Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (T-m's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At T-m Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at T-m with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a P-fold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

Solution structural features of N-acyl homoserine lactones

Here we demonstrate that in interbacterial quorum signal moderators, N-acylhomoserine lactones (AHLs), the stabilization of bioactive pharmacophore lactone against lysis is through the e(-) withdrawing N-acyl motif which reduces lactone carbonyl polarization. This lysis is assisted by weak (<0.05 kcal mol(-1)) contacts between N-acyl O and lactone C'. The interactions that preclude this weak contact, in the free and receptor-bound AHLs, improve lactone halflife and hence are key to the design of the antibacterial AHL analogues. (C) 2015 Elsevier Ltd. All rights reserved.

Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (beta/alpha)(8)-triosephosphate isomerase barrel enzyme

Although several factors have been suggested to contribute to thermostability, the stabilization strategies used by proteins are still enigmatic. Studies on a recombinant xylanase from Bacilllus sp. NG-27 (RBSX), which has the ubiquitous (beta/alpha)(8)-triosephosphate isomerase barrel fold, showed that just a single mutation, V1L, although not located in any secondary structural element, markedly enhanced the stability from 70 degrees C to 75 degrees C without loss of catalytic activity. Conversely, the V1A mutation at the same position decreased the stability of the enzyme from 70 degrees C to 68 degrees C. To gain structural insights into how a single extreme N-terminus mutation can markedly influence the thermostability of the enzyme, we determined the crystal structure of RBSX and the two mutants. On the basis of computational analysis of their crystal structures, including residue interaction networks, we established a link between N-terminal to C-terminal contacts and RBSX thermostability. Our study reveals that augmenting N-terminal to C-terminal noncovalent interactions is associated with enhancement of the stability of the enzyme. In addition, we discuss several lines of evidence supporting a connection between N-terminal to C-terminal noncovalent interactions and protein stability in different proteins. We propose that the strategy of mutations at the termini could be exploited with a view to modulate stability without compromising enzymatic activity, or in general, protein function in diverse folds where N and C termini are in close proximity. Database The coordinates of RBSX, V1A and V1L have been deposited in the PDB database under the accession numbers 4QCE, 4QCF, and 4QDM, respectively

Transport properties of solution processed Cu2SnS3/AZnO heterostructure for low cost photovoltaics

Cu2SnS3 thin films were deposited by a facile sot-gel technique followed by annealing. The annealed films were structurally characterized by grazing incidence X-ray diffraction (GIXRD) and transmission electron microscopy (TEM). The crystal structure was found to be tetragonal with crystallite sizes of 2.4-3 nm. Texture coefficient calculations from the GIXRD revealed the preferential orientation of the film along the (112) plane. The morphological investigations of the films were carried out using field emission scanning electron microscopy (FESEM) and the composition using electron dispersive spectroscopy (EDS). The temperature dependent current, voltage characteristics of the Cu2SnS3/AZnO heterostructure were studied. The log I-log V plot exhibited three regions of different slopes showing linear ohmic behavior and non-linear behavior following the power law. The temperature dependent current voltage characteristics revealed the variation in ideality factor and barrier height with temperature. The Richardson constant was calculated and its deviation from the theoretical value revealed the inhomogeneity of the barrier heights. Transport characteristics were modeled using the thermionic emission model. The Gaussian distribution of barrier heights was applied and from the modified Richardson plot the value of the Richardson constant was found to be 47.18 A cm(-2) K-2. (c) 2015 Elsevier B.V. All rights reserved.

Injection barrier induced deviations in space charge limited conduction in doped poly(3-methylthiophene) based devices

The carrier density dependent current-voltage (J V) characteristics of electrochemically prepared poly(3-methylthiophene) (P3MeT) have been investigated in Pt/P3MeT/Al devices, as a function of temperature from 280 to 84 K. In these devices, the charge transport is found to be mainly governed by different transport regimes of space charge limited conduction (SCLC). In a lightly doped device, SCLC controlled by exponentially distributed traps (Vl+1 law, l > 1) is observed in the intermediate voltage range (0.5-2 V) at all temperatures. However, at higher bias (> 2 V), the current deviates from the usual Vl+1 law where the slope is found to be less than 2 of the logJ-logV plot, which is attributed to the presence of the injection barrier. These deviations gradually disappear at higher doping level due to reduction in the injection barrier. Numerical simulations of the Vl+1 law by introducing the injection barrier show good agreement with experimental data. The results show that carrier density can tune the charge transport mechanism in Pt/P3MeT/Al devices to understand the non-Ohmic behavior. The plausible reasons for the origin of injection barrier and the transitions in the transport mechanism with carrier density are discussed. (C) 2015 AIP Publishing LLC.

Quantitative In Situ Analysis of Deformation in Sliding Metals: Effect of Initial Strain State

Using in situ, high-speed imaging of a hard wedge sliding against pure aluminum, and image analysis by particle image velocimetry, the deformation field in sliding is mapped at high resolution. This model system is representative of asperity contacts on engineered surfaces and die-workpiece contacts in deformation and machining processes. It is shown that large, uniform plastic strains of 1-5 can be imposed at the Al surface, up to depths of 500 mu m, under suitable sliding conditions. The spatial strain and strain rate distributions are significantly influenced by the initial deformation state of the Al, e.g., extent of work hardening, and sliding incidence angle. Uniform straining occurs only under conditions of steady laminar flow in the metal. Large pre-strains and higher sliding angles promote breakdown in laminar flow due to surface fold formation or flow localization in the form of shear bands, thus imposing limits on uniform straining by sliding. Avoidance of unsteady sliding conditions, and selection of parameters like sliding angle, thus provides a way to control the deformation field. Key characteristics of the sliding deformation such as strain and strain rate, laminar flow, folding and prow formation are well predicted by finite element simulation. The deformation field provides a quantitative basis for interpreting wear particle formation. Implications for engineering functionally graded surfaces, sliding wear and ductile failure in metals are discussed.

Intrinsic Limit for Contact Resistance in Exfoliated Multilayered MoS2 FET

A new method for the separation of contact resistance (R-contact) into Schottky barrier resistance (R-SB) and interlayer resistance (R-IL) is proposed for multilayered MoS2 FETs. While R-SB varies exponentially with Schottky barrier height (Phi(bn)), R-IL essentially remains unchanged. An empirical model utilizing this dependence of R-contact versus Phi(bn) is proposed and fits to the experimental data. The results, on comparison with the existing reports of lowest R-contact, suggest that the extracted R-IL (1.53 k Omega.mu m) for an unaltered channel would determine the lower limit of intrinsic R-contact even for barrierless contacts for multilayered exfoliated MoS2 FETs.

Prospects of zero Schottky barrier height in a graphene-inserted MoS2-metal interface

A low Schottky barrier height (SBH) at source/drain contact is essential for achieving high drive current in atomic layer MoS(2-)channel-based field effect transistors. Approaches such as choosing metals with appropriate work functions and chemical doping are employed previously to improve the carrier injection from the contact electrodes to the channel and to mitigate the SBH between the MoS2 and metal. Recent experiments demonstrate significant SBH reduction when graphene layer is inserted between metal slab (Ti and Ni) and MoS2. However, the physical or chemical origin of this phenomenon is not yet clearly understood. In this work, density functional theory simulations are performed, employing pseudopotentials with very high basis sets to get insights of the charge transfer between metal and monolayer MoS2 through the inserted graphene layer. Our atomistic simulations on 16 different interfaces involving five different metals (Ti, Ag, Ru, Au, and Pt) reveal that (i) such a decrease in SBH is not consistent among various metals, rather an increase in SBH is observed in case of Au and Pt; (ii) unlike MoS2-metal interface, the projected dispersion of MoS2 remains preserved in any MoS2-graphene- metal system with shift in the bands on the energy axis. (iii) A proper choice of metal (e.g., Ru) may exhibit ohmic nature in a graphene-inserted MoS2-metal contact. These understandings would provide a direction in developing high-performance transistors involving heteroatomic layers as contact electrodes. (c) 2016 AIP Publishing LLC.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the Xray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.

General Solution to Two-Dimensional Nonslipping JKR Model with a Pulling Force in an Arbitrary Direction

In this paper, a generalized JKR model is investigated, in which an elastic cylinder adhesively contacts with an elastic half space and the contact region is assumed to be perfect bonding. An external pulling force is acted on the cylinder in an arbitrary direction. The contact area changes during the pull-off process, which can be predicted using the dynamic Griffith energy balance criterion as the contact edge shifts. Full coupled solution with an oscillatory singularity is obtained and analyzed by numerical calculations. The effect of Dundurs' parameter on the pull-off process is analyzed, which shows that a nonoscillatory solution can approximate the general one under some conditions, i.e., larger pulling angle (pi/2 is the maximum value), smaller a/R or larger nondimensional parameter value of Delta gamma/E*R. Relations among the contact half width, the external pulling force and the pulling angle are used to determine the pull-off force and pull-off contact half width explicitly. All the results in the present paper as basic solutions are helpful and applicable for experimenters and engineers.

Scanning gate microscopy of current-annealed single layer graphene

We have used scanning gate microscopy to explore the local conductivity of a current-annealed graphene flake. A map of the local neutrality point (NP) after annealing at low current density exhibits micron-sized inhomogeneities. Broadening of the local e-h transition is also correlated with the inhomogeneity of the NP. Annealing at higher current density reduces the NP inhomogeneity, but we still observe some asymmetry in the e-h conduction. We attribute this to a hole-doped domain close to one of the metal contacts combined with underlying striations in the local NP. © 2010 American Institute of Physics.

Nonlinear Mechanical Modeling Of Cell Adhesion

Cell adhesion, which is mediated by the receptor-ligand bonds, plays an essential role in various biological processes. Previous studies often described the force-extension relationship of receptor-ligand bond with linear assumption. However, the force-extension relationship of the bond is intrinsically nonlinear, which should have significant influence on the mechanical behavior of cell adhesion. In this work, a nonlinear mechanical model for cell adhesion is developed, and the adhesive strength was studied at various bond distributions. We find that the nonlinear mechanical behavior of the receptor-ligand bonds is crucial to the adhesive strength and stability. This nonlinear behavior allows more bonds to achieve large bond force simultaneously, and therefore the adhesive strength becomes less sensitive to the change of bond density at the outmost periphery of the adhesive area. In this way, the strength and stability of cell adhesion are soundly enhanced. The nonlinear model describes the cell detachment behavior better than the linear model. (C) 2007 Elsevier Ltd. All rights reserved.

Pedir ayuda a “Los otros” : algunas consideraciones en torno a la primera embajada bizantina en Córdoba (s. IX)

Resumen: El presente artículo estudia las motivaciones que tuvo Téofilo, Emperador bizantino, para entrar en contacto con el Emirato Independiente de Córdoba. Desde ese punto de vista, se presentan algunas cuestiones en torno a la imagen del musulmán construidas por la apologética bizantina, haciendo especial mención a la obra de Constantino VII Porfirogénito, De administrando Imperio. Es a partir de allí que se trata de analizar los motivos que mueven al Basileus a enviar la primera embajada bizantina en Córdoba, comprobando con esto que , cuando se trata de salvaguardar la seguridad del imperio, no habrán motivos para evitar contactos con aquel que , incluso, pueda ser un enemigo.

Social Interactions and Subjective Well-Being: Evidence from Latin America

In this paper, we seek to examine the effect of comparisons and social capital on subjective well-being. Furthermore, we test if, through social influence and exposure, social capital is either an enhancer or appeaser of the comparison effect. Using the Latinobarómetro Survey (2007) we find that in contrast to most previous studies, the comparison effect on well-being is positive; that is, the better others perform, the happier the individual is. We also find that social capital is among the strongest correlates of individuals’ subjective well-being in Latin American countries. Furthermore, our findings suggest that social contacts may enhance the comparison effect on individual’s happiness, which is more intense for those who perform worse in their reference group.