Novel pppGpp binding site at the C-terminal region of the Rel enzyme from Mycobacterium smegmatis

Mycobacterium tuberculosis elicits the stringent response under unfavorable growth conditions, such as those encountered by the pathogen inside the host. The hallmark of this response is production of guanosine tetra-and pentaphosphates, collectively termed (p)ppGpp, which have pleiotropic effects on the bacterial physiology. As the stringent response is connected to survival under stress, it is now being targeted for developing inhibitors against bacterial persistence. The Rel enzyme in mycobacteria has two catalytic domains at its N-terminus that are involved in the synthesis and hydrolysis of (p)ppGpp, respectively. However, the function of the C-terminal region of the protein remained unknown. Here, we have identified a binding site for pppGpp in the C-terminal region of Rel. The binding affinity of pppGpp was quantified by isothermal titration calorimetry. The binding site was determined by crosslinking using the nucleotide analog azido-pppGpp, and examining the crosslink product by mass spectrometry. Additionally, mutations in the Rel protein were created to confirm the site of pppGpp binding by isothermal titration calorimetry. These mutants showed increased pppGpp synthesis and reduced hydrolytic activity. We believe that binding of pppGpp to Rel provides a feedback mechanism that allows the protein to detect and adjust the (p)ppGpp level in the cell. Our work suggests that such sites should also be considered while designing inhibitors to target the stringent response.

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

Functional roles of N-terminal and C-terminal domains in the overall activity of a novel single-stranded DNA binding protein of Deinococcus radiodurans

Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: Ssb(N) (N-terminal without connector), Ssb(NC) (N-terminal with connector) and Ssb(C) (C-terminal), each harboring one OB fold. Both Ssb(N) and Ssb(NC) displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (Ssb(FL)). The level of ssDNA binding activity displayed by SsbC was intermediate between Ssb(FL) and Ssb(N). Ssb(C) and Ssb(FL) predominantly existed as homo-dimers while Ssb(NC)/Ssb(N) formed different oligomeric forms. In vitro, Ssb(NC) or Ssb(N) formed a binary complex with Ssb(C) that displayed enhanced ssDNA binding activity. Unlike Ssb(FL), Ssb variants were able to differentially modulate topoisomerase-I activity, but failed to stimulate Deinococcal RecA-promoted DNA strand exchange. The results suggest that the C-terminal OB fold is primarily responsible for ssDNA binding. The N-terminal OB fold binds weakly to ssDNA but is involved in multimerization. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license.

Ischaemic concentrations of lactate increase TREK1 channel activity by interacting with a single histidine residue in the carboxy terminal domain

Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change. AbstractA rise in lactate concentration and the leak potassium channel TREK1 have been independently associated with cerebral ischaemia. Recent literature suggests lactate to be neuroprotective and TREK1 knockout mice show an increased sensitivity to brain and spinal cord ischaemia; however, the connecting link between the two is missing. Therefore we hypothesized that lactate might interact with TREK1 channels. In the present study, we show that lactate at ischaemic concentrations (15-30mm) at pH7.4 increases TREK1 current in CA1 stratum radiatum astrocytes and causes membrane hyperpolarization. We confirm the intracellular action of lactate on TREK1 in hippocampal slices using monocarboxylate transporter blockers and at single channel level in cell-free inside-out membrane patches. The intracellular effect of lactate on TREK1 is specific since other monocarboxylates such as pyruvate and acetate at pH7.4 failed to increase TREK1 current. Deletion and point mutation experiments suggest that lactate decreases the longer close dwell time incrementally with increase in lactate concentration by interacting with the histidine residue at position 328 (H328) in the carboxy terminal domain of the TREK1 channel. The interaction of lactate with H328 is dependent on the charge on the histidine residue since isosteric mutation of H328 to glutamine did not show an increase in TREK1 channel activity with lactate. This is the first demonstration of a direct effect of lactate on ion channel activity. The action of lactate on the TREK1 channel signifies a separate neuroprotective mechanism in ischaemia since it was found to be independent of the effect of acidic pH on channel activity. Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change.

Instability Analysis of Nonlinear Surface Waves in a Circular Cylindrical Container Subjected to a Vertical Excitation

Singular perturbation theory of two-time scale expansions was developed both in inviscid and weak viscous fluids to investigate the motion of single surface standing wave in a liquid-filled circular cylindrical vessel, which is subject to a vertical periodical oscillation. Firstly, it is assumed that the fluid in the circular cylindrical vessel is inviscid, incompressible and the motion is irrotational, a nonlinear evolution equation of slowly varying complex amplitude, which incorporates cubic nonlinear term, external excitation and the influence of surface tension, was derived from solvability condition of high-order approximation. It shows that when forced frequency is low, the effect of surface tension on mode selection of surface wave is not important. However, when forced frequency is high, the influence of surface tension is significant, and can not be neglected. This proved that the surface tension has the function, which causes free surface returning to equilibrium location. Theoretical results much close to experimental results when the surface tension is considered. In fact, the damping will appear in actual physical system due to dissipation of viscosity of fluid. Based upon weakly viscous fluids assumption, the fluid field was divided into an outer potential flow region and an inner boundary layer region. A linear amplitude equation of slowly varying complex amplitude, which incorporates damping term and external excitation, was derived from linearized Navier-Stokes equation. The analytical expression of damping coefficient was determined and the relation between damping and other related parameters (such as viscosity, forced amplitude and depth of fluid) was presented. The nonlinear amplitude equation and a dispersion, which had been derived from the inviscid fluid approximation, were modified by adding linear damping. It was found that the modified results much reasonably close to experimental results. Moreover, the influence both of the surface tension and the weak viscosity on the mode formation was described by comparing theoretical and experimental results. The results show that when the forcing frequency is low, the viscosity of the fluid is prominent for the mode selection. However, when the forcing frequency is high, the surface tension of the fluid is prominent. Finally, instability of the surface wave is analyzed and properties of the solutions of the modified amplitude equation are determined together with phase-plane trajectories. A necessary condition of forming stable surface wave is obtained and unstable regions are illustrated. (c) 2005 Elsevier SAS. All rights reserved.

Nonlinear Faraday Waves in a Parametrically Excited Circular Cylindrical Container

In the cylindrical coordinate system, a singular perturbation theory of multiple-scale asymptotic expansions was developed to study single standing water wave mode by solving potential equations of water waves in a rigid circular cylinder, which is subjec

Defensa de la vida física del paciente en estado terminal : entre la dignidad y la autonomía

Resumen: Proponemos un análisis crítico de los fundamentos que sustentan la llamada “Ley de Muerte Digna” incorporada en la Ley que consagra la regulación de los derechos del paciente, historia clínica, consentimiento informado, (Art. 2º, inc. “e” párr. 2º de la Ley 26.529 modificada por la Ley 26.742), que introduce en nuestro país la existencia real de un sistema eutanásico formal sin fundamentos de orden científico, éticos e incluso jurídicos. ¿Es moralmente lícito suprimir la vida del enfermo terminal?, ¿la legalización de esta práctica eutanásica es la primera piedra de una nueva “cultura” de la vida? Entendemos que la llamada “tesis de la autonomía”, fundante de la reforma legislativa en cuestión, desde una óptica Bioética personalista, merece serias objeciones bioéticas ya que puede distorsionar gravemente el ejercicio de la medicina y la relación médico paciente.

Estatuto antropológico de la enfermedad y el dolor en el enfermo terminal

Resumen: Los conceptos de dolor, enfermedad y enfermedad terminal exceden plenamente el ámbito meramente biológico y solo pueden abordarse acabadamente desde una perspectiva hilemorfista de persona humana. El enfoque integral de estos conceptos permite descubrir un significado antropológico de los mismos. Su comprensión adecuada constituye un imperativo moral en el cuidado del paciente terminal. En este sentido, es posible rescatar el valor de los cuidados paliativos como una modalidad de atención integral del paciente. En este contexto surge el proyecto de la Casa de la Bondad Salta, que pertenece a la Fundación Manos Abiertas. La Casa de la Bondad tiene como objetivo implementar cuidados paliativos a enfermos terminales. Se parte de la necesidad de realizar un abordaje integral del enfermo desde un enfoque transdisciplinar.

Computer Simulation Of Random Sphere Packing In An Arbitrarily Shaped Container

Most simulations of random sphere packing concern a cubic or cylindric container with periodic boundary, containers of other shapes are rarely studied. In this paper, a new relaxation algorithm with pre-expanding procedure for random sphere packing in an arbitrarily shaped container is presented. Boundaries of the container are simulated by overlapping spheres which covers the boundary surface of the container. We find 0.4 similar to 0.6 of the overlap rate is a proper value for boundary spheres. The algorithm begins with a random distribution of small internal spheres. Then the expansion and relaxation procedures are performed alternately to increase the packing density. The pre-expanding procedure stops when the packing density of internal spheres reaches a preset value. Following the pre-expanding procedure, the relaxation and shrinking iterations are carried out alternately to reduce the overlaps of internal spheres. The pre-expanding procedure avoids the overflow problem and gives a uniform distribution of initial spheres. Efficiency of the algorithm is increased with the cubic cell background system and double link data structure. Examples show the packing results agree well with both computational and experimental results. Packing density about 0.63 is obtained by the algorithm for random sphere packing in containers of various shapes.

Surface waves in a vertically excited circular cylindrical container

The nonlinear free surface amplitude equation, which has been derived from the inviscid fluid by solving the potential equation of water waves with a singular perturbation theory in a vertically oscillating rigid circular cylinder, is investigated successively in the fourth-order Runge-Kutta approach with an equivalent time-step. Computational results include the evolution of the amplitude with time, the characteristics of phase plane determined by the real and imaginary parts of the amplitude, the single-mode selection rules of the surface waves in different forced frequencies, contours of free surface displacement and corresponding three-dimensional evolution of surface waves, etc. In addition, the comparison of the surface wave modes is made between theoretical calculations and experimental measurements, and the results are reasonable although there are some differences in the forced frequency.

Instability of the vertically forced surface wave in a circular cylindrical container

The nonlinear amplitude equation, which was derived by Jian Yongjun employing expansion of two-time scales in inviscid fluids in a vertically oscillating circular cylindrical vessel, is modified by introducing a damping term due to the viscous dissipation of this system. Instability of the surface wave is analysed and properties of the solutions of the modified equation are determined together with phase-plane trajectories. A necessary condition of forming a stable surface wave is obtained and unstable regions are illustrated. Research results show that the stable pattern of surface wave will not lose its stability to an infinitesimal disturbance.

Dynamic interaction of an elastic container with fluid

The vibration analysis of an elastic container with partially filled fluid was investigated in this paper. The container is made of a thin cylinder and two circular plates at the ends. The axis of the cylinder is in the horizontal direction. It is difficult to solve this problem because the complex system is not axially symmetric. The equations of motion for this system were derived. An incompressible and ideal fluid model is used in the present work. Solutions of the equations were obtained by the generalized variational method. The solution was expressed in a series of normalized generalized Fourier's functions. This series converged rapidly, and so its approximate solution was obtained with high precision. The agreement of the calculated values with the experimental result is good. It should be mentioned that with our method, the computer time is less than that with the finite-element method.

A snapshot of digitisation and OCR Developments

One of the goals of Knowledge Exchange (www.knowledge-exchange.info) is to help partners to share knowledge and expertise and facilitate the build of expert networks. In the area of digitisation, including non-textual and 3-D-digitisation, a first step is to provide a snapshot of current activities and challenges in the KE partner countries. This paper is a synthesis of the information gathered in a questionnaire that was sent to 15 infrastructure institutions, e.g. libraries and also funders, within the five partner countries of Knowledge Exchange: Denmark (DK), Finland (FIN), Germany (GER), the Netherlands (NL) and the United Kingdom (UK). The paper is based on the answers provided by 6 respondents from four countries:  DK o Danish Agency of Culture (Henrik Jarl Hansen) o State and University Library (Tonny Skovgård Jensen)  GER o German research foundation, DFG (Franziska Regner)  NL o Royal Library (Hildelies Balk) o Leiden University Library (Saskia van Bergen)  UK o Jisc (Paola Marchionni, Peter Findlay) The absence of Finnish responses may be due to Finland participating in the recent Enumerate Core Survey II that also addressed digitisation. We have included some of the outcomes of this survey to present a richer picture.