Chimeras of Escherichia coli and Mycobacterium tuberculosis Single-Stranded DNA Binding Proteins: Characterization and Function in Escherichia coli

Single stranded DNA binding proteins (SSBs) are vital for the survival of organisms. Studies on SSBs from the prototype, Escherichia coli (EcoSSB) and, an important human pathogen, Mycobacterium tuberculosis (MtuSSB) had shown that despite significant variations in their quaternary structures, the DNA binding and oligomerization properties of the two are similar. Here, we used the X-ray crystal structure data of the two SSBs to design a series of chimeric proteins (m beta 1, m beta 1'beta 2, m beta 1-beta 5, m beta 1-beta 6 and m beta 4-beta 5) by transplanting beta 1, beta 1'beta 2, beta 1-beta 5, beta 1-beta 6 and beta 4-beta 5 regions, respectively of the N-terminal (DNA binding) domain of MtuSSB for the corresponding sequences in EcoSSB. In addition, m beta 1'beta 2(ESWR) SSB was generated by mutating the MtuSSB specific `PRIY' sequence in the beta 2 strand of m beta 1'beta 2 SSB to EcoSSB specific `ESWR' sequence. Biochemical characterization revealed that except for m beta 1 SSB, all chimeras and a control construct lacking the C-terminal domain (Delta C SSB) bound DNA in modes corresponding to limited and unlimited modes of binding. However, the DNA on MtuSSB may follow a different path than the EcoSSB. Structural probing by protease digestion revealed that unlike other SSBs used, m beta 1 SSB was also hypersensitive to chymotrypsin treatment. Further, to check for their biological activities, we developed a sensitive assay, and observed that m beta 1-beta 6, MtuSSB, m beta 1'beta 2 and m beta 1-beta 5 SSBs complemented E. coli Delta ssb in a dose dependent manner. Complementation by the m beta 1-beta 5 SSB was poor. In contrast, m beta 1'beta 2(ESWR) SSB complemented E. coli as well as EcoSSB. The inefficiently functioning SSBs resulted in an elongated cell/filamentation phenotype of E. coli. Taken together, our observations suggest that specific interactions within the DNA binding domain of the homotetrameric SSBs are crucial for their biological function.

Distributed Function Computation over Fields and Rings via Linear Compression of Sources

The setting considered in this paper is one of distributed function computation. More specifically, there is a collection of N sources possessing correlated information and a destination that would like to acquire a specific linear combination of the N sources. We address both the case when the common alphabet of the sources is a finite field and the case when it is a finite, commutative principal ideal ring with identity. The goal is to minimize the total amount of information needed to be transmitted by the N sources while enabling reliable recovery at the destination of the linear combination sought. One means of achieving this goal is for each of the sources to compress all the information it possesses and transmit this to the receiver. The Slepian-Wolf theorem of information theory governs the minimum rate at which each source must transmit while enabling all data to be reliably recovered at the receiver. However, recovering all the data at the destination is often wasteful of resources since the destination is only interested in computing a specific linear combination. An alternative explored here is one in which each source is compressed using a common linear mapping and then transmitted to the destination which then proceeds to use linearity to directly recover the needed linear combination. The article is part review and presents in part, new results. The portion of the paper that deals with finite fields is previously known material, while that dealing with rings is mostly new.Attempting to find the best linear map that will enable function computation forces us to consider the linear compression of source. While in the finite field case, it is known that a source can be linearly compressed down to its entropy, it turns out that the same does not hold in the case of rings. An explanation for this curious interplay between algebra and information theory is also provided in this paper.

Abstract Characteristic Function

The characteristic function for a contraction is a classical complete unitary invariant devised by Sz.-Nagy and Foias. Just as a contraction is related to the Szego kernel k(S)(z, w) = ( 1 - z(w)over bar)- 1 for |z|, |w| < 1, by means of (1/k(S))( T, T *) = 0, we consider an arbitrary open connected domain Omega in C(n), a kernel k on Omega so that 1/k is a polynomial and a tuple T = (T(1), T(2), ... , T(n)) of commuting bounded operators on a complex separable Hilbert spaceHsuch that (1/k)( T, T *) >= 0. Under some standard assumptions on k, it turns out that whether a characteristic function can be associated with T or not depends not only on T, but also on the kernel k. We give a necessary and sufficient condition. When this condition is satisfied, a functional model can be constructed. Moreover, the characteristic function then is a complete unitary invariant for a suitable class of tuples T.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Barrier crossing by a flexible long chain molecule - The kink mechanism

The problem and related earlier work All the above problems involve the passage of a long chain molecule, through a region in space, where the free energy per segment is higher, thus effectively presenting a barrier for the motion of the molecule. This is what we refer to as the Kramers proble...

From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Learning polyhedral classifiers using logistic function

In this paper we propose a new algorithm for learning polyhedral classifiers. In contrast to existing methods for learning polyhedral classifier which solve a constrained optimization problem, our method solves an unconstrained optimization problem. Our method is based on a logistic function based model for the posterior probability function. We propose an alternating optimization algorithm, namely, SPLA1 (Single Polyhedral Learning Algorithm1) which maximizes the loglikelihood of the training data to learn the parameters. We also extend our method to make it independent of any user specified parameter (e.g., number of hyperplanes required to form a polyhedral set) in SPLA2. We show the effectiveness of our approach with experiments on various synthetic and real world datasets and compare our approach with a standard decision tree method (OC1) and a constrained optimization based method for learning polyhedral sets.

DeNOx Study in Diesel Engine Exhaust Using Barrier Discharge Corona Assisted by V2O5/TiO2 Catalyst

A plasma-assisted catalytic reactor was used to remove nitrogen oxides (NOx) from diesel engine exhaust operated under different load conditions. Initial studies were focused on plasma reactor (a dielectric barrier discharge reactor) treatment of diesel exhaust at various temperatures. The nitric oxide (NO) removal efficiency was lowered when high temperature exhaust was treated using plasma reactor. Also, NO removal efficiency decreased when 45% load exhaust was treated. Studies were then made with plasma reactor combined with a catalytic reactor consisting of a selective catalytic reduction (SCR) catalyst, V2O5/TiO2. Ammonia was used as a reducing agent for SCR process in a ratio of 1:1 to NOx. The studies were focused on temperatures of the SCR catalytic reactor below 200°C. The plasma-assisted catalytic reactor was operated well to remove NOx under no-load and load conditions. For an energy input of 96 J/l, the NOx removal efficiencies obtained under no-load and load conditions were 90% and 72% respectively at an exhaust temperature of 100°C.

Treatment of NOx from Diesel Engine Exhaust by Dielectric Barrier Discharge Method

This paper reports improved performance of discharge plasma in filtered engine exhaust treatment. Our paper deals about the removal of NOX emissions from the diesel exhaust by electric discharge plasma. For the treatment of diesel exhaust a new type of reactor referred to as crossflow dielectric barrier discharge reactor has been used, where the gas flow is perpendicular to the corona electrode. Experiments were conducted at different flow rates ranging from 2 l/min to 10 l/min. The discharge plasma assisted barrier discharge reactor has shown promising results in NOX removal at high flow rates.

Barrier Inhomogeneity and Electrical Properties of InN Nanodots/Si Heterojunction Diodes

The electrical transport behavior of n-n indium nitride nanodot-silicon (InN ND-Si) heterostructure Schottky diodes is reported here, which have been fabricated by plasma-assisted molecular beam epitaxy. InN ND structures were grown on a 20 nm InN buffer layer on Si substrates. These dots were found to be single crystalline and grown along [0 0 0 1] direction. Temperature-dependent current density-voltage plots (J-V-T) reveal that the ideality factor (eta) and Schottky barrier height (SBH) (Phi(B)) are temperature dependent. The incorrect values of the Richardson constant (A**) produced suggest an inhomogeneous barrier. Descriptions of the experimental results were explained by using two models. First one is barrier height inhomogeneities (BHIs) model, in which considering an effective area of the inhomogeneous contact provided a procedure for a correct determination of A**. The Richardson constant is extracted similar to 110 A cm(-2) K(-2) using the BHI model and that is in very good agreement with the theoretical value of 112 A cm(-2) K(-2). The second model uses Gaussian statistics and by this, mean barrier height Phi(0) and A** were found to be 0.69 eV and 113 A cm(-2) K(-2), respectively.

Treatment of NOx from Diesel Engine Exhaust by Dielectric Barrier Discharge Method

This paper reports improved performance of advantages when compared to its counterpart as it is cost discharge plasma in filtered engine exhaust treatment. Our effective, low capital and operation costs, salable by- paper deals about the removal of NOX emissions from the diesel products, and integration with the existing systems. In this exhaust by electric discharge plasma. For the treatment of diesel paper we describe an alternate reactor geometry referred to exhaust a new type of reactor referred to as cross-flow dielectric as cross-flow DBD reactor, where the exhaust gas flow barrier discharge reactor has been used, where the gas flow is perpendicular to the wire-cylinder reaction chamber. This perpendicular to the corona electrode. Experiments were reactor is used to treat the actual exhaust of a 3.75 kW diesel- conducted at different flow rates ranging from 2 l/min to 10 l/ generator set. The main emphasis is laid on the NOX treatment min. The discharge plasma assisted barrier discharge reactor of diesel engine exhaust. Experiments were carried out at has shown promising results in NOX removal at high flow rates.

Construction of equivalent circuit of a transformer winding from driving-point impedance function - analytical approach

Analytical solution is presented to convert a given driving-point impedance function (in s-domain) into a physically realisable ladder network with inductive coupling between any two sections and losses considered. The number of sections in the ladder network can vary, but its topology is assumed fixed. A study of the coefficients of the numerator and denominator polynomials of the driving-point impedance function of the ladder network, for increasing number of sections, led to the identification of certain coefficients, which exhibit very special properties. Generalised expressions for these specific coefficients have also been derived. Exploiting their properties, it is demonstrated that the synthesis method essentially turns out to be an exercise of solving a set of linear, simultaneous, algebraic equations, whose solution directly yields the ladder network elements. The proposed solution is novel, simple and guarantees a unique network. Presently, the formulation can synthesise a unique ladder network up to six sections.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Chitosan-polyvinyl alcohol-sulfonated polyethersulfone mixed-matrix membranes as methanol-barrier electrolytes for DMFCs

Chitosan (CS)-polyvinyl alcohol (PVA) cross-linked with sulfosuccinic acid (SSA) and modified with sulfonated polyethersulfone (SPES) mixed-matrix membranes are reported for their application in direct methanol fuel cells (DMFCs). Polyethersulfone (PES) is sulfonated by chlorosulfonic acid and factors affecting the sulfonation reaction, such as time and temperature, are studied. The ion-exchange capacity, degree of sulfonation, sorption, and proton conductivity for the mixed-matrix membranes are investigated. The mixed-matrix membranes are also characterised for their mechanical and thermal properties. The methanol-crossover flux across the mixed-matrix membranes is studied by measuring the mass balance of methanol using the density meter. The methanol cross-over for these membranes is found to be about 33% lower in relation to Nafion-117 membrane. The DMFC employing CS-PVA-SPES mixed-matrix membrane with an optimum content of 25 wt % SPES delivers a peak power-density of 5.5 mW cm-2 at a load current-density of 25 mA cm-2 while operating at 70 degrees C. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Insights into differential modulation of receptor function by hinge region using novel agonistic lutropin receptor and inverse agonistic thyrotropin receptor antibodies

We report two antibodies, scFv 13B1 and MAb PD1.37, against the hinge regions of LHR and TSHR, respectively, which have similar epitopes but different effects on receptor function. While neither of them affected hormone binding, with marginal effects on hormone response, scFv 13B1 stimulated LHR in a dose-dependent manner, whereas MAb PD1.37 acted as an inverse agonist of TSHR. Moreover, PD1.37 could decrease the basal activity of hinge region CAMs, but had varied effects on those present in ECLs, whereas 13B1 was refractory to any CAMs in LHR. Using truncation mutants and peptide phage display, we compared the differential roles of the hinge region cysteine box-2/3 as well as the exoloops in the activation of these two homologus receptors. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.