Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, R-g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R-g from the FRET efficiency. FRET experiments estimate approximate to 6 angstrom decrease in R-g when the actual decrease is approximate to 3 angstrom on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The approximate to 3 angstrom decrease is close to the statistical uncertainties of the R-g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Psi-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.

Stabilization of Cu-7 clusters in azide networks: syntheses, structures and magnetic behaviour

Two new azide bridged copper(II) coordination polymer compounds, Cu-7(N-3)(14)(C3H10N2)(C4H13N3)]n (I) and Cu-7(N-3)(14)(C3H10N2)(C5H15N3)(2)](n) (II) where C3H10N2 = 1,2-diaminopropane (1,2-DAP); C4H13N3 = di-ethylenetriamine (DETA); C5H15N3 = N-2-aminoethyl-1,3-propanediamine (AEDAP)] were prepared by employing a room temperature diffusion technique involving three layers. Single crystal studies reveal that both compounds I and II, have similar connectivity forming Cu7 clusters through end-on (EO) bonding of the azide. The Cu-7 clusters are connected through end-to-end (EE) connectivity of the azides forming three-dimensional structures. Magnetic studies confirmed the ferromagnetic interactions within the Cu-7 units and revealed the occurrence of concomitant ferro- and antiferro-magnetic interactions between these clusters. As a result I behaves as a weak-ferromagnet with T-C = 10 K.

RPRDC: Reliable Proliferation Routing with low Duty-Cycle in Wireless Sensor Networks

Ensuring reliable energy efficient data communication in resource constrained Wireless Sensor Networks (WSNs) is of primary concern. Traditionally, two types of re-transmission have been proposed for the data-loss, namely, End-to-End loss recovery (E2E) and per hop. In these mechanisms, lost packets are re-transmitted from a source node or an intermediate node with a low success rate. The proliferation routing(1) for QoS provisioning in WSNs low End-to-End reliability, not energy efficient and works only for transmissions from sensors to sink. This paper proposes a Reliable Proliferation Routing with low Duty Cycle RPRDC] in WSNs that integrates three core concepts namely, (i) reliable path finder, (ii) a randomized dispersity, and (iii) forwarding. Simulation results demonstrates that packet successful delivery rate can be maintained upto 93% in RPRDC and outperform Proliferation Routing(1). (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Thermodynamics of ligand (substrate end product) binding to endoxylanase from Chainia sp. (NCL-82-5-1): isothermal calorimetry and fluorescence titration studies

The binding of xylo-oligosaccharides to Chainia endoxylanase resulted in a decrease in fluorescence intensity of the enzyme with the formation of 1:1 complex. Equilibrium and thermodynamic parameters of ligand binding were determined by fluorescence titrations and titration calorimetry. The affinity of xylanase for the oligosaccharides increases in the order X-2 < X-3 < X-4 less than or equal to X-5. Contributions from the enthalpy towards the free energy change decreased with increasing chain length from X-2 to X-4, whereas an increase in entropy was observed, the change in enthalpy and entropy of binding being compensatory. The entropically driven binding process suggested that hydrophobic interactions as well as hydrogen bonds play a predominant role in ligand binding.

A playful side to twelfth-century mathematics

As editors of the book Lilavati's Daughters: The Women Scientists of India, reviewed by Asha Gopinathan (Nature 460, 1082; 2009), we would like to elaborate on the background to its title. Lilavati was a mathematical treatise of the twelfth century, composed by the mathematician and astronomer Bhaskaracharya (1114–85) — also known as Bhaskara II — who was a teacher of repute and author of several other texts. The name Lilavati, which literally means 'playful', is a surprising title for an early scientific book. Some of the mathematical problems posed in the book are in verse form, and are addressed to a girl, the eponymous Lilavati. However, there is little real evidence concerning Lilavati's historicity. Tradition holds that she was Bhaskaracharya's daughter and that he wrote the treatise to console her after an accident that left her unable to marry. But this could be a later interpolation, as the idea was first mentioned in a Persian commentary. An alternative view has it that Lilavati was married at an inauspicious time and was widowed shortly afterwards. Other sources have implied that Lilavati was Bhaskaracharya's wife, or even one of his students — raising the possibility that women in parts of the Indian subcontinent could have participated in higher education as early as eight centuries ago. However, given that Bhaskara was a poet and pedagogue, it is also possible that he chose to address his mathematical problems to a doe-eyed girl simply as a whimsical and charming literary device.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Thermal sresses in afinite solid cylinder due to steady temperature variation along the curved and end surface

An exact solution for determining the thermal stresses in a finite short cylinder due to an axisymmetric steady temperature field along the curved surface has been given. It is shown that a part of the solution obtained for this problem can be used to determine the thermal stresses in a finite solid cylinder heated over the end surfaces. Numerical results for a finite cylinder symmetrically heated over a portion on the curved surface and heated over the complete end surfaces have been given.

Thermal stresses in a finite hollow cylinder due to an axisymmetric temperature field at the end surface

A three-dimensional exact solution for determining the thermal stresses in a finite hollow cylinder subject to a steady state axisymmetric temperature field over one of its end surfaces has been given. Numerical results for a hollow cylinder, having lenght to outer diameter ratio equal to one and inner to outer diameter ratio equal to 0.75, subjected to a symmetric temperature variation over the end surfaces of the cylinder have been given.

Thermal stresses in a finite solid cylinder due to an axisymmetric temperature field at the end surface.

A three-dimensional rigorous solution for determining thermal stresses in a finite solid cylinder due to a steady state axisymmetric temperature field over one of its end surfaces is given. Numerical results for a solid cylinder having a length to diameter ratio equal to one and subjected to a symmetric temperature variation over half the radius of the cylinder at the end surfaces are included. These results have been compared with the results of the approximate solution given by W. Nowacki.

Acoustic emission technique for leak detection in an end shield of a pressurised heavy water reactor

This paper discusses a successful application of the Acoustic Emission Technique (AET) for the detection and location of leak paths present on an inaccessible side of an end shield of a Pressurised Heavy Water Reactor (PHWR). The methodology was based on the fact that air- and water-leak AE signals have different characteristic features. Baseline data was generated from a sound end shield of a PHWR for characterising the background noise. A mock-up end shield system with saw-cut leak paths was used to verify the validity of the methodology. It was found that air-leak signals under pressurisation (as low as 3 psi) could be detected by frequency domain analysis. Signals due to air leaks from various locations of defective end shield were acquired and analysed. It was possible to detect and locate leak paths. The presence of detected leak paths was further confirmed by an alternative test.

Five-level inverter scheme for an open-end winding induction machine with less number of switches

Higher level of inversion is achieved with a less number of switches in the proposed scheme. The scheme proposes a five-level inverter for an open-end winding induction motor which uses only two DC-link rectifiers of voltage rating of Vdc/4, a neutral-point clamped (NPC) three-level inverter and a two-level inverter. Even though the two-level inverter is connected to the high-voltage side, it is always in square-wave operation. Since the two-level inverter is not switching in a pulse width modulated fashion and the magnitude of switching transient is only half compared to the convention three-level NPC inverter, the switching losses and electromagnetic interference is not so high. The scheme is experimentally verified on a 2.5 kW induction machine.

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

A Compliant End-Effector to Passively Limit the Force in Tele-Operated Tissue-Cutting

This paper presents a compliant end-effector that cuts soft tissues and senses the cutting forces. The end-effector is designed to have an upper threshold on cutting forces to facilitate safe handling of tissue during automated cutting. This is demonstrated with nonlinear finite element analysis and experimental results obtained by cutting inhomogeneous phantom tissue. The cutting forces are estimated using a vision-based technique that uses amplified elastic deformation of the compliant end-effector. We also demonstrate an immersive tele-operated tissue-cutting system together with a haptic device that gives real-time force feedback to the user. DOI: 10.1115/1.4007638]

Three-dimensional acoustic analysis of an elliptical chamber muffler with a side inlet and a side outlet

The acoustical behaviour of an elliptical chamber muffler having a side inlet and side outlet port is analyzed in this paper, wherein a uniform velocity piston source is assumed to model the 3-D acoustic field in the elliptical chamber cavity. Towards this end, we consider the modal expansion of the acoustic pressure field in the elliptical cavity in terms of the angular and radial Mathieu func-tions, subjected to the rigid wall condition. Then, the Green's function due to the point source lo-cated on the side (curved) surface of the elliptical chamber is obtained. On integrating this function over the elliptical piston area on the curved surface of the elliptical chamber and subsequent divi-sion by the area of the elliptic piston, one obtains the acoustic pressure field due to the piston driven source which is equivalent to considering plane wave propagation in the side ports. Thus, one can obtain the acoustic pressure response functions, i.e., the impedance matrix (Z) parameters due to the sources (ports) located on the side surface, from which one may also obtain a progressive wave rep-resentation in terms of the scattering matrix (S). Finally, the acoustic performance of the muffler is evaluated in terms of the Transmission loss (TL) which is computed in terms of the scattering pa-rameters. The effect of the axial length of the muffler and the angular location of the ports on the TL characteristics is studied in detail. The acoustically long chambers show dominant axial plane wave propagation while the TL spectrum of short chambers indicates the dominance of the trans-versal modes. The 3-D analytical results are compared with the 3-D FEM simulations carried on a commercial software and are shown to be in an excellent agreement, thereby validating the analyti-cal procedure suggested in this work.

SeaMo plus : a virtual real-time multimedia service framework on handhelds to enable remote real-time patient monitoring for mobile doctors

The key requirements for enabling real-time remote healthcare service on a mobile platform, in the present day heterogeneous wireless access network environment, are uninterrupted and continuous access to the online patient vital medical data, monitor the physical condition of the patient through video streaming, and so on. For an application, this continuity has to be sufficiently transparent both from a performance perspective as well as a Quality of Experience (QoE) perspective. While mobility protocols (MIPv6, HIP, SCTP, DSMIP, PMIP, and SIP) strive to provide both and do so, limited or non-availability (deployment) of these protocols on provider networks and server side infrastructure has impeded adoption of mobility on end user platforms. Add to this, the cumbersome OS configuration procedures required to enable mobility protocol support on end user devices and the user's enthusiasm to add this support is lost. Considering the lack of proper mobility implementations that meet the remote healthcare requirements above, we propose SeaMo+ that comprises a light-weight application layer framework, termed as the Virtual Real-time Multimedia Service (VRMS) for mobile devices to provide an uninterrupted real-time multimedia information access to the mobile user. VRMS is easy to configure, platform independent, and does not require additional network infrastructure unlike other existing schemes. We illustrate the working of SeaMo+ in two realistic remote patient monitoring application scenarios.