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This study examined the impact of narrative and emotion on processing of African American breast cancer survivor messages. We employed a two (narrative: present/absent) × three (emotional valence: pleasant/unpleasant/mixed) × four (message repetition) within-subjects experimental design. Findings indicated narrative messages with both pleasant and unpleasant emotional content (mixed) showed the greatest attention (heart rate deceleration) and negative emotional response (corrugator supercillii) while unpleasant narratives showed the least. Surprisingly, non-narrative messages showed the opposite pattern of results, where unpleasant messages showed the greatest attention and emotional response while non-narrative messages with mixed emotional content showed the least. These data initially point to the conclusion that attention for narrative material depends on the valence of emotion expressed in the message, which has both theoretical and practical implications.

The spread and uptake of new ideas (diffusion of innovations) is critical for organizations to adapt over time, but there is little evidence of how this happens within organizations and to their broader community. To address this, we analyzed how individuals accessed information about a recent science innovation at a large, international, biodiversity conservation non-profit-The Nature Conservancy-and then traced the flow of how this information was shared within the organization and externally, drawing on an exceptionally data-rich environment. We used surveys and tracking of individual internet activity to understand mechanisms for early-stage diffusion (knowledge seeking and sharing) following the integration of social science and evidence principles into the institutional planning framework: Conservation by Design (CbD 2.0). Communications sent to all employees effectively catalyzed 56.4% to exhibit knowledge seeking behavior, measured by individual downloads from and visits to a restricted-access site. Individuals who self-reported through a survey that they shared information about CbD 2.0 internally were more likely to have both received and sought out information about the framework. Such individuals tended to hold positions within a higher job grade, were more likely to train others on CbD as part of their job, and to enroll in other online professional development offerings. Communication strategies targeting external audiences did not appear to influence information seeking behavior. Staff who engaged in internal knowledge sharing and adopting "evidence" practices from CbD 2.0 were more likely to have shared the document externally. We found a negative correlation with external sharing behavior and in-person trainings. Our findings suggest repeated, direct email communications aimed at wide audiences can effectively promote diffusion of new ideas. We also found a wide range of employee characteristics and circumstances to be associated with knowledge diffusion behavior (at both an organizational and individual level).

Abstract Background Dietary fibers have been proposed to play a role in cardiovascular risk as well as body weight management. Flaxseeds are a good source of dietary fibers, and a large proportion of these are water-soluble viscous fibers. Method Here, we examine the effect of flaxseed dietary fibers in different food matrices on blood lipids and fecal excretion of fat and energy in a double-blind randomized crossover study with 17 subjects. Three different 7-d diets were tested: a low-fiber control diet (Control), a diet with flaxseed fiber drink (3/day) (Flax drink), and a diet with flaxseed fiber bread (3/day) (Flax bread). Total fat and energy excretion was measured in feces, blood samples were collected before and after each period, and appetite sensation registered 3 times daily before main meals. Results Compared to control, Flax drink lowered fasting total-cholesterol and LDL-cholesterol by 12 and 15%, respectively, (p < 0.01), whereas Flax bread only produced a reduction of 7 and 9%, respectively (p < 0.05). Fecal fat and energy excretion increased by 50 and 23% with Flax drink consumption compared to control (p < 0.05), but only fecal fat excretion was increased with Flax bread compared to control (p < 0.05). Conclusion Both Flax drink and Flax bread resulted in decreased plasma total and LDL-cholesterol and increased fat excretion, but the food matrix and/or processing may be of importance. Viscous flaxseed dietary fibers may be a useful tool for lowering blood cholesterol and potentially play a role in energy balance. Trial Registration ClinicalTrials.gov: NCT00953004

Abstract Background Sex hormones closely regulate development of the male genital organs during fetal life. The hypothesis that xenobiotics may disrupt endogenous hormonal signalling has received considerable scientific attention, but human evidence is scarce. Objectives We analyse occurrence of hypospadias and cryptorchidism according to maternal and paternal occupational exposure to possible endocrine disrupting chemicals. Methods We conducted a follow-up study of 45,341 male singleton deliveries in the Danish National Birth Cohort during 1997-2009. Information on work during pregnancy was obtained by telephone interviews around gestational week 16. Parents' job titles were classified according to DISCO-88. A job exposure matrix for endocrine disrupting chemicals (EDCs) was implemented to assess occupational exposures. The Medical Birth and National Hospital Register provided data on congenital anomalies diagnosed at birth or during follow-up, which ended in 2009. Crude and adjusted hazard ratios (HR) were obtained from Cox regression models. Results Among all pregnancies, 6.3% were classified as possibly or probably exposed to EDCs. The most prevalent occupations conferring possible exposure were cleaners, laboratory technicians, hairdressers and agricultural workers (58% of all potentially exposed). The final cumulative incidence of cryptorchidism in boys was 2.2% (1002 cases), and of hypospadias 0.6% (262 cases). The occurrence of hypospadias increased when mothers were probably [HRa = 1.8 (95% CI 1.0-2.6)] or possibly exposed to one or more EDCs [HRa = 2.6 (95% CI 1.8-3.4). Possible paternal exposure to heavy metals increased the risk of hypospadias [HRa 2.2 (95% CI: 1.0-3.4)] and cryptorchidism [HRa 1.9 (95% CI: 1.1-2.7)]. None of the exposure groups reached statistical significance. Conclusion The study provides some but limited evidence that occupational exposure to possible endocrine disrupting chemicals during pregnancy increases the risk of hypospadias.

Abstract Background Echocardiography is the method of choice when one wishes to examine myocardial function. Qualitative assessment of the 2D grey scale images obtained is subjective, and objective methods are required. Speckle Tracking Ultrasound is an emerging technology, offering an objective mean of quantifying left ventricular wall motion. However, before a new ultrasound technology can be adopted in the clinic, accuracy and reproducibility needs to be investigated. Aim It was hypothesized that the collection of ultrasound sample data from an in vitro model could be automated. The aim was to optimize an in vitro model to allow for efficient collection of sample data. Material & Methods A tissue-mimicking phantom was made from water, gelatin powder, psyllium fibers and a preservative. Sonomicrometry crystals were molded into the phantom. The solid phantom was mounted in a stable stand and cyclically compressed. Peak strain was then measured by Speckle Tracking Ultrasound and sonomicrometry. Results We succeeded in automating the acquisition and analysis of sample data. Sample data was collected at a rate of 200 measurement pairs in 30 minutes. We found good agreement between Speckle Tracking Ultrasound and sonomicrometry in the in vitro model. Best agreement was 0.83 ± 0.70%. Worst agreement was -1.13 ± 6.46%. Conclusions It has been shown possible to automate a model that can be used for evaluating the in vitro accuracy and precision of ultrasound modalities measuring deformation. Sonomicrometry and Speckle Tracking Ultrasound had acceptable agreement.

Abstract Background General practitioners (GPs) and patients find it difficult to talk about risk of future disease, especially when patients have asymptomatic conditions, and treatment options are unlikely to cause immediate perceptible improvements in well-being. Further studies in risk communication training are needed. Aim:1) to systematically develop, describe and evaluate a complex intervention comprising a training programme for GPs in risk communication and shared decision-making, 2) to evaluate the effect of the training programme on real-life consultations between GPs and patients with high cholesterol levels, and 3) to evaluate patients' reactions during and after the consultations. Methods/Design The effect of the complex intervention, based around a training programme, will be evaluated in a cluster-randomised controlled trial with an intervention group and an active control group with 40 GPs and 280 patients in each group. The GPs will receive a questionnaire at baseline and after 6 months about attitudes towards risk communication and cholesterol-reducing medication. After each consultation with a participating high cholesterol-patient, the GPs will complete a questionnaire about decision satisfaction (Provider Decision Process Assessment Instrument). The patients will receive a questionnaire at baseline and after 3 and 6 months. It includes questions about adherence to chosen treatment (Morisky Compliance Scale), self-rated health (SF-12), enablement (Patient Enablement Instrument), and risk communication and decision-making effectiveness (COMRADE Scale). Prescriptions, contacts to the health services, and cholesterol level will be drawn from the registers. In each group, 12 consultations will be observed and tape-recorded. The patients from these 24 consultations will be interviewed immediately after the consultation and re-interviewed after 6 months. Eight purposefully selected GPs from the intervention group will be interviewed in a focus group 6 months after participation in the training programme. The process and context of the RISAP-study will be investigated in detail using an action research approach, in order to analyse adaptation of the intervention model to the specific context. Discussion This study aims at providing GPs and patients with a firm basis for active deliberation about preventive treatment options, with a view to optimising adherence to chosen treatment. Trial registration ClinicalTrials.gov Protocol Registration System NCT01187056

Social anxiety disorder (SAD) is one of the most common anxiety disorders among adolescents. It is associated with extensive distress and negative long-term consequences. Generic cognitive behavioral therapy (CBT) is one of the preferred treatments for anxiety disorders, but it has shown poorer outcome for adolescents with SAD than for other anxiety disorders.

Abstract Background Androgens are crucial for normal testicular descent. Studies show that some pesticides have estrogenic or antiandrogenic effects, and that female workers exposed to pesticides have increased risk of having a boy with cryptorchidism. The main objective of the present study was to investigate whether pregnant women exposed to pesticides due to their work in horticulture experience excess risk of having sons with cryptorchidism. Methods We conducted a cohort study of pregnant women working in horticulture using four cohorts including one cohort established with data from the departments of occupational medicine in Jutland and Funen and three existing mother-child cohorts (n = 1,468). A reference group was established from the entire Danish population of boys born in the period of 1986-2007 (n = 783,817). Nationwide Danish health registers provided information on birth outcome, cryptorchidism diagnosis and orchiopexy. The level of occupational exposure to pesticides was assessed by expert judgment blinded towards outcome status. Risk of cryptorchidism among exposed horticulture workers compared to the background population and to unexposed horticulture workers was assessed by Cox regression models. Results Pesticide exposed women employed in horticulture had a hazard ratio (HR) of having cryptorchid sons of 1.39 (95% CI 0.84; 2.31) and a HR of orchiopexy of 1.34 (0.72; 2.49) compared to the background population. Analysis divided into separate cohorts revealed a significantly increased risk of cryptorchidism in cohort 2: HR 2.58 (1.07;6.20) and increased risk of orchiopexy in cohort 4: HR 2.76 (1.03;7.35), but no significant associations in the other cohorts. Compared to unexposed women working in horticulture, pesticide exposed women had a risk of having sons with cryptorchidism of 1.34 (0.30; 5.96) and of orchiopexy of 1.93 (0.24;15.4). Conclusions The data are compatible with a slightly increased risk of cryptorchidism in sons of women exposed to pesticides by working in horticulture.

The cation channel TRPA1 is a potentially important drug target, and characterization of TRPA1 functional dynamics might help guide structure-based drug design. Here, we present results from long-timescale molecular dynamics simulations of TRPA1 with an allosteric activator, allyl isothiocyanate (AITC), in which we observed spontaneous transitions from a closed, non-conducting channel conformation into an open, conducting conformation. Based on these transitions, we propose a gating mechanism in which movement of a regulatory TRP-like domain allosterically translates into pore opening in a manner reminiscent of pore opening in voltage-gated ion channels. In subsequent experiments, we found that mutations that disrupt packing of the S4-S5 linker-TRP-like domain and the S5 and S6 helices also affected channel activity. In simulations, we also observed A-967079, a known allosteric inhibitor, binding between helices S5 and S6, suggesting that A-967079 may suppress activity by stabilizing a non-conducting pore conformation-a finding consistent with our proposed gating mechanism., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

To perform their physiological functions, amino methyl propionic acid receptors (AMPARs) cycle through active, resting, and desensitized states, and dysfunction in AMPAR activity is associated with various neurological disorders. Transitions among AMPAR functional states, however, are largely uncharacterized at atomic resolution and are difficult to examine experimentally. Here, we report long-timescale molecular dynamics simulations of dimerized AMPAR ligand-binding domains (LBDs), whose conformational changes are tightly coupled to changes in AMPAR functional states, in which we observed LBD dimer activation and deactivation upon ligand binding and unbinding at atomic resolution. Importantly, we observed the ligand-bound LBD dimer transition from the active conformation to several other conformations, which may correspond with distinct desensitized conformations. We also identified a linker region whose structural rearrangements heavily affected the transitions to and among these putative desensitized conformations, and confirmed, using electrophysiology experiments, the importance of the linker region in these functional transitions., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Inward-rectifier potassium channels (Kirs) are lipid-gated ion channels that differ from other K+ channels in that they allow K+ ions to flow more easily into, rather than out of, the cell. Inward rectification is known to result from endogenous magnesium ions or polyamines (e.g., spermine) binding to Kirs, resulting in a block of outward potassium currents, but questions remain regarding the structural and dynamic basis of the rectification process and lipid-dependent channel activation. Here, we present the results of long-timescale molecular dynamics simulations starting from a crystal structure of phosphatidylinositol 4,5-bisphosphate (PIP2)-bound chicken Kir2.2 with a non-conducting pore. After introducing a mutation (G178R) that is known to increase the open probability of a homologous channel, we were able to observe transitions to a stably open, ion-conducting pore, during which key conformational changes occurred in the main activation gate and the cytoplasmic domain. PIP2 binding appeared to increase stability of the pore in its open and conducting state, as PIP2 removal resulted in pore closure, with a median closure time about half of that with PIP2 present. To investigate structural details of inward rectification, we simulated spermine binding to and unbinding from the open pore conformation at positive and negative voltages, respectively, and identified a spermine-binding site located near a previously hypothesized site between the pore cavity and the selectivity filter. We also studied the effects of long-range electrostatics on conduction and spermine binding by mutating charged residues in the cytoplasmic domain and found that a finely tuned charge density, arising from basic and acidic residues within the cytoplasmic domain, modulated conduction and rectification., (© 2022 Jogini et al.)

Background and Aims: The potassium channel Kv1.3 is a potentially attractive therapeutic target in T cell-mediated inflammatory diseases, as the activity of antigen-activated T cells is selectively impeded by Kv1.3 inhibition. In this study, we examined Kv1.3 as a potential therapeutic intervention point for ulcerative colitis [UC], and studied the efficacy of DES1, a small-molecule inhibitor of Kv1.3, in vitro and in vivo., Methods: Kv1.3 expression on T cells in peripheral blood mononuclear cells [PBMCs] isolated from donors with and without UC was examined by flow cytometry. In biopsies from UC patients, Kv1.3-expressing CD4+ T cells were detected by flow cytometry and immunohistochemistry. In vitro, we determined the ability of DES1 to inhibit anti-CD3-driven activation of T cells. In vivo, the efficacy of DES1 was determined in a humanised mouse model of UC and compared with infliximab and tofacitinib in head-to-head studies., Results: Kv1.3 expression was elevated in PBMCs from UC patients and correlated with the prevalence of TH1 and TH2 T cells. Kv1.3 expression was also detected on T cells from biopsies of UC patients. In vitro, DES1 suppressed anti-CD3-driven activation of T cells in a concentration-dependent manner. In vivo, DES1 significantly ameliorated inflammation in the UC model and most effectively so when PBMCs from donors with higher levels of activated T cells were selected for reconstitution. The efficacy of DES1 was comparable to that of either infliximab or tofacitinib., Conclusion: Inhibition of Kv1.3 [by DES1, for instance] appears to be a potential therapeutic intervention strategy for UC patients., (© The Author(s) 2021. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.)

The NMDA (N-methyl-D-aspartate) receptor transduces the binding of glutamate and glycine, coupling it to the opening of a calcium-permeable ion channel 1 . Owing to the lack of high-resolution structural studies of the NMDA receptor, the mechanism by which ion-channel blockers occlude ion permeation is not well understood. Here we show that removal of the amino-terminal domains from the GluN1-GluN2B NMDA receptor yields a functional receptor and crystals with good diffraction properties, allowing us to map the binding site of the NMDA receptor blocker, MK-801. This crystal structure, together with long-timescale molecular dynamics simulations, shows how MK-801 and memantine (a drug approved for the treatment of Alzheimer's disease) bind within the vestibule of the ion channel, promote closure of the ion channel gate and lodge between the M3-helix-bundle crossing and the M2-pore loops, physically blocking ion permeation.

Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with [Formula: see text]CT. Experimental data from the in vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed leaflet dynamics, and force vectors from the in vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements enable validating and adjusting material parameters to improve the accuracy of computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

Purpose: To demonstrate the first use of a novel technology for quantifying suture forces on annuloplasty rings to better understand the mechanisms of ring dehiscence., Description: Force transducers were developed, attached to a size 24 Physio ring, and implanted in the mitral annulus of an ovine animal. Ring suture forces were measured after implantation and for cardiac cycles reaching peak left ventricular pressures (LVP) of 100, 125, and 150 mm Hg., Evaluation: After implantation of the undersized ring to the flaccid annulus, the mean suture force was 2.0±0.6 N. During cyclic contraction, the anterior ring suture forces were greater than the posterior ring suture forces at peak LVPs of 100 mm Hg (4.9±2.0 N vs 2.1±1.1 N), 125 mm Hg (5.4±2.3 N vs 2.3±1.2 N), and 150 mm Hg (5.7±2.4 N vs 2.4±1.1 N). The largest force was 7.4 N at 150 mm Hg., Conclusions: The preliminary results demonstrate trends in annuloplasty suture forces and their variation with location and LVP. Future studies will significantly contribute to clinical knowledge by elucidating the mechanisms of ring dehiscence while improving annuloplasty ring design and surgical repair techniques., (Copyright © 2014 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

The difficulty in characterizing ion conduction through membrane channels at the level of individual permeation events has made it challenging to elucidate the mechanistic principles underpinning this fundamental physiological process. Using long, all-atom simulations enabled by special-purpose hardware, we studied K(+) permeation across the KV1.2/2.1 voltage-gated potassium channel. At experimentally accessible voltages, which include the physiological range, the simulated permeation rate was substantially lower than the experimentally observed rate. The current-voltage relationship was also nonlinear but became linear at much higher voltages. We observed permeation consistent with a "knock-on" mechanism at all voltages. At high voltages, the permeation rate was in accordance with our previously reported KV1.2 pore-only simulations, after the simulated voltages from the previous study were recalculated using the correct method, new insight into which is provided here. Including the voltage-sensing domains in the simulated channel brought the linear current-voltage regime closer to the experimentally accessible voltages. The simulated permeation rate, however, still underestimated the experimental rate, because formation of the knock-on intermediate occurred too infrequently. Reducing the interaction strength between the ion and the selectivity filter did not increase conductance. In complementary simulations of gramicidin A, similar changes in interaction strength did increase the observed permeation rate. Permeation nevertheless remained substantially below the experimental value, largely because of infrequent ion recruitment into the pore lumen. Despite the need to apply large voltages to simulate the permeation process, the apparent voltage insensitivity of the permeation mechanism suggests that the direct simulation of permeation at the single-ion level can provide fundamental physiological insight into ion channel function. Notably, our simulations suggest that the knock-on permeation mechanisms in KV1.2 and KcsA may be different.

The mechanism of ion channel voltage gating-how channels open and close in response to voltage changes-has been debated since Hodgkin and Huxley's seminal discovery that the crux of nerve conduction is ion flow across cellular membranes. Using all-atom molecular dynamics simulations, we show how a voltage-gated potassium channel (KV) switches between activated and deactivated states. On deactivation, pore hydrophobic collapse rapidly halts ion flow. Subsequent voltage-sensing domain (VSD) relaxation, including inward, 15-angstrom S4-helix motion, completes the transition. On activation, outward S4 motion tightens the VSD-pore linker, perturbing linker-S6-helix packing. Fluctuations allow water, then potassium ions, to reenter the pore; linker-S6 repacking stabilizes the open pore. We propose a mechanistic model for the sodium/potassium/calcium voltage-gated ion channel superfamily that reconciles apparently conflicting experimental data.

Although the Escherichia coli ammonia transporter B (AmtB) protein has been the focus of several recent studies, there are still many questions and controversies regarding substrate binding and recognition. Specifically, how and where AmtB differentiates between substrates is not yet fully understood. The present computational study addresses the importance of intermolecular interactions with respect to substrate recruitment and recognition by means of ab initio QM/MM simulations. On the basis of calculations with substrates NH(3), NH(4)(+), Na(+), and K(+) positioned at the periplasmic binding site (Am1) and NH(3) and NH(4)(+) at intraluminal binding sites (Am1a/b), we conclude that D160 is the single most important residue for substrate recruitment, whereas cation-π interactions to W148 and F107 are found to be less important. Regarding substrate recruitment and recognition, we find that only NH(4)(+) and K(+) reach the Am1 site. However, NH(4)(+) has the largest affinity for this site due to its better dehydration compensation, while charge stabilization effects favor the binding of NH(4)(+) over NH(3) (i.e., if NH(3) would enter the Am1 site, it is likely to be protonated). Therefore, we conclude that the Am1 site selects NH(4)(+) over Na(+), K(+) and NH(3). Our calculations also suggest that translocation of NH(4)(+) from Am1 into the channel lumen is driven by rotation of the A162-G163 peptide bond, which coordinates NH(4)(+) but not NH(3) at both Am1 and Am1a/b sites.

Since the behavior of biomolecules can be sensitive to temperature, the ability to accurately calculate and control the temperature in molecular dynamics (MD) simulations is important. Standard analysis of equilibrium MD simulations-even constant-energy simulations with negligible long-term energy drift-often yields different calculated temperatures for different motions, however, in apparent violation of the statistical mechanical principle of equipartition of energy. Although such analysis provides a valuable warning that other simulation artifacts may exist, it leaves the actual value of the temperature uncertain. We observe that Tolman's generalized equipartition theorem should hold for long stable simulations performed using velocity-Verlet or other symplectic integrators, because the simulated trajectory is thought to sample almost exactly from a continuous trajectory generated by a shadow Hamiltonian. From this we conclude that all motions should share a single simulation temperature, and we provide a new temperature estimator that we test numerically in simulations of a diatomic fluid and of a solvated protein. Apparent temperature variations between different motions observed using standard estimators do indeed disappear when using the new estimator. We use our estimator to better understand how thermostats and barostats can exacerbate integration errors. In particular, we find that with large (albeit widely used) time steps, the common practice of using two thermostats to remedy so-called hot solvent-cold solute problems can have the counterintuitive effect of causing temperature imbalances. Our results, moreover, highlight the utility of multiple-time step integrators for accurate and efficient simulation.

We present the first atomic-resolution observations of permeation and gating in a K(+) channel, based on molecular dynamics simulations of the Kv1.2 pore domain. Analysis of hundreds of simulated permeation events revealed a detailed conduction mechanism, resembling the Hodgkin-Keynes "knock-on" model, in which translocation of two selectivity filter-bound ions is driven by a third ion; formation of this knock-on intermediate is rate determining. In addition, at reverse or zero voltages, we observed pore closure by a novel "hydrophobic gating" mechanism: A dewetting transition of the hydrophobic pore cavity-fastest when K(+) was not bound in selectivity filter sites nearest the cavity-caused the open, conducting pore to collapse into a closed, nonconducting conformation. Such pore closure corroborates the idea that voltage sensors can act to prevent pore collapse into the intrinsically more stable, closed conformation, and it further suggests that molecular-scale dewetting facilitates a specific biological function: K(+) channel gating. Existing experimental data support our hypothesis that hydrophobic gating may be a fundamental principle underlying the gating of voltage-sensitive K(+) channels. We suggest that hydrophobic gating explains, in part, why diverse ion channels conserve hydrophobic pore cavities, and we speculate that modulation of cavity hydration could enable structural determination of both open and closed channels.

The spinach plant aquaporin SoPIP2;1 is a gated water channel, which switches between open and closed states depending on the conformation of a 20-residue cytoplasmic loop, the D-loop. Using fully atomistic molecular dynamics simulations, we have investigated the possibility of driving the conformational equilibrium of the protein toward a constitutively open state. We introduce two separate mutations in the D-loop, while being in the closed conformation. We show that the single channel permeability of both mutants is comparable to that of the open conformation. This Article provides new molecular insight into the gating mechanism of SoPIP2;1. It is proposed that residues Arg190, Asp191, and Ser36 might play important roles in the gating of the protein.

Fully understanding the mechanisms of signaling proteins such as G protein-coupled receptors (GPCRs) will require the characterization of their conformational states and the pathways connecting those states. The recent crystal structures of the beta(2)- and beta(1)-adrenergic receptors in a nominally inactive state constituted a major advance toward this goal, but also raised new questions. Although earlier biochemical observations had suggested that these receptors possessed a set of contacts between helices 3 and 6, known as the ionic lock, which was believed to form a molecular switch for receptor activation, the crystal structures lacked these contacts. The unexpectedly broken ionic lock has raised questions about the true conformation(s) of the inactive state and the role of the ionic lock in receptor activation and signaling. To address these questions, we performed microsecond-timescale molecular dynamics simulations of the beta(2)-adrenergic receptor (beta(2)AR) in multiple wild-type and mutant forms. In wild-type simulations, the ionic lock formed reproducibly, bringing the intracellular ends of helices 3 and 6 together to adopt a conformation similar to that found in inactive rhodopsin. Our results suggest that inactive beta(2)AR exists in equilibrium between conformations with the lock formed and the lock broken, whether or not the cocrystallized ligand is present. These findings, along with the formation of several secondary structural elements in the beta(2)AR loops during our simulations, may provide a more comprehensive picture of the inactive state of the beta-adrenergic receptors, reconciling the crystal structures with biochemical studies.

In many protein kinases, a characteristic conformational change (the "DFG flip") connects catalytically active and inactive conformations. Many kinase inhibitors--including the cancer drug imatinib--selectively target a specific DFG conformation, but the function and mechanism of the flip remain unclear. Using long molecular dynamics simulations of the Abl kinase, we visualized the DFG flip in atomic-level detail and formulated an energetic model predicting that protonation of the DFG aspartate controls the flip. Consistent with our model's predictions, we demonstrated experimentally that the kinetics of imatinib binding to Abl kinase have a pH dependence that disappears when the DFG aspartate is mutated. Our model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.

Recent advances in algorithms, software, and hardware for molecular dynamics (MD) simulations have brought previously inaccessible simulation timescales within reach, allowing the use of MD simulation to address a substantially broader set of questions regarding protein function. MD has proved particularly useful in elucidating the functional mechanisms of membrane proteins, whose dynamics are especially difficult to characterize experimentally. Here, we illustrate the utility of state-of-the-art high-performance MD simulations in the study of membrane proteins, using as examples a G-protein-coupled receptor, an aquaporin, and an antiporter. In each case, we used MD either to deduce an atomic-level mechanism for protein function or to reconcile apparent discrepancies among recent experimental observations.

Aquaporin 0 (AQP0), the most abundant membrane protein in mammalian lens fiber cells, not only serves as the primary water channel in this tissue but also appears to mediate the formation of thin junctions between fiber cells. AQP0 is remarkably less water permeable than other aquaporins, but the structural basis and biological significance of this low permeability remain uncertain, as does the permeability of the protein in a reported junctional form. To address these issues, we performed molecular dynamics (MD) simulations of water transport through membrane-embedded AQP0 in both its (octameric) junctional and (tetrameric) nonjunctional forms. From our simulations, we measured an osmotic permeability for the nonjunctional form that agrees with experiment and found that the distinct dynamics of the conserved, lumen-protruding side chains of Tyr-23 and Tyr-149 modulate water passage, accounting for the slow permeation. The junctional and nonjunctional forms conducted water equivalently, in contrast to a previous suggestion based on static crystal structures that water conduction is lost on junction formation. Our analysis suggests that the low water permeability of AQP0 may help maintain the mechanical stability of the junction. We hypothesize that the structural features leading to low permeability may have evolved in part to allow AQP0 to form junctions that both conduct water and contribute to the organizational structure of the fiber cell tissue and microcirculation within it, as required to maintain transparency of the lens.

A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than that of the overall rotational diffusion of ubiquitin and whose effects would not be apparent in experimentally derived order parameters. A coupled analysis of internal and overall motion yields simulated order parameters substantially closer to the experimentally determined values than is the case for a conventional analysis of internal motion alone. Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations.

Background and Aim of the Study: Increasing mitral valve repair durability requires successful restoration and support with annuloplasty rings. The stress distribution in these devices indirectly determines the success of the repair. It is hypothesized that changes in annular geometry throughout the cardiac cycle result in adverse strain distribution in stiff, flat annuloplasty rings, and hence non-physiological loading of the myocardium. The study aim was to identify the three-dimensional (3-D) force distribution in mitral annuloplasty rings., Methods: Eight animals were included in an acute porcine study. The mitral annulus 3-D dynamic geometry was assessed with sonomicrometry prior to ring insertion. Strain gauges mounted on dedicated D-shaped rigid flat annuloplasty rings enabled dynamic force measurements to be made perpendicular to the annulus plane., Results: The average systolic annular height to commissural width ratio before ring implantation was 13.7 +/- 1.4%. Following ring implantation, the annulus was fixed in the diastolic flat configuration (p <0.01). Force accumulation was seen from the anterior (0.7 +/- 0.4 N) and commissural (1.4 +/- 1.0 N) annular segments; both forces were acting in opposite directions and were statistically significantly larger than zero (p <0.01; n = 8)., Conclusion: These data demonstrate highest strains at the anterior and commissural areas of flat mitral annuloplasty rings, and support the hypothesis that the mitral valve annulus and its attached valvular and subvalvular structures apply systolic torque onto the flat annuloplasty ring in an attempt to conform it into the saddle-shaped configuration.

Background and Aim of the Study: The assessment of three-dimensional (3-D) mitral valve geometry in patients with chronic functional ischemic mitral valve regurgitation (FIMR) has been hampered by a lack of adequate imaging techniques. The study aim was to use a clinically applicable cardiac magnetic resonance imaging (MRI) technique to assess the 3-D mitral annular, leaflet and papillary muscle geometry in pigs with chronic FIMR., Methods: Ten pigs with moderate chronic FIMR induced by catheter-based coiling of the circumflex artery, were examined using cardiac MRI. The reconstruction of 3-D data from two-dimensional cardiac MRI scans allowed the mitral annulus and leaflet geometries to be assessed. Using 3-D morphology scans, the spatial position of the posterior papillary muscle (PPM) relative to the anterior papillary muscle (APM), mitral annulus and anterior (A-trig) and posterior (P-trig) trigones was assessed. Using dedicated software for image analysis, data were transferred to a Cartesian coordinate system (x,y,z) for geometric analysis. Ten healthy pigs served as controls., Results: Compared to controls, at end-systole in the chronic FIMR group the PPM was significantly displaced (p <0.05) from the APM (38 +/- 2 versus 23 +/- 1 mm), A-trig (48 +/- 2 versus 36 +/- 1 mm) and P-trig (41 +/-1 versus 33 +/- 1 mm). There was no significant apical PPM displacement (20 +/- 2 versus 20 +/- 1 mm). The annular area (1,240 +/- 90 versus 850 +/- 90 mm2), septolateral distance (36 +/- 2 versus 26 +/- 1 mm), commissure-to-commissure distance (38 +/- 2 versus 33 +/- 1 mm), mean tenting height (8 +/- 1 versus 5 +/- 0 mm), maximum tenting height (10 +/- 1 versus 7 +/- 0 mm), tenting volume (2,600 +/- 400 versus 1,500 +/- 200 mm3), and occlusional leaflet area (1,820 +/- 110 versus 1,120 +/- 70 mm2) were each significantly increased., Conclusion: This clinically applicable cardiac MRI modality permitted a detailed geometric insight to be made into the mitral annular, leaflet and PPM geometries that cause FIMR. Such a reliable tool for geometric mitral valve analysis has previously been demonstrated only by using invasive techniques. Hence, this approach holds promise for further clarifying the pathogenesis of chronic FIMR and improving preoperative surgical planning.

Na+/H+ antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia coli NhaA was recently determined, but its mechanisms of transport and pH regulation remain elusive. We performed molecular dynamics simulations of NhaA that, with existing experimental data, enabled us to propose an atomically detailed model of antiporter function. Three conserved aspartates are key to our proposed mechanism: Asp164 (D164) is the Na+-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+. Additional mutagenesis experiments further validated the model.

Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of the narrowest parts of the channel during permeation, the widening being largest within the periplasmic half-channel. During permeation, the water-filled lumen of LacY only partially hydrates lactose, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly interacts with hydrophobic channel lining residues, whereas in the cytoplasmic half-channel key protein-substrate interactions are mediated by ionic residues. A major energy barrier against transport is found within a tight segment of the periplasmic half-channel where sugar hydration is minimal and protein-sugar interaction maximal. Upon unbinding from the binding pocket, lactose undergoes a rotation to permeate either half-channel with its long axis aligned parallel to the channel axis. The results hint at the possibility of a transport mechanism, in which lactose permeates LacY through a narrow periplasmic half-channel and a wide cytoplasmic half-channel, the opening of which is controlled by changes in protonation states of key protein side groups.

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

The nucleotide-induced structural rearrangements in ATP binding cassette (ABC) transporters, leading to substrate translocation, are largely unknown. We have modeled nucleotide binding and release in the vitamin B(12) importer BtuCD using perturbed elastic network calculations and biased molecular dynamics simulations. Both models predict that nucleotide release decreases the tilt between the two transmembrane domains and opens the cytoplasmic gate. Nucleotide binding has the opposite effect. The observed coupling may be relevant for all ABC transporters because of the conservation of nucleotide binding domains and the shared role of ATP in ABC transporters. The rearrangements in the cytoplasmic gate region do not provide enough space for B(12) to diffuse from the transporter pore into the cytoplasm, which could suggest that peristaltic forces are needed to exclude B(12) from the transporter pore.

To investigate substrate recruitment and transport across the Escherichia coli Ammonia transporter B (AmtB) protein, we performed molecular dynamics simulations of the AmtB trimer. We have identified residues important in recruitment of ammonium and intraluminal binding sites selective of ammonium, which provide a means of cation selectivity. Our results indicate that A162 guides translocation of an extraluminal ammonium into the pore lumen. We propose a mechanism for transporting the intraluminally recruited proton back to periplasm. Our mechanism conforms to net transport of ammonia and can explain why ammonia conduction is lost upon mutation of the conserved residue D160. We unify previous suggestions of D160 having either a structural or an ammonium binding function. Finally, our simulations show that the channel lumen is hydrated from the cytoplasmic side via the formation of single file water, while the F107/F215 stack at the inner-most part of the periplasmic vestibule constitutes a hydrophobic filter preventing AmtB from conducting water.

Lactose permease is an integral membrane protein that uses the cell membrane's proton gradient for import of lactose. Based on extensive biochemical data and a substrate-bound crystal structure, intermediates involved in lactose/H(+) co-transport have been suggested. Yet, the transport mechanism, especially the coupling of protonation states of essential residues and protein conformational changes involved in the transport, is not understood. Here we report molecular-dynamics simulations of membrane-embedded lactose permease in different protonation states, both in the presence and in the absence of lactose. The results analyzed in terms of pore diameter, salt-bridge formation, and substrate motion, strongly implicate Glu(269) as one of the main proton translocation sites, whose protonation state controls several key steps of the transport process. A critical ion pair (Glu(269) and Arg(144)) was found to keep the cytoplasmic entrance open, but via a different mechanism than the currently accepted model. After protonation of Glu(269), the salt bridge between Glu(269) and Arg(144) was found to break, and Arg(144) to move away from Glu(269), establishing a new salt bridge with Glu(126); furthermore, neutralization of Glu(269) and the displacement of Arg(144) and consequently of water molecules from the interdomain region was seen to initiate the closing of the cytoplasmic half channel (2.6-4.0 A reduction in diameter in the cytoplasmic constriction region in 10 ns) by allowing hydrophobic surfaces of the N- and C-domains to fuse. Charged Glu(269) was found to strongly bind the lactose permeant, indicating that proton transfer from water or another residue to Glu(269) is a prerequisite for unbinding of lactose from the binding pocket.

From equilibrium molecular dynamics simulations we have determined single-channel water permeabilities for Escherichia coli aquaporin Z (AqpZ) and aquaglyceroporin GlpF with the channels embedded in lipid bilayers. GlpF's osmotic water permeability constant pf exceeds by 2-3 times that of AqpZ and the diffusive permeability constant (pd) of GlpF is found to exceed that of AqpZ 2-9-fold. Achieving complete water selectivity in AqpZ consequently implies lower transport rates overall relative to the less selective, wider channel of GlpF. For AqpZ, the ratio pf/pd congruent with 12 is close to the average number of water molecules in the channel lumen, whereas for GlpF, pf/pd congruent with 4. This implies that single-file structure of the luminal water is more pronounced for AqpZ, the narrower channel of the two. Electrostatics profiles across the pore lumens reveal that AqpZ significantly reinforces water-channel interactions, and weaker water-water interactions in turn suppress water-water correlations relative to GlpF. Consequently, suppressed water-water correlations across the narrow selectivity filter become a key structural determinant for water permeation causing luminal water to permeate slower across AqpZ.

Integral membrane proteins are characterized by having a preference for aromatic residues, e.g., tryptophan (W), at the interface between the lipid bilayer core and the aqueous phase. The reason for this is not clear, but it seems that the preference is related to a complex interplay between steric and electrostatic forces. The flat rigid paddle-like structure of tryptophan, associated with a quadrupolar moment (aromaticity) arising from the pi-electron cloud of the indole, interacts primarily with moieties in the lipid headgroup region hardly penetrating into the bilayer core. We have studied the interaction between the nitrogen moiety of lipid molecule headgroups and the pi-electron distribution of gramicidin (gA) tryptophan residues (W9, W11, W13, and W15) using molecular dynamics (MD) simulations of gA embedded in two hydrated lipid bilayers composed of 1-palmitoyl-2-oleoylphosphatidylethanolamine (POPE) and 1-palmitoyl-2-oleoylphosphatidyl-choline (POPC), respectively. We use a force field model for tryptophan in which polarizability is only implicit, but we believe that classical molecular dynamics force fields are sufficient to capture the most prominent features of the cation-pi interaction. Our criteria for cation-pi interactions are based on distance and angular requirements, and the results from our model suggest that cation-pi interactions are relevant for W(PE)1), W(PE)13, W(PE)15, and, to some extent, W(PC)11 and W(PC)13. In our model, W9 does not seem to engage in cation-pi interactions with lipids, neither in POPE nor POPC. The criteria for the cation-pi effect are satisfied more often in POPE than in POPC, whereas the H-bonding ability between the indole donor and the carbonyl acceptor is similar in POPE and POPC. This suggests an increased affinity for lipids with ethanolamine headgroups to transmembrane proteins enriched in interfacial tryptophans.

The thermotropic phase behavior and lateral structure of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers containing an acylated peptide has been characterized by differential scanning calorimetry (DSC) on vesicles and atomic force microscopy (AFM) on mica-supported bilayers. The acylated peptide, which is a synthetic decapeptide N-terminally linked to a C14 acyl chain (C14-peptide), is incorporated into DPPC bilayers in amounts ranging from 0-20 mol %. The calorimetric scans of the two-component system demonstrate a distinct influence of the C14-peptide on the lipid bilayer thermodynamics. This is manifested as a concentration-dependent downshift of both the main phase transition and the pretransition. In addition, the main phase transition peak is significantly broadened, indicating phase coexistence. In the AFM imaging scans we found that the C14-peptide, when added to supported gel phase DPPC bilayers, inserts preferentially into preexisting defect regions and has a noticeable influence on the organization of the surrounding lipids. The presence of the C14-peptide gives rise to a laterally heterogeneous bilayer structure with coexisting lipid domains characterized by a 10 A height difference. The AFM images also show that the appearance of the ripple phase of the DPPC lipid bilayers is unaffected by the C14-peptide. The experimental results are supported by molecular dynamics simulations, which show that the C14-peptide has a disordering effect on the lipid acyl chains and causes a lateral expansion of the lipid bilayer. These effects are most pronounced for gel-like bilayer structures and support the observed downshift in the phase-transition temperature. Moreover, the molecular dynamics data indicate a tendency of a tryptophan residue in the peptide sequence to position itself in the bilayer headgroup region.

Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contiguous set of water-water hydrogen bonds in which polarization of the water molecules vary with position along the channel axis. Deprotonation of the water chain promotes the reorientation of water molecules while the hydroxide ion rapidly migrates by sequentially accepting protons from the neighboring water molecules. The hydroxide ion is not attracted by a conserved, channel-lining arginine residue, but is immobilized at two centrally located, conserved Asparagine-Proline-Alanine motifs where fourfold coordination stabilizes the ion. Hydroxide transition from the channel vestibules into the channel lumen is strongly influenced by electrostatic coupling to two conserved oppositely aligned macrodipoles. This suggests that the macrodipole's negative poles play a role in preventing hydroxide ions from entering into the channel's inner vestibules. Water protonation within the lumen facilitates water reorientation and subsequent proton expelling occurs. In the periplasmic half-channel, expelling occurs via the Grotthuss mechanism. Protonation within the cytoplasmic half-channel implies wire-breakage at the Asn-Pro-Ala motifs. The proton is here diffusively rejected as (H(5)O(2))(+).

A topical review of the current state of lipid-protein interactions is given with focus on the physical interactions between lipids and integral proteins in lipid-bilayer membranes. The concepts of hydrophobic matching and curvature stress are revisited in light of recent data obtained from experimental and theoretical studies which demonstrate that not only do integral proteins perturb the lipids, but the physical state of the lipids does also actively influence protein function. The case of the trans-membrane water-channel protein aquaporin GlpF from E. coli imbedded in lipid-bilayer membranes is discussed in some detail. Numerical data obtained from Molecular Dynamics simulations show on the one side that the lipid bilayer adapts to the channel by a hydrophobic matching condition which reflects the propensity of the lipid molecules for forming curved structures. On the other side, it is demonstrated that the transport function of the channel is modulated by the matching condition and/or the curvature stress in a lipid-specific manner.

A three-dimensional structure of a model decapeptide is obtained by performing molecular dynamics simulations of the peptide in explicit water. Interactions between an N-myristoylated form of the folded peptide anchored to dipalmitoylphosphatidylcholine fluid phase lipid membranes are studied at different applied surface tensions by molecular dynamics simulations. The lipid membrane environment influences the conformational space explored by the peptide. The overall secondary structure of the anchored peptide is found to deviate at times from its structure in aqueous solution through reversible conformational transitions. The peptide is, despite the anchor, highly mobile at the membrane surface with the peptide motion along the bilayer normal being integrated into the collective modes of the membrane. Peptide anchoring moderately alters the lateral compressibility of the bilayer by changing the equilibrium area of the membrane. Although membrane anchoring moderately affects the elastic properties of the bilayer, the model peptide studied here exhibits conformational flexibility and our results therefore suggest that peptide acylation is a feasible way to reinforce peptide-membrane interactions whereby, e.g., the lifetime of receptor-ligand interactions can be prolonged.

Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C(36)H(74) or n-alcohol C(35)H(71)OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together with a partial drying of the surfaces are more indicative of the hydrophobic effect than structural ordering, which we suggest to be independent of surface topology., ((c) 2004 American Institute of Physics.)

Water permeation and electrostatic interactions between water and channel are investigated in the Escherichia coli glycerol uptake facilitator GlpF, a member of the aquaporin water channel family, by molecular dynamics simulations. A tetrameric model of the channel embedded in a 16:0/18:1c9-palmitoyloleylphosphatidylethanolamine membrane was used for the simulations. During the simulations, water molecules pass through the channel in single file. The movement of the single file water molecules through the channel is concerted, and we show that it can be described by a continuous-time random-walk model. The integrity of the single file remains intact during the permeation, indicating that a disrupted water chain is unlikely to be the mechanism of proton exclusion in aquaporins. Specific hydrogen bonds between permeating water and protein at the channel center (at two conserved Asp-Pro-Ala "NPA" motifs), together with the protein electrostatic fields enforce a bipolar water configuration inside the channel with dipole inversion at the NPA motifs. At the NPA motifs water-protein electrostatic interactions facilitate this inversion. Furthermore, water-water electrostatic interactions are in all regions inside the channel stronger than water-protein interactions, except near a conserved, positively charged Arg residue. We find that variations of the protein electrostatic field through the channel, owing to preserved structural features, completely explain the bipolar orientation of water. This orientation persists despite water translocation in single file and blocks proton transport. Furthermore, we find that for permeation of a cation, ion-protein electrostatic interactions are more unfavorable at the conserved NPA motifs than at the conserved Arg, suggesting that the major barrier against proton transport in aquaporins is faced at the NPA motifs.

The structure of enkephalin, a small neuropeptide with five amino acids, has been simulated on computers using molecular dynamics. Such simulations exhibit a few stable conformations, which also have been identified experimentally. The simulations provide the possibility to perform cluster analysis in the space defined by potentially pharmacophoric measures such as dihedral angles, side-chain orientation, etc. By analyzing the statistics of the resulting clusters, the probability distribution of the side-chain conformations may be determined. These probabilities allow us to predict the selectivity of [Leu]enkephalin and [Met]enkephalin to the known mu- and delta-type opiate receptors to which they bind as agonists. Other plausible consequences of these probability distributions are discussed in relation to the way in which they may influence the dynamics of the synapse., (Copyright 2003 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 71: 577-592, 2003)

Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain less fine structural information than the calculated profiles because the resolution of the experiment is limited by the intrinsic surface roughness of water. Least squares fits of the calculated profiles to the experimental profiles provide areas per adsorbed enzyme and suggest that Thermomyces lanuginosa lipase adsorbs to the air-water interface in a semiopen conformation with the lid oriented away from the interface.

Aquaglyceroporin GlpF selectively conducts water and linear polyalcohols, such as glycerol, across the inner membrane of Escherichia coli. We report steered molecular dynamics simulations of glycerol conduction through GlpF, in which external forces accelerate the transchannel conduction in a manner that preserves the intrinsic conduction mechanism. The simulations reveal channel-glycerol hydrogen bonding interactions and the stereoselectivity of the channel. Employing Jarzynski's identity between free energy and irreversible work, we reconstruct the potential of mean force along the conduction pathway through a time series analysis of molecular dynamics trajectories. This potential locates binding sites and barriers inside the channel; it also reveals a low energy periplasmic vestibule suited for efficient uptake of glycerol from the environment.

Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.

Nonequilibrium molecular dynamics simulations are applied to investigate the rheological properties of coplanar nanopore systems of amphiphilic chain molecules with the tails grafted to the walls of the nanopore and with the head-group ends immersed in a solvent inside the nanopore. In particular, the effects of modifying the interaction between the amphiphilic head-groups by repulsive dipolar interactions or directly covalently linking pairs of chains at the head-groups have been studied. Different grafting densities are considered. The chains are modeled by a harmonic bead-spring model, and all particles interact through the repulsive part of a shifted Lennard-Jones potential. Head-group linking is also governed by a bead-spring potential. A harmonic potential models the lattice vibrations of the atomic boundaries. The rheological properties are studied by a shearing process in which the heat generated is conducted away from the system through the walls by applying a Nosé-Hoover thermostat. Computed geometric parameters such as average chain length and average tilt angle indicate reduction in chain flexibility at large dipole moments. Dipolar repulsion is found to broaden the density profiles of the solvent. This effect is opposed by chain linking. For increasing head-group repulsion, the amphiphile-solvent interfaces become less diffusive that leads to systematic variations in viscosities with increasing dipole moments. Friction forces become stronger at large grafting density and for larger dipole moments. The changes in rheological properties for fixed grafting density are essentially governed by the change in the response of the normal pressure to the applied shear field. The velocity gradients depend strongly on the degree of grafting density but appear to be less sensitive to the strength of the interactions between the head groups.