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The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.RAS binding to RAF’s RBDCRD domain on lipid bilayers cooperatively induces nanoclustering, slowing complex diffusion—an essential mechanism in initial signal activation. [ABSTRACT FROM AUTHOR]

Climate despair—a sense of hopelessness about humanity’s ability to pursue a sustainable future—is emerging as a psychosocial threat. Psychological science conceptualizes hopelessness as a cognitive schema characterized by negative expectancies. Climate hopelessness, then, may be conceptualized as a mental model that represents climate change as a massive problem with futile response options. It manifests in negative expectancies about the future. Here we show that learning about eco-innovations—novel climate-response options—can decrease climate hopelessness. Across 11 experiments (N = 3224), we found that adults (mostly from the USA) reported lower climate hopelessness after viewing videos that depicted eco-innovations (such as a high-tech, net-zero-energy city) than they did in various control conditions, including those that were unrelated to climate (such as a no-video control) and those that depicted more familiar, schema-consistent climate responses (such as living in a rural, intentional community). This research provides causal evidence that thinking about novel climate responses can contribute to a more hopeful outlook, and it identifies technological innovation as one possible seed for such messaging. [ABSTRACT FROM AUTHOR]

Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications. [ABSTRACT FROM AUTHOR]

Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a “gatekeeper” for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.Understanding of GPCR activation is limited as the structural information fails to present the full spectrum of energy landscape. Here, authors establish a series of conformation-biased mutants that represent five conformational states lying along adenosine A2A receptor (A2AR) activation. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A2A receptor (A2AR) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A2AR to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 2296.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A2AR, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-Gs). Most notably, the agonist binding and the coupling to mini-Gs accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y2887.53, and Y2907.55) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 2296.31 on TM6. This study provides a quantitative description of conformational dynamics in A2AR and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor. [ABSTRACT FROM AUTHOR]

The first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation. The molecular details of the RAS-RAF interaction are still not fully understood. Here, the authors present crystal structures of wild-type and mutant KRAS in complex with the RAS-binding and membrane-interacting cysteine-rich domains of RAF1, and propose a model of the membrane-bound RAS-RAF complex. [ABSTRACT FROM AUTHOR]

Cations play key roles in regulating G-protein-coupled receptors (GPCRs), although their mechanisms are poorly understood. Here, 19F NMR is used to delineate the effects of cations on functional states of the adenosine A2A GPCR. While Na+ reinforces an inactive ensemble and a partial-agonist stabilized state, Ca2+ and Mg2+ shift the equilibrium toward active states. Positive allosteric effects of divalent cations are more pronounced with agonist and a G-protein-derived peptide. In cell membranes, divalent cations enhance both the affinity and fraction of the high affinity agonist-bound state. Molecular dynamics simulations suggest high concentrations of divalent cations bridge specific extracellular acidic residues, bringing TM5 and TM6 together at the extracellular surface and allosterically driving open the G-protein-binding cleft as shown by rigidity-transmission allostery theory. An understanding of cation allostery should enable the design of allosteric agents and enhance our understanding of GPCR regulation in the cellular milieu. [ABSTRACT FROM AUTHOR]

This research directly assesses older people's neural activation in response to a changing urban environment while walking, as measured by electroencephalography (EEG). The study builds on previous research that shows changes in cortical activity while moving through different urban settings. The current study extends this methodology to explore previously unstudied outcomes in older people aged 65 years or more (n = 95). Participants were recruited to walk one of six scenarios pairing urban busy (a commercial street with traffic), urban quiet (a residential street) and urban green (a public park) spaces in a counterbalanced design, wearing a mobile Emotiv EEG headset to record real-time neural responses to place. Each walk lasted around 15 min and was undertaken at the pace of the participant. We report on the outputs for these responses derived from the Emotiv Affectiv Suite software, which creates emotional parameters ('excitement', 'frustration', 'engagement' and 'meditation') with a real-time value assigned to them. The six walking scenarios were compared using a form of high dimensional correlated component regression (CCR) on difference data, capturing the change between one setting and another. The results showed that levels of 'engagement' were higher in the urban green space compared to those of the urban busy and urban quiet spaces, whereas levels of 'excitement' were higher in the urban busy environment compared with those of the urban green space and quiet urban space. In both cases, this effect is shown regardless of the order of exposure to these different environments. These results suggest that there are neural signatures associated with the experience of different urban spaces which may reflect the older age of the sample as well as the condition of the spaces themselves. The urban green space appears to have a restorative effect on this group of older adults. [ABSTRACT FROM AUTHOR]

Rationale: Caffeine exerts positive effects on cognitive and behavioral processes, especially in sub-optimal conditions when arousal is low. Apart from caffeine, coffee contains other compounds including the phenolic compounds ferulic acid, caffeic acid, and the chlorogenic acids, which have purported antioxidant properties. The chlorogenic acids are the most abundant family of compounds found in coffee, yet their effects on cognition and mood have not been investigated. Objectives: This study aims to ascertain whether a coffee rich in chlorogenic acid modulates brain function. Methods: The present pilot study examined the acute effects of decaffeinated coffee with regular chlorogenic acid content and decaffeinated coffee with high chlorogenic acid content on mood and cognitive processes, as measured by behavioral tasks and event-related potentials (ERPs). Performance and ERP responses to a battery of cognitive tasks were recorded at baseline and following the equivalent of three cups of coffee in a randomized, double-blind, crossover study of 39 healthy older participants. Results: Compared with the decaffeinated coffee with regular chlorogenic acid and placebo, caffeinated coffee showed a robust positive effect on higher-level mood and attention processes. To a lesser extent, the decaffeinated coffee high in chlorogenic acid also improved some mood and behavioral measures, relative to regular decaffeinated coffee. Conclusions: Our pilot results suggest that non-caffeine compounds in coffee such as the chlorogenic acids may be capable of exerting some acute behavioral effects, thus warranting further investigation. [ABSTRACT FROM AUTHOR]

Please note that the legend to Fig. 1 has been modified since this article was originally published, and also that in Tables 2, 3 and 4, R[2] was corrected to (the now correct) R squared. [ABSTRACT FROM AUTHOR]