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Living systems use chemical fuel to process information, assemble structures and maintain fluxes. Many of these processes are dissipative: energy is consumed purely to maintain non-equilibrium steady-state outputs. How efficiently the input energy is transduced toward the output dissipation as opposed to being lost during intermediate steps, and whether the efficiency is constrained by general principles or specific fine-tuning, are open questions. Here, applying a recent mapping from non-equilibrium systems to battery-resistor circuits, an analytic expression for the efficiency of any dissipative molecular machine driven by a chemical potential difference is derived. This expression disentangles the chemical potential from the machine's details, whose effect on the efficiency is fully specified by a constant called the load resistance. The efficiency passes through an inflection point separating totally inefficient machines from efficient machines if the balance between chemical potential difference and load resistance exceeds thermal noise. This explains all-or-none dynein stepping with increasing ATP concentration observed in single-molecule experiments. These results indicate that energy transduction in living systems is efficient not because of idiosyncratic optimization of biomolecules, but rather because the concentration of chemical fuel is kept above a threshold level. [ABSTRACT FROM AUTHOR]

Protein self-assembly is fundamental to biological function and disease. Experimentally, the atomic-level structure is difficult to obtain and the assembly mechanism is poorly understood. The large number of possible states accessible to such systems limits computational prediction. Here, I introduce a new computational approach that enforces conformational symmetry, whereby all chains in the system adopt the same conformation. Using this approach on a 2D lattice, a designed multi-chain conformation is found more than four orders of magnitude faster than existing approaches. Furthermore, the free energy landscape can be efficiently computed, showing potential for enabling atomistic prediction of protein self-assembly. [ABSTRACT FROM AUTHOR]

How protein structure encodes functionality is not fully understood. For example, long-range intraprotein communication can occur without measurable conformational change and is often not captured by existing structural correlation functions. It is shown here that important functional information is encoded in the timing of protein motions, rather than motion itself. I introduce the conditional activity function to quantify such timing correlations among the degrees of freedom within proteins. For three proteins, the conditional activities between side-chain dihedral angles were computed using the output of microseconds-long atomistic simulations. The new approach demonstrates that a sparse fraction of side-chain pairs are dynamically correlated over long distances (spanning protein lengths up to 7 nm), in sharp contrast to structural correlations, which are short-ranged (<1 nm). Regions of high self- and inter-side-chain dynamical correlations are found, corresponding to experimentally determined functional modules and allosteric connections, respectively. [ABSTRACT FROM AUTHOR]

Helices are the "hydrogen atoms" of biomolecular complexity; the DNA/RNA double hairpin and protein a-helix ubiquitously form the building blocks of life's constituents at the nanometer scale. Nevertheless, the formation processes of these structures, especially the dynamical pathways and rates, remain challenging to predict and control. Here, we present a general analytical method for constructing dynamical free-energy landscapes of helices. Such landscapes contain information about the thermodynamic stabilities of the possible macromolecular conformations, as well as about the dynamic connectivity, thus enabling the visualization and computation of folding pathways and timescales. We elucidate the methodology using the folding of polyalanine, and demonstrate that its a-helix folding kinetics is dominated by misfolded intermediates. At the physiological temperature of T = 298 K and midfolding time t = 250 ns, the fraction of structures in the native-state (α-helical) basin equals 22%, which is in good agreement with time-resolved experiments and massively distributed, ensemble-convergent molecular-dynamics simulations. We discuss the prominent role of β-strand-like intermediates in flight toward the native fold, and in relation to the primary conformational change precipitating aggregation in some neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated primarily by inherent physical forces, whereas natural selection determines the native state. [ABSTRACT FROM AUTHOR]

Among the macromolecular patterns of biological significance, right-handed a-helices are perhaps the most abundant structural motifs. Here, guided by experimental findings, we discuss both ultrafast initial steps and longer-time-scale structural dynamics of helix-coil transitions induced by a range of temperature jumps in large, isolated macromolecular ensembles of an a-helical protein segment thymosin β9 (Tβ9), and elucidate the comprehensive picture of (un)folding. In continuation of an earlier theoretical work from this laboratory that utilized a simplistic structure-scrambling algorithm combined with a variety of self-avoidance thresholds to approximately model helix-coil transitions in Tβ9, in the present contribution we focus on the actual dynamics of unfolding as obtained from massively distributed ensemble-convergent MD simulations which provide an unprecedented scope of information on the nature of transient macromolecular structures, and with atomic-scale spatiotemporal resolution. In addition to the use of radial distribution functions of ultrafast electron diffraction (UED) simulations in gaining an insight into the elementary steps of conformational interconversions, we also investigate the structural dynamics of the protein via the native (a-helical) hydrogen bonding contact metric which is an intuitive coarse graining approach. Importantly, the decay of a-helical motifs and the (globular) conformational annealing in Tβ9 occur consecutively or competitively, depending on the magnitude of temperature jump. [ABSTRACT FROM AUTHOR]

As the simplest and most prevalent motif of protein folding, a-helix initiation is the starting point of macromolecular complexity. In this work, helix initiation was directly measured via ultrafast temperature-jump spectroscopy on the smallest possible helix nucleus for which only the first turn is formed. The rate's dependence on sequence, length, and temperature reveals the fastest possible events in protein folding dynamics, and it was possible to separate the rate-limiting torsional (conformational) diffusion from the fast annealing of the helix. An analytic coarse-grained model for this process, which predicts the initiation rate as a function of temperature, confirms this picture. Moreover, the stipulations of the model were verified by ensemble-converging all-atom molecular dynamics simulations, which reproduced both the picosecond annealing and the nanosecond diffusion processes observed experimentally. [ABSTRACT FROM AUTHOR]

AbstractThe reflection of an obliquely incident electromagnetic pulse from a moving plasma half-space is studied. Using the Lorentz transformations, covariance of Maxwell's equations and the principle of phase invariance to transform between the rest frame and the moving frame, calculations can be conveniently performed in the moving frame. An analytical formula for the linear reflected waveform as a function of the incident angle shows temporal compression and pulse amplification at relativistic velocities of relevance for the generation of ultra-short laser optical pulses. [ABSTRACT FROM AUTHOR]

The article presents a study on No Store Queue (NoSQ) microarchitecture to perform in-flight store-load forwarding structures. It explores the speculative memory bypassing (SMB) in converting in-window store-load communication. NoSQ mentions that it repurposes the register read ports and address generation units, which is used to execute stores in the out-of-order core to now execute stores in order. It features other proposed core data path design that contains no dedicated in-flight store-load communication structure. It highlights that NoSQ uses SMB to replace the conventional store-load forwarding path in an out-of-order processor.

Abstract: In this Letter, we report on the direct mapping of helicity in the helix-to-coil structural transitions by theoretically simulating the ultrafast electron diffraction (UED) technique for isolated proteins with thousands of possible conformations. A novel approach for producing random coil structures of a given helical protein is presented with proper account of the steric avoidance threshold. A ‘resonance’ is manifested in the UED patterns of the helical structures. This resonance erodes as the transition to random coils becomes dominant, indicating that the residual helicity in the sample and the ensemble-averaged radius of gyration can be obtained and related to structural dynamics of isolated proteins. [Copyright &y& Elsevier]

Multiprocessors commonly use private per-processor caches that buffer blocks of the shared memory to improve both effective memory latency and bandwidth. A cache coherence protocol manages the read and write permissions if data in caches to ensure all processors observe a consistent view of shared memory. Unfortunately, emerging workload and technology trends reduce the attractiveness of this existing solution. Authors propose Token Coherence framework, which directly enforces the coherence invariant by counting tokens. This token-counting approach enables correct protocols that do not rely on request ordering and can operate with alternative policies that seek to improve the performance of future multiprocessors.

Predicting the behavior of heterogeneous nonequilibrium systems is currently analytically intractable. Consequently, complex biological systems have resisted unifying principles. Here, I introduce a mapping from dynamical systems to battery-resistor circuits. I show that in these transformed variables (i) arbitrary numbers of heterogeneous dynamical transitions can be reduced to a Thevenin equivalent resistor which is invariant to driving from equilibrium, (ii) resistors (together with the external driving sources) are sufficient to describe system behavior, and (iii) the resistor's directional symmetry leads to universal theorems of nonequilibrium behavior. This mapping is used to derive two general steady-state relations. First, for any cyclic process, the maximum amplification of any state is tightly bounded by the total dissipation of all states; experimental data are used to show that the master signal protein Ras achieves this bound. Second, for any process, the response of any reaction due to driving any other reaction is identical to the reciprocal response rescaled by the ratio of the corresponding Thevenin resistors. This result generalizes Onsager's reciprocal relation to the strongly driven regime and makes a testable prediction about how systems should be designed or evolved to maximize response. These analytic results represent a new perspective applicable to biological complexity and suggest that this mapping provides the natural variables to study heterogeneous nonequilibrium systems. [ABSTRACT FROM AUTHOR]

The SNAP receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin mediate neurotransmitter release by forming tight SNARE complexes that fuse synaptic vesicles with the plasma membranes in microseconds. Membrane fusion is generally explained by the action of proteins on macroscopic membrane properties such as curvature, elastic modulus, and tension, and a widespread model envisions that the SNARE motifs, juxtamembrane linkers, and C-terminal transmembrane regions of synaptobrevin and syntaxin-1 form continuous helices that act mechanically as semirigid rods, squeezing the membranes together as they assemble ("zipper") from the N to the C termini. However, the mechanism underlying fast SNARE-induced membrane fusion remains unknown. We have used all-atom molecular dynamics simulations to investigate this mechanism. Our results need to be interpreted with caution because of the limited number and length of the simulations, but they suggest a model of membrane fusion that has a natural physicochemical basis, emphasizes local molecular events over general membrane properties, and explains extensive experimental data. In this model, the central event that initiates fast (microsecond scale) membrane fusion occurs when the SNARE helices zipper into the juxtamembrane linkers which, together with the adjacent transmembrane regions, promote encounters of acyl chains from both bilayers at the polar interface. The resulting hydrophobic nucleus rapidly expands into stalk-like structures that gradually progress to form a fusion pore, aided by the SNARE transmembrane regions and without clearly discernible intermediates. The propensity of polyunsaturated lipids to participate in encounters that initiate fusion suggests that these lipids may be important for the high speed of neurotransmitter release. [ABSTRACT FROM AUTHOR]

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts human immunodeficiency virus type 1 (HIV-1) infection by reducing the intracellular dNTP pool. We have shown that SAMHD1 suppresses nuclear factor kappa-B activation and type I interferon (IFN-I) induction by viral infection and inflammatory stimuli. However, the mechanism by which SAMHD1 inhibits IFN-I remains unclear. Here, we show that SAMHD1 inhibits IFN-I activation induced by the mitochondrial antiviral-signaling protein (MAVS). SAMHD1 interacted with MAVS and suppressed MAVS aggregation in response to Sendai virus infection in human monocytic THP-1 cells. This resulted in increased phosphorylation of TANK binding kinase 1 (TBK1), inhibitor of nuclear factor kappa-B kinase epsilon (IKKe), and IFN regulatory factor 3 (IRF3). SAMHD1 suppressed IFN-I activation induced by IKKe and prevented IRF7 binding to the kinase domain of IKKe. We found that SAMHD1 interaction with the inhibitory domain (ID) of IRF7 (IRF7-ID) was necessary and sufficient for SAMHD1 suppression of IRF7-mediated IFN-I activation in HEK293T cells. Computational docking and molecular dynamics simulations revealed possible binding sites between IRF7-ID and full-length SAMHD1. Individual substitution of F411, E416, or V460 in IRF7-ID significantly reduced IRF7 transactivation activity and SAMHD1 binding. Furthermore, we investigated the role of SAMHD1 inhibition of IRF7-mediated IFN-I induction during HIV-1 infection. We found that THP-1 cells lacking IRF7 expression had reduced HIV-1 infection and viral transcription compared to control cells, indicating a positive role of IRF7 in HIV-1 infection. Our findings suggest that SAMHD1 suppresses IFN-I induction through the MAVS, IKKe, and IRF7 signaling axis. [ABSTRACT FROM AUTHOR]

Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Synaptotagmin-1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Synaptotagmin-1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Synaptotagmin-1-SNARE-complexin-1 complex. The simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Synaptotagmin-1 C2B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces, but keeps the system ready for fast fusion upon Ca2+ influx. [ABSTRACT FROM AUTHOR]

Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in solvent dynamics. which is coupled to the change in protein structure, is observed at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent hydrophobicity and bulk solvent viscosity. [ABSTRACT FROM AUTHOR]

Abstract: The search for molecular mechanisms to stimulate sensory regeneration in the mammalian inner ear is commonly based upon developmental studies. This has revealed many genes that regulate the differentiation of sensory cells. A major challenge is to place these genes into the context of functional networks that describe developmental processes more fully and increase the chances of identifying useful therapeutic targets. We used a novel approach to identify genes that are functionally related to the transcription factor gata2. Temporal profiles of gene expression were derived from three conditionally immortal cell lines and clustered to those of gata2 by applying the gamma model for oligonucleotide signals, a statistical method that allows quantitative analysis of oligonucleotide array data. We derived an objective list of 28 genes that clustered with gata2 in all three cell lines. A number of these genes have known functional links with gata2. Genes encoding CCAAT/enhancer binding proteins (C/EBP) and signal transducer and activation of transcription 3 (Stat3) are especially interesting as they are known to bind gata proteins directly. The results provide strong evidence that our experimental approach can reveal functional relationships between genes that regulate fundamental processes in the differentiation of sensory cells in the inner ear. [Copyright &y& Elsevier]

T cells can be controllably stimulated through antigen-specific or nonspecific protocols. Accompanying functional hallmarks of T cell activation can include cytoskeletal reorganization, cell size increase, and cytokine secretion. Photon-induced near-field electron microscopy (PINEM) is used to image and quantify evanescent electric fields at the surface of T cells as a function of various stimulation conditions. While PINEM signal strength scales with multiple of the biophysical changes associated with T cell functional activation, it mostly strongly correlates with antigen-engagement of the T cell receptors, even under conditions that do not lead to functional T cell activation. PINEM image analysis suggests that a stimulation-induced reorganization of T cell surface structure, especially over length scales of a few hundred nanometers, is the dominant contributor to these PINEM signal changes. These experiments reveal that PINEM can provide a sensitive label-free probe of nanoscale cellular surface structures. [ABSTRACT FROM AUTHOR]

Computational sprinting activates dark silicon to improve responsiveness by briefly but intensely exceeding a system's sustainable power limit. This article focuses on the energy implications of sprinting. The authors observe that sprinting can save energy even while improving responsiveness by enabling execution in chip configurations that, though thermally unsustainable, improve energy efficiency. Surprisingly, this energy savings can translate to throughput improvements even for long-running computations. Repeatedly alternating between sprint and idle modes while maintaining sustainable average power can outperform steady-state computation at the platform's thermal limit. [ABSTRACT FROM PUBLISHER]

Aims Several studies have investigated the effects of metformin treatment in patients with type 1 diabetes mellitus ( T1DM). No study has hitherto examined its effects on endothelial function in these patients. In this study we sought to evaluate the effect of metformin on endothelial function in type 1 diabetic patients. Methods Forty-two uncomplicated T1DM patients were randomized in a placebo-controlled, double-blind, 6-month trial to treatment with either metformin or placebo. Glycometabolic and clinical parameters as well as flow-mediated dilation ( FMD) and nitrate-mediated dilation ( NMD) of the right brachial artery were measured at baseline and at the end of the study. Glycaemic variability ( GV, calculated from continuous glucose monitoring data) and a biomarker of oxidative stress [urinary 8-iso-prostaglandin F2 α ( PGF2 α)] were also assessed. Results Baseline data were similar in the two groups. Compared with placebo, metformin significantly reduced body weight [−2.27 kg (95% confidence interval: −3.99; −0.54); p = 0.012] whilst improved FMD [1.32% (0.30; 2.43); p = 0.013] and increased PGF2 α [149 pg/mg creatinine (50; 248); p = 0.004]. Notably, the improvement of FMD did not correlate with the decrease of body weight (r2 < 1%). NMD, haemoglobin A1c, GV, daily insulin dose and other parameters did not significantly change after the treatment comparing the two groups. Conclusions Our pilot trial showed that, in uncomplicated type 1 diabetic subjects, metformin improved FMD and increased PGF2 α, a marker of oxidative stress, irrespective of its effects on glycaemic control and body weight. Randomized, blinded clinical trials are needed to evaluate the benefits and risks of metformin added to insulin in type 1 diabetes. [ABSTRACT FROM AUTHOR]

To control viral infection, vertebrates rely on both inducible interferon responses and less well-characterized cell-intrinsic responses composed of "at the ready" antiviral effector proteins. Here, we show that E3 ubiquitin ligase TRIM7 is a cell-intrinsic antiviral effector that restricts multiple human enteroviruses by targeting viral 2BC, a membrane remodeling protein, for ubiquitination and proteasome-dependent degradation. Selective pressure exerted by TRIM7 results in emergence of a TRIM7-resistant coxsackievirus with a single point mutation in the viral 2C ATPase/helicase. In cultured cells, the mutation helps the virus evade TRIM7 but impairs optimal viral replication, and this correlates with a hyperactive and structurally plastic 2C ATPase. Unexpectedly, the TRIM7-resistant virus has a replication advantage in mice and causes lethal pancreatitis. These findings reveal a unique mechanism for targeting enterovirus replication and provide molecular insight into the benefits and trade-offs of viral evolution imposed by a host restriction factor. [Display omitted] • cDNA screen reveals E3 ligase TRIM7 as a potent inhibitor of human enteroviruses • TRIM7 targets viral 2BC protein for ubiquitination and degradation • A single T323A amino acid change in viral 2C protein confers resistance to TRIM7 • TRIM7-resistant viral variant replicates robustly in mice and causes severe disease The E3 ubiquitin ligase TRIM7 is an antiviral effector that restricts multiple human enteroviruses. [ABSTRACT FROM AUTHOR]

Cofilin and ADF are cytoskeleton remodeling proteins that cooperatively bind and fragment actin filaments. Bound cofilin molecules do not directly interact with each other, indicating that cooperative binding of cofilin is mediated by the actin filament lattice. Cofilactin is therefore a model system for studying allosteric regulation of self-assembly. How cofilin binding changes structural and mechanical properties of actin filaments is well established. Less is known about the interaction energies and the thermodynamics of filament fragmentation, which describes the collective manner in which the cofilin concentration controls mean actin filament length. Here, we provide a general thermodynamic framework for allosteric regulation of self-assembly, and we use the theory to predict the interaction energies of experimental actin filament length distributions over a broad range of cofilin binding densities and for multiple cofilactin variants. We find that bound cofilin induces changes in nearby actin-actin interactions, and that these allosteric effects are propagated along the filament to affect up to four neighboring cofilin-binding sites (i.e., beyond nearest-neighbor allostery). The model also predicts that cofilin differentially stabilizes and destabilizes longitudinal versus lateral actin-actin interactions, and that the magnitude, range, asymmetry, and even the sign of these interaction energies can be altered using different actin and cofilin mutational variants. These results demonstrate that the theoretical framework presented here can provide quantitative thermodynamic information governing cooperative protein binding and filament length regulation, thus revealing nanometer length-scale interactions from micron length-scale "wet-lab" measurements. [ABSTRACT FROM AUTHOR]

Introduction Acute coronary syndrome (ACS) is the cause of over 114 000 UK hospital admissions and a cost to the NHS of over €3.9 billion every year. Advances in microarray technology allow a detailed understanding of genome-wide expression profiles of pathological processes. We hypothesised that analysis of ACS, at the time of an acute event and throughout recovery, would provide insight into pathology, as well as identify genes as potential drug targets and both diagnostic and prognostic markers. Methods 50 patients presenting with chest pain consistent with ACS were recruited within 48 h of admission. 3 ml of peripheral whole blood was collected using Tempus RNA tubes at days 1, 3, 7, 30 and 90. Total RNA was extracted, cleared of globin mRNA and arrayed using Affymetrix HG_U133 plusv.2 GeneChips. Data were analysed using open source software PUMA. Results We used principal component analysis (PCA) to visualise the data. With clinical information incorporated, it was found that the data discriminated between patients, putting them into troponin-positive and troponin-negative groups across all time points. Hierarchical clustering, comparing the expression profiles between groups, identified different clusters of genes that increased in expression over time in the troponin-positive group. Pathway analysis of the clusters showed overexpression of Rho GTPase cytoskeletal, endothelin signalling, integrin signalling, G-protein signalling and inflammation-mediated pathways. Conclusions Microarray analysis identified expression differences between troponin-positive and troponin-negative patients over time. Specific biological pathways possibly showing the late effects of acute events can be used to discover biomarkers of coronary heart disease. [ABSTRACT FROM AUTHOR]