Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

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.

Monatomic ions influence substrate permeation across bacterial microcompartment shells

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.

Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery

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.

Exploring CRD mobility during RAS/RAF engagement at the membrane

During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.

Drug Discovery by Automated Adaptation of Chemical Structure and Identity

Computer-aided drug design offers the potential to dramatically reduce the cost and effort required for drug discovery. While screening-based methods are valuable in the early stages of hit identification, they are frequently succeeded by iterative, hypothesis-driven computations that require recurrent investment of human time and intuition. To increase automation, we introduce a computational method for lead refinement that combines concerted dynamics of the ligand/protein complex via molecular dynamics simulations with integrated Monte Carlo-based changes in the chemical formula of the ligand. This approach, which we refer to as ligand-exchange Monte Carlo molecular dynamics, accounts for solvent- and entropy-based contributions to competitive binding free energies by coupling the energetics of bound and unbound states during the ligand-exchange attempt. Quantitative comparison of relative binding free energies to reference values from free energy perturbation, conducted in vacuum, indicates that ligand-exchange Monte Carlo molecular dynamics simulations sample relevant conformational ensembles and are capable of identifying strongly binding compounds. Additional simulations demonstrate the use of an implicit solvent model. We speculate that the use of chemical graphs in which exchanges are only permitted between ligands with sufficient similarity may enable an automated search to capture some of the benefits provided by human intuition during hypothesis-guided lead refinement.

Corrigendum: Assessing Inequalities in Wellbeing at a Neighbourhood Scale in Low-Middle-Income-Country Secondary Cities and Their Implications for Long-Term Livability

[This corrects the article DOI: 10.3389/fsoc.2021.729453.].

Assessing Inequalities in Wellbeing at a Neighbourhood Scale in Low-Middle-Income-Country Secondary Cities and Their Implications for Long-Term Livability

To ensure future sustainability, cities need to consider concepts of livability and resident wellbeing alongside environmental, economic and infrastructure development equity. The current rapid urbanization experienced in many regions is leading to sustainability challenges, but also offers the opportunity to deliver infrastructure supporting the social aspects of cities and the services that underpin them alongside economic growth. Unfortunately, evidence of what is needed to deliver urban wellbeing is largely absent from the global south. This paper contributes to filling this knowledge gap through a novel interdisciplinary mixed methods study undertaken in two rapidly changing cities (one Thai and one Kenyan) using qualitative surveys, subjective wellbeing and stress measurements, and spatial analysis of urban infrastructure distribution. We find the absence of basic infrastructure (including waste removal, water availability and quality) unsurprisingly causes significant stress for city residents. However, once these services are in place, smaller variations (inequalities) in social (crime, tenure) and environmental (noise, air quality) conditions begin to play a greater role in determining differences in subjective wellbeing across a city. Our results indicate that spending time in urban greenspaces can mitigate the stressful impacts of city living even for residents of informal neighborhoods. Our data also highlights the importance of places that enable social interactions supporting wellbeing-whether green or built. These results demonstrate the need for diversity and equity in the provision of public realm spaces to ensure social and spatial justice. These findings strengthen the need to promote long term livability in LMIC urban planning alongside economic growth, environmental sustainability, and resilience.

Can an Ice-Cream Based Supplement Help Address Malnutrition in Orthogeriatric Patients?

Using a Plan-Do-Study-Act (PDSA) methodology, we describe our first cycle of a project using an ice-cream oral nutritional supplement (ONS ice-cream) to address malnutrition in older patients. A Scandishake-based^® (Nutricia) vanilla flavored ice-cream was developed and piloted on a cohort of orthopedic patients over 3 days. All suitable patients were offered 100 g ice-cream portions (240 kcal/per portion). Acceptability and energy intake were our primary outcomes. Over 3 days, the ONS ice-cream was accepted in 77% (n = 27, median age, 75 years, IQR 12.5) of the times offered. Among these patients the average energy intake per day including the ONS ice-cream was 1006 kcal, a 41% increase in energy intake compared to an initial nutritional survey among the older orthopedic patients (714 kcal, p = 0.010). When surveyed 84% (n = 16) of patients stated they would have the ONS ice-cream again. An ONS ice-cream intervention to improve energy intake in older adults is feasible.

The RIT1 C-terminus associates with lipid bilayers via charge complementarity

RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. We used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.

The Urban Built Environment, Walking and Mental Health Outcomes Among Older Adults: A Pilot Study

The benefits of walking in older age include improved cognitive health (e.g., mental alertness, improved memory functioning) and a reduced risk of stress, depression and dementia. However, research capturing the benefits of walking among older people in real-time as they navigate their world is currently very limited. This study explores cognitive health and well-being outcomes in older people as they walk in their local neighborhood environment. Residents from an independent living facility for older people (mean age 65, n = 11) walked from their home in two dichotomous settings, selected on the basis of significantly different infrastructure, varying levels of noise, traffic and percentage of green space. Employing a repeated-measures, cross over design, participants were randomly allocated to one of two groups, and walked on different days in an urban busy “gray” district (a busy, built up commercial street) vs. an urban quiet “green” district (a quiet residential area with front gardens and street trees). Our study captured real-time air quality and noise data using hand-held Airbeam sensors and physiologic health data using a smart watch to capture heart rate variability (a biomarker of stress). Cognitive health outcome measures were a pre- and post-walk short cognitive reaction time (SRT) test and memory recall of the route walked (captured via a drawn mental map). Emotional well-being outcomes were a pre- and post-walk mood scale capturing perceived stress, happiness and arousal levels. Findings showed significant positive health benefits from walking in the urban green district on emotional well-being (happiness levels) and stress physiology (p < 0.05), accompanied by faster cognitive reaction times post-walk, albeit not statistically significant in this small sample. Cognitive recall of the route varied between urban gray and urban green conditions, as participants were more likely to rely on natural features to define their routes when present. The environmental and physiologic data sets were converged to show a significant effect of ambient noise and urban conditions on stress activation as measured by heart rate variability. Findings are discussed in relation to the complexity of combining real-time environmental and physiologic data and the implications for follow-on studies. Overall, our study demonstrates the viability of using older people as citizen scientists in the capture of environmental and physiologic stress data and establishes a new protocol for exploring relationships between the built environment and cognitive health in older people.

How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes

RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected 1 ms of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding modes with an RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remains unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposed to cytosolic RAF. Particularly, on the membrane having PIP2, we found nonlinear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.

The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling

Mutant Ras proteins are important drivers of human cancers, yet no approved drugs act directly on this difficult target. Over the last decade, the idea has emerged that oncogenic signaling can be diminished by molecules that drive Ras into orientations in which effector-binding interfaces are occluded by the cell membrane. To support this approach to drug discovery, we characterize the orientational preferences of membrane-bound K-Ras4B in 1.45-ms aggregate time of atomistic molecular dynamics simulations. Individual simulations probe active or inactive states of Ras on membranes with or without anionic lipids. We find that the membrane orientation of Ras is relatively insensitive to its bound guanine nucleotide and activation state but depends strongly on interactions with anionic phosphatidylserine lipids. These lipids slow Ras' translational and orientational diffusion and promote a discrete population in which small changes in orientation control Ras' competence to bind multiple regulator and effector proteins. Our results suggest that compound-directed conversion of constitutively active mutant Ras into functionally inactive forms may be accessible via subtle perturbations of Ras' orientational preferences at the membrane surface.

The Application of Wearable Technology to Quantify Health and Wellbeing Co-benefits From Urban Wetlands

Improved nature provision in urban environments offers great potential for achieving both biodiversity conservation and public health objectives. Yet there are few experimental studies that address links between specific natural environments and physiological and/or psychological changes that could contribute to the health and wellbeing co-benefits of urban nature. In addition, relative to green space, the salutogenic impact of aquatic environments are understudied. Here, we present a feasibility study examining the use of low-cost wearable technology to quantify the psychophysiological effects of short-term exposure to urban wetlands. The study took place at the WWT London Wetland Centre, which is characterized by its contrasting biodiverse wetland habitat and surrounding urban setting. Thirty-six healthy participants experienced counterbalanced exposures to an indoor space, a wetland, an urban site. We continuously recorded electroencephalographic (EEG) data and real-time physiological stress responses; with additional monitoring of post-exposure self-reported mood states. We found a significant effect of site on mean resting heart rate (HR), with increased HR in the urban setting, although this was only observed in participants with pre-existing high stress. We found no significant differences in other measures of physiological stress responses (heart rate variability and electrodermal activity). The EEG data showed modulation of high beta band activity only in the wetland setting, potentially related to changes in attention. However, the EEG findings were confounded by low quality signals and artifacts caused by movement and environmental interference. Assessments of self-reported mood states demonstrated an increase in positive feelings in the wetland setting. A pronounced decrease in negative feelings in the wetland setting was observed in stressed individuals only. Our results suggest that pre-existing stress levels may be an important modulator of the salutogenic effect of blue-green space. We provide partial support for the hypothesis that exposure to blue-green space promotes stress recovery and for the use of low-cost psychophysiological measurements to quantify the potential stress-reducing effects of blue–green space exposure in urban dwellers. Further technological refinement is required for this approach to become a viable tool to support evidence-based decision-making for public health and green/blue space provision.

Exploring the potential of virtual reality technology to investigate the health and well being benefits of group singing

There is a growing body of academic research aiming to quantify and understand the associated health and well being benefits of group singing. The social interaction is known to strongly contribute to perceived improvements to mental and physical health but there are also indications that singing together elicits better well being outcomes than other community activities. This paper introduces the Vocal Interaction in an Immersive Virtual Acoustic (VIIVA) system, which allows the user to take part in a group singing activity in 360 degree virtual reality, hearing themselves in the recorded venue alongside the other singers. The VIIVA is intended to make group singing accessible to those unable to attend real community choirs but also as a tool for experimental research into the health and well being benefits of group singing. This paper describes the VIIVA system and presents a number of methodologies and applications which are discussed in relation to three ongoing research projects. Preliminary work indicates that the VIIVA system provides a promising tool with which to study the health and well being benefits of group singing, and in particular to control for the social interactions inherent in real group singing activities.

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B

Ras protein colocalization at the plasma membrane is implicated in the activation of signaling cascades that promote cell growth, survival, and motility. However, the mechanisms that underpin Ras self-association remain unclear. We use molecular dynamics simulations to show how basic and hydrophobic components of the disordered C-terminal membrane tether of K-Ras4B combine to regulate its membrane interactions. Specifically, anionic lipids attract lysine residues to the membrane surface, thereby splitting the peptide population into two states that exchange on the microsecond time scale. These states differ in the membrane insertion of a methionine residue, which is influenced by local membrane composition. As a result, these states may impose context-dependent biases on the disposition of Ras' signaling domain, with possible implications for the accessibility of its effector binding surfaces. We investigate Ras' ability to nanocluster by fly-casting for patches of anionic lipids and find that while anionic lipids promote the intermolecular association of K-Ras4B membrane tethers, at short range this appears to be a passive process in which anionic lipids electrostatically screen these cationic peptides to mitigate their natural repulsion. Together with the sub-microsecond stability of interpeptide contacts, this result suggests that experimentally observed K-Ras4B nanoclustering is not driven by direct intermolecular contact of its membrane tethers.

Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain

Activation of RAF kinase involves the association of its RAS-binding domain (RBD) and cysteine-rich domain (CRD) with membrane-anchored RAS. However, the overall architecture of the RAS/RBD/CRD ternary complex and the orientations of its constituent domains at the membrane remain unclear. Here, we have combined all-atom and coarse-grained molecular dynamics (MD) simulations with experimental data to construct and validate a model of membrane-anchored CRD, and used this as a basis to explore models of membrane-anchored RAS/RBD/CRD complex. First, simulations of the CRD revealed that it anchors to the membrane via insertion of its two hydrophobic loops, which is consistent with our NMR measurements of CRD bound to nanodiscs. Simulations of the CRD in the context of membrane-anchored RAS/RBD then show how CRD association with either RAS or RBD could play an unexpected role in guiding the membrane orientations of RAS/RBD. This finding has implications for the formation of RAS-RAS dimers, as different membrane orientations of RAS expose distinct putative dimerization interfaces.

Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations

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.

Molecular recognition and packing frustration in a helical protein

Biomolecular recognition entails attractive forces for the functional native states and discrimination against potential nonnative interactions that favor alternate stable configurations. The challenge posed by the competition of nonnative stabilization against native-centric forces is conceptualized as frustration. Experiment indicates that frustration is often minimal in evolved biological systems although nonnative possibilities are intuitively abundant. Much of the physical basis of minimal frustration in protein folding thus remains to be elucidated. Here we make progress by studying the colicin immunity protein Im9. To assess the energetic favorability of nonnative versus native interactions, we compute free energies of association of various combinations of the four helices in Im9 (referred to as H1, H2, H3, and H4) by extensive explicit-water molecular dynamics simulations (total simulated time > 300 μs), focusing primarily on the pairs with the largest native contact surfaces, H1-H2 and H1-H4. Frustration is detected in H1-H2 packing in that a nonnative packing orientation is significantly stabilized relative to native, whereas such a prominent nonnative effect is not observed for H1-H4 packing. However, in contrast to the favored nonnative H1-H2 packing in isolation, the native H1-H2 packing orientation is stabilized by H3 and loop residues surrounding H4. Taken together, these results showcase the contextual nature of molecular recognition, and suggest further that nonnative effects in H1-H2 packing may be largely avoided by the experimentally inferred Im9 folding transition state with native packing most developed at the H1-H4 rather than the H1-H2 interface.

Biomolecules need to recognize one another with high specificity: promoting “native” functional intermolecular binding events while avoiding detrimental “nonnative” bound configurations; i.e., “frustration”—the tendency for nonnative interactions—has to be minimized. Folding of globular proteins entails a similar discrimination. To gain physical insight, we computed the binding affinities of helical structures of the protein Im9 in various native or nonnative configurations by atomic simulations, discovering that partial packing of the Im9 core is frustrated. This frustration is overcome when the entire core of the protein is assembled, consistent with experiment indicating no significant kinetic trapping in Im9 folding. Our systematic analysis thus reveals a subtle, contextual aspect of biomolecular recognition and provides a general approach to characterize folding frustration.

The Aging Urban Brain: Analyzing Outdoor Physical Activity Using the Emotiv Affectiv Suite in Older People

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.

Correction to: The Aging Urban Brain: Analyzing Outdoor Physical Activity Using the Emotiv Affectiv Suite in Older People

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.

Older People's Experiences of Mobility and Mood in an Urban Environment: A Mixed Methods Approach Using Electroencephalography (EEG) and Interviews

There are concerns about mental wellbeing in later life in older people as the global population becomes older and more urbanised. Mobility in the built environment has a role to play in improving quality of life and wellbeing, as it facilitates independence and social interaction. Recent studies using neuroimaging methods in environmental psychology research have shown that different types of urban environments may be associated with distinctive patterns of brain activity, suggesting that we interact differently with varying environments. This paper reports on research that explores older people’s responses to urban places and their mobility in and around the built environment. The project aim was to understand how older people experience different urban environments using a mixed methods approach including electroencephalography (EEG), self-reported measures, and interview results. We found that older participants experience changing levels of “excitement”, “engagement” and “frustration” (as interpreted by proprietary EEG software) whilst walking between a busy built urban environment and an urban green space environment. These changes were further reflected in the qualitative themes that emerged from transcribed interviews undertaken one week post-walk. There has been no research to date that has directly assessed neural responses to an urban environment combined with qualitative interview analysis. A synergy of methods offers a deeper understanding of the changing moods of older people across time whilst walking in city settings.

Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.

Peptide Bond Isomerization in High-Temperature Simulations

Force fields for molecular simulation are generally optimized to model macromolecules such as proteins at ambient temperature and pressure. Nevertheless, elevated temperatures are frequently used to enhance conformational sampling, either during system setup or as a component of an advanced sampling technique such as temperature replica exchange. Because macromolecular force fields are now put upon to simulate temperatures and time scales that greatly exceed their original design specifications, it is appropriate to re-evaluate whether these force fields are up to the task. Here, we quantify the rates of peptide bond isomerization in high-temperature simulations of three octameric peptides and a small fast-folding protein. We show that peptide octamers with and without proline residues undergo cis/trans isomerization every 1-5 ns at 800 K with three classical atomistic force fields (AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L). On the low microsecond time scale, these force fields permit isomerization of nonprolyl peptide bonds at temperatures ≥500 K, and the CHARMM22/CMAP force field permits isomerization of prolyl peptide bonds ≥400 K. Moreover, the OPLS-AA/L force field allows chiral inversion about the Cα atom at 800 K. Finally, we show that temperature replica exchange permits cis peptide bonds developed at 540 K to subsequently migrate back to the 300 K ensemble, where cis peptide bonds are present in 2 ± 1% of the population of Trp-cage TC5b, including up to 4% of its folded state. Further work is required to assess the accuracy of cis/trans isomerization in the current generation of protein force fields.

Sampling errors in free energy simulations of small molecules in lipid bilayers

Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Functional Activation during the Rapid Visual Information Processing Task in a Middle Aged Cohort: An fMRI Study

The Rapid Visual Information Processing (RVIP) task, a serial discrimination task where task performance believed to reflect sustained attention capabilities, is widely used in behavioural research and increasingly in neuroimaging studies. To date, functional neuroimaging research into the RVIP has been undertaken using block analyses, reflecting the sustained processing involved in the task, but not necessarily the transient processes associated with individual trial performance. Furthermore, this research has been limited to young cohorts. This study assessed the behavioural and functional magnetic resonance imaging (fMRI) outcomes of the RVIP task using both block and event-related analyses in a healthy middle aged cohort (mean age = 53.56 years, n = 16). The results show that the version of the RVIP used here is sensitive to changes in attentional demand processes with participants achieving a 43% accuracy hit rate in the experimental task compared with 96% accuracy in the control task. As shown by previous research, the block analysis revealed an increase in activation in a network of frontal, parietal, occipital and cerebellar regions. The event related analysis showed a similar network of activation, seemingly omitting regions involved in the processing of the task (as shown in the block analysis), such as occipital areas and the thalamus, providing an indication of a network of regions involved in correct trial performance. Frontal (superior and inferior frontal gryi), parietal (precuenus, inferior parietal lobe) and cerebellar regions were shown to be active in both the block and event-related analyses, suggesting their importance in sustained attention/vigilance. These networks and the differences between them are discussed in detail, as well as implications for future research in middle aged cohorts.

Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering

The interactions of the basic, cell-penetrating region (Y47GRKKRRQRRR57) of the HIV-1 Tat protein with dioleoylphosphatidylcholine (DOPC) bilayers were previously assessed by comparing experimental X-ray diffuse scattering with atomistic molecular dynamics simulations. Here, we extend this investigation by evaluating the influence of phosphatidylethanolamine (PE) lipids. Using experimental bilayer form factors derivedfrom X-ray diffuse scattering data as a guide, our simulations indicate that Tat peptides localize close to the carbonyl-glycerol group in the headgroup region of bilayers composed of either DOPC or DOPC:DOPE (1:1) lipid. Our results also suggest that Tat peptides may more frequently insert into the hydrophobic core of bilayers composed of PC:PE (1:1) lipids than into bilayers composed entirely of PC lipids. PE lipids may facilitate peptide translocation across a lipid bilayer by stabilizing intermediate states in which hydrated peptides span the bilayer.

Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA

Ion channels catalyze ionic permeation across membranes via water-filled pores. To understand how changes in intracellular magnesium concentration regulate the influx of Mg²⁺ into cells, we examine early events in the relaxation of Mg²⁺ channel CorA toward its open state using massively-repeated molecular dynamics simulations conducted either with or without regulatory ions. The pore of CorA contains a 2-nm-long hydrophobic bottleneck which remained dehydrated in most simulations. However, rapid hydration or “wetting” events concurrent with small-amplitude fluctuations in pore diameter occurred spontaneously and reversibly. In the absence of regulatory ions, wetting transitions are more likely and include a wet state that is significantly more stable and more hydrated. The free energy profile for Mg²⁺ permeation presents a barrier whose magnitude is anticorrelated to pore diameter and the extent of hydrophobic hydration. These findings support an allosteric mechanism whereby wetting of a hydrophobic gate couples changes in intracellular magnesium concentration to the onset of ionic conduction.

This study shows how rapid wetting/dewetting transitions in the pores of ion channels participate in the control of biological ion permeation. Ion channels catalyze ionic permeation across non-polar membranes via water-filled pores. However, non-polar stretches or hydrophobic bottlenecks are present in the pores of many ion channels. To clarify the relationship between channel regulation, pore hydration, and ion permeation, we examine how the slow relaxation of magnesium channel CorA from its closed state towards its open state modulates wetting of its hydrophobic bottleneck. Results provide a quantitative description of wetting and dewetting probabilities and kinetics and a quantitative relationship between the extent of pore hydration and the energetics of ion permeation, consistent with a mechanism of hydrophobic gating.

Anti-stress effects of lemon balm-containing foods

Lemon balm (Melissa officinalis) has been used historically and contemporarily as a modulator of mood and cognitive function, with anxiolytic effects following administration of capsules, coated tablets and topical application. Following a pilot study with lemon balm extract administered as a water based drink, which confirmed absorption of rosmarinic acid effects on mood and cognitive function, we conducted two similar double-blind, placebo-controlled, crossover studies. These evaluated the mood and cognitive effects of a standardised M. officinalis preparation administered in palatable forms in a beverage and in yoghurt. In each study a cohort of healthy young adults' self-rated aspects of mood were measured before and after a multi-tasking framework (MTF) administered one hour and three hours following one of four treatments. Both active lemon balm treatments were generally associated with improvements in mood and/or cognitive performance, though there were some behavioral "costs" at other doses and these effects depended to some degree on the delivery matrix.

Acute effects of different multivitamin mineral preparations with and without Guaraná on mood, cognitive performance and functional brain activation

Previous work has identified the positive effects of the acute administration of a multivitamin-guaraná preparation during an effortful executive/working memory task. Here, we aimed to differentiate the effects of multivitamins with and without guaraná and to examine the neural substrates of such effects using functional magnetic resonance imaging (fMRI). Following a double-blind, placebo-controlled, randomised, balanced crossover design, 20 participants (mean age 29 ± 5.54 years) consumed multivitamin preparations with or without guaraná (Berocca^® Performance and Boost, respectively) and a placebo. Thirty minutes post-treatment, they underwent neurocognitive assessment, consisting of a 10 min Cognitive Demand Battery, with mood ratings taken immediately before and after the battery. Five additional participants underwent post-treatment fMRI scanning during Rapid Visual Information Processing and Inspection Time activation tasks. The multivitamin with guaraná treatment was associated with significantly enhanced Serial Threes performance and self-rated contentment. fMRI revealed that both multivitamin treatments increased activation in areas associated with working memory and attentional processing, with the effect being greater in the multivitamin with guaraná condition. These data confirm the acute benefits of multivitamins with guaraná on mood and cognitive performance. Furthermore, they demonstrate for the first time increased brain activation from multivitamin preparations both with and without guaraná, as measured using fMRI.

Detergent-mediated protein aggregation

Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation.

Cognitive effects of two nutraceuticals Ginseng and Bacopa benchmarked against modafinil: a review and comparison of effect sizes

Over recent years there has been increasing research into both pharmaceutical and nutraceutical cognition enhancers. Here we aimed to calculate the effect sizes of positive cognitive effect of the pharmaceutical modafinil in order to benchmark the effect of two widely used nutraceuticals Ginseng and Bacopa (which have consistent acute and chronic cognitive effects, respectively). A search strategy was implemented to capture clinical studies into the neurocognitive effects of modafinil, Ginseng and Bacopa. Studies undertaken on healthy human subjects using a double-blind, placebo-controlled design were included. For each study where appropriate data were included, effect sizes (Cohen's d) were calculated for measures showing significant positive and negative effects of treatment over placebo. The highest effect sizes for cognitive outcomes were 0.77 for modafinil (visuospatial memory accuracy), 0.86 for Ginseng (simple reaction time) and 0.95 for Bacopa (delayed word recall). These data confirm that neurocognitive enhancement from well characterized nutraceuticals can produce cognition enhancing effects of similar magnitude to those from pharmaceutical interventions. Future research should compare these effects directly in clinical trials.

Characterization of disordered proteins with ENSEMBLE

ENSEMBLE is a computational approach for determining a set of conformations that represents the structural ensemble of a disordered protein based on input experimental data. The disordered protein can be an unfolded or intrinsically disordered state. Here, we introduce the latest version of the program, which has been enhanced to facilitate its general release and includes an intuitive user interface, as well as new approaches to treat data and analyse results.

AVAILABILITY AND IMPLEMENTATION

ENSEMBLE is a program implemented in C and embedded in a Perl wrapper. It is supported on main Linux distributions. Source codes and installation files, including a detailed example, can be freely downloaded at http://abragam.med.utoronto.ca/∼JFKlab.

Neurocognitive and mood effects of alcohol in a naturalistic setting

OBJECTIVE

The current pilot study aimed to assess the effects of drinking alcohol in a naturalistic setting on aspects of performance.

METHODS

Thirty individuals were approached and tested individually in a university campus bar. They provided details regarding alcoholic drinks consumption. Each was breathalysed before and after completion of a computerised test battery administered on a handheld device. The battery consisted of visual analogue mood scales, a series of alcohol-sensitive psychomotor and cognitive tests.

RESULTS

There were highly significant correlations between measured blood alcohol concentrations, estimated units of alcohol consumed and scores on a 'sober-drunk' VAS (p < 0.001 in all cases). For performance, there was a characteristic alcohol-associated shift in the speed/accuracy trade-off (SATO), which was reflected as significantly more errors with less effect on speed across several measures (including maze performance and Serial Sevens). Individuals who were more intoxicated were also significantly less alert.

CONCLUSIONS

The data suggest that controlled laboratory tests into the effects of alcohol intoxication may have ecological validity, with SATO shifts amongst the characteristic impairments seen in both controlled and naturalistic settings.

The cognitive-enhancing effects of Bacopa monnieri: a systematic review of randomized, controlled human clinical trials

OBJECTIVES

Traditional knowledge suggests that Bacopa monnieri enhances cognitive performance. Such traditional beliefs have now been scientifically tested through a handful of randomized, controlled human clinical trials. The current systematic review aimed to examine the scientific evidence as to whether Bacopa can enhance cognitive performance in humans.

DESIGN

A systematic review of randomized controlled trials is presented. Multiple databases were systematically searched by multiple authors. Relevant trials were objectively assessed for methodological quality.

SUBJECTS

The subjects studied were adult humans without dementia or significant cognitive impairment.

INTERVENTIONS

B. monnieri, including Bacopa extracts, were administered over long-term supplementation periods.

OUTCOME MEASURES

Any validated cognitive test, whether a primary or secondary outcome.

RESULTS

Six (6) studies met the final inclusion criteria and were included in review. Trials were all conducted over 12 weeks. Across trials, three different Bacopa extracts were used at dosages of 300-450 mg extract per day. All reviewed trials examined the effects of Bacopa on memory, while other cognitive domains were less well studied. There were no cognitive tests in the areas of auditory perceptual abilities or idea production and only a paucity of research in the domains of reasoning, number facility, and language behavior. Across studies, Bacopa improved performance on 9 of 17 tests in the domain of memory free recall. There was little evidence of enhancement in any other cognitive domains.

CONCLUSIONS

There is some evidence to suggest that Bacopa improves memory free recall with evidence for enhancement in other cognitive abilities currently lacking perhaps due to inconsistent measures employed by studies across these cognitive domains. Research into the nootropic effects of Bacopa is in its infancy, with research still yet to investigate the effects of Bacopa across all human cognitive abilities. Similarly, future research should examine the nootropic effects of Bacopa at varied dosages and across different extracts.