihydrated dimer. The data underscore the key role of H‐bonding in the stability of Chla‐H₂O adducts and, in particular, the great importance of the Chla monomeric dihydrated species in the hydration and dimerization of Chla in aqueous media. Clearly, the Chla dihydrates (Chla‐2 H₂O) are found more stable than the monohydrates (Chla‐H₂O) and the Chla dimers (Chla₂), owing to a particular structure in which cooperative interactions occur between the H₂O molecules and Chla. Calculations also indicate that the most thermodynamically preferred pathway for the formation of Chla dimer hydrates can be represented by two steps: the first corresponds to the formation of Chla monomeric dihydrates and the second is the dimerization of the dihydrates on to tetrahydrated Chla dimers. These results allow to obtain a new possible pathway for Chla dimer formation processes and could provide new insights to the aggregation of chlorophyll (a) in solution.     

A diverse set of oligomeric class II MHC-peptide complexes for probing T-cell receptor interactions

BACKGROUND: T-cells are activated by engagement of their clonotypic cell surface receptors with peptide complexes of major histocompatibility complex (MHC) proteins, in a poorly understood process that involves receptor clustering on the membrane surface. Few tools are available to study the molecular mechanisms responsible for initiation of activation processes in T-cells. RESULTS: A topologically diverse set of oligomers of the human MHC protein HLA-DR1, varying in size from dimers to tetramers, was produced by varying the location of an introduced cysteine residue and the number and spacing of sulfhydryl-reactive groups carried on novel and commercially available cross-linking reagents. Fluorescent probes incorporated into the cross-linking reagents facilitated measurement of oligomer binding to the T-cell surface. Oligomeric MHC-peptide complexes, including a variety of MHC dimers, trimers and tetramers, bound to T-cells and initiated T-cell activation processes in an antigen-specific manner. CONCLUSION: T-cell receptor dimerization on the cell surface is sufficient to initiate intracellular signaling processes, as a variety of MHC-peptide dimers differing in intramolecular spacing and orientation were each able to trigger early T-cell activation events. The relative binding affinities within a homologous series of MHC-peptide oligomers suggest that T-cell receptors may rearrange in the plane of the membrane concurrent with oligomer binding.     

酸性分子筛催化乙烯二聚反应

应用密度泛函理论(DFT), 采用5T簇模型来模拟分子筛催化剂的酸性位, 在B3LYP/6-311+G(3df, 2p)的条件下通过理论计算研究了乙烯在酸性分子筛上的二聚反应. 对反应各驻点进行了全局优化, 经过零点能校正后, 计算得出乙烯二聚反应的活化能. 研究表明, 乙烯在分子筛上的二聚反应分三步进行: 单个乙烯分子化学吸附→第二个乙烯分子的物理吸附→两乙烯分子二聚反应. 乙烯化学吸附生成的烷氧化合物与物理吸附的乙烯分子发生二聚反应生成新的C—C键同时生成新的烷氧化合物. 计算得到的乙烯化学吸附和二聚反应的反应能垒分别为108和149 kJ·mol-1. 反应的逆过程也就是1-丁烯在酸性分子筛表面的1-丁基烷氧化合物发生β分裂反应, 计算所得相应的1-丁烯β分裂反应的能垒为217 kJ·mol-1, 远高于相应的乙烯二聚反应能垒. 此外还进一步研究了所用基组对计算结果的影响.     

Aspects of the photodimerization mechanism of 2,4-dichlorocinnamic acid studied by kinetic photocrystallography

Photoinduced structural variations in single crystals of 2,4-dichloro-trans-cinnamic acid (C9H6Cl2O2, DiClCA) have been investigated using X-ray diffraction (photocrystallography) and optical spectroscopic methods. During UV irradiation, which initiates the irreversible dimerization reaction, a loss of the long-range order of the reactant single crystal was found, i.e., that the dimerization is a heterogeneous one. This unexpected result emphasizes the still-existing problem of predicting changes or of remaining periodicity during chemical reactions in the solid state. On the basis of the experimental results, we propose a qualitative kinetic reaction scheme for DiClCA heterogeneous dimerization reaction.     

Structural tuning intra- versus inter-molecular proton transfer reaction in the excited state

A series of 2-pyridyl-pyrazole derivatives 1-4 possessing five-membered ring hydrogen bonding configuration are synthesized, the structural flexibility of which is strategically tuned to be in the order of 1 > 2 > 3 > 4. This system then serves as an ideal chemical model to investigate the correlation between excited-state intramolecular proton transfer (ESIPT) reaction and molecular skeleton motion associated with hydrogen bonds. The resulting luminescence data reveal that the rate of ESIPT decreases upon increasing the structural constraint. At sufficiently low concentration where negligible dimerization is observed, ESIPT takes place in 1 and 2 but is prohibited in 3 and 4, for which high geometry constraint is imposed. The results imply that certain structural bending motions associated with hydrogen bonding angle/distance play a key role in ESIPT. This trend is also well supported by the DFT computational approach, in which the barrier associated with ESIPT is in the order of 1 < 2 < 3 < 4. Upon increasing the concentration in cyclohexane, except for 2, the rest of the title compounds undergo ground-state dimerization, from which the double proton transfer takes place in the excited state, resulting in a relatively blue shifted dimeric tautomer emission (cf. the monomer tautomer emission). The lack of dimerization in 2 is rationalized by substantial energy required to adjust the angle of hydrogen bond via twisting the propylene bridge prior to dimerization.     

Structural and thermodynamic behavior of eukaryotic initiation factor 4E in supramolecular formation with 4E-binding protein 1 and mRNA cap analogue, studied by spectroscopic methods

The structural and thermodynamic behavior of the complex formation of eIF4E with either or both mRNA cap analogue (m7GTP, m7GpppA, or m7GpppG) and 4EBP1 has been investigated by spectroscopic measurements. Although the circular dichroism (CD) spectrum of eIF4E was little affected by the association with any cap analogue, the association constant of eIF4E with m7GpppA/G, estimated from the fluorescence quenching, was about 10 times larger than that with m7GTP. The van't Hoff analyses showed that the m7GpppA/G binding is enthalpy-driven with a large negative deltaH(o), and this is in contrast with the entropy-driven binding of m7GTP, where the positive deltaS(o) is large enough to overcome an increase of deltaH(o). This different behavior obviously originates in the interaction of the second nucleotide in m7GpppA with eIF4E, suggesting the importance of the nucleotide sequence linked to the m7Gppp terminal moiety, in addition to the specific interaction with the m7G base, for the recognition of mRNA cap structure by eIF4E. On the other hand, the CD spectra indicated that the binding of 4EBP1, an endogenous eIF4E-regulatory protein without having any defined secondary structure, shifted the m7GTP- or m7GpppA/G-bound eIF4E to an irregular structure, although such a structural change was not observed for eIF4E alone. The association constant of 4EBP1 with m7GTP- or m7GpppA/G-bound eIF4E was by two orders of magnitude larger than that with eIF4E alone. These results suggest the close interrelation in the supramolecular formation of 4EBP-eIF4E-mRNA cap structure.     

Investigation of ethylene dimerization over faujasite zeolite by the ONIOM method.

Ethylene dimerization was investigated by using an 84T cluster of faujasite zeolite modeled by the ONIOM3(MP2/6-311++G(d,p):HF/6-31G(d):UFF) method. Concerted and stepwise mechanisms were evaluated. In the stepwise mechanism, the reaction proceeds by protonation of ethylene to form the surface ethoxide and then C--C bond formation between the ethoxide and the second ethylene molecule to give the butoxide product. The first step is rate-determining and has an activation barrier of 30.06 kcal mol(-1). The ethoxide intermediate is rather reactive and readily reacts with another ethylene molecule with a smaller activation energy of 28.87 kcal mol(-1). In the concerted mechanism, the reaction occurs in one step of simultaneous protonation and C--C bond formation. The activation barrier is calculated to be 38.08 kcal mol(-1). Therefore, the stepwise mechanism should dominate in ethylene dimerization.     

Protein-Targeted Glycan Editing on Living Cells Disrupts KRAS Signaling

The frequent mutation of KRAS oncogene in some of the most lethal human cancers has spurred incredible efforts to develop KRAS inhibitors, yet only one covalent inhibitor for the KRAS^G12C mutant has been approved to date. New venues to interfere with KRAS signaling are desperately needed. Here, we report a “localized oxidation-coupling” strategy to achieve protein-specific glycan editing on living cells for disrupting KRAS signaling. This glycan remodeling method exhibits excellent protein and sugar specificity and is applicable to different donor sugars and cell types. Attachment of mannotriose to the terminal galactose/N-acetyl-D-galactosamine epitopes of integrin α_vβ₃, a membrane receptor upstream of KRAS, blocks its binding to galectin-3, suppresses the activation of KRAS and downstream effectors, and mitigates KRAS-driven malignant phenotypes. Our work represents the first successful attempt to interfere with KRAS activity by manipulating membrane receptor glycosylation.