Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Markov Chain Model for Cracking Behavior of Reinforced Concrete Beams

In this paper, nonhomogeneous Markov chains are proposed for modeling the cracking behavior of reinforced concrete beams subjected to monotonically increasing loads. The model facilitates prediction of the maximum crackwidth at a given load given the crackwidth at a lower load level, and thus leads to a better understanding of the cracking phenomenon. To illustrate the methodology developed, the results of three reinforced concrete beams tested in the laboratory are analyzed and presented.

Grid interfacing of a photovoltaic system using a chain cell converter

With the rapid development of photovoltaic system installations and increased number of grid connected power systems, it has become imperative to develop an efficient grid interfacing instrumentation suitable for photovoltaic systems ensuring maximum power transfer. The losses in the power converter play an important role in the overall efficiency of a PV system. Chain cell converter is considered to be efficient as compared to PWM converters due to lower switching losses, modularized circuit layout, reduced voltage rating of the converter switches, reduced EMI. The structure of separate dc sources in chain cell converter is well suited for photovoltaic systems as there will b several separate PV modules in the PV array which can act as an individual dc source. In this work, a single phase multilevel chain cell converter is used to interface the photovoltaic array to a single phase grid at a frequency of 50Hz. Control algorithms are developed for efficient interfacing of the PV system with grid and isolating the PV system from grid under faulty conditions. Digital signal processor TMS320F 2812 is used to implement the control algorithms developed and for the generation of other control signals.

An unusual C-H center dot center dot center dot O hydrogen bond mediated reversal of polypeptide chain direction in a synthetic peptide helix

An unusual C-terminal conformation has been detected in a synthetic decapeptide designed to analyze the stereochemistry of helix termination in polypeptides. The crystal structure of the decapeptide Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe reveals a helical segment spanning residues 1-7 and helix termination by formation of a Schellman motif, generated by (D)Ala(8) adopting the left-handed helical (alpha(L)) conformation. The extended conformation at (D)Leu(9) results in a compact folded structure, stabilized by a potentially strong C-H ... O hydrogen bond between Ala(4) (CH)-H-alpha and (D)Leu(9)CO. The parameters for C-H ... O interaction are Ala(4) (CH)-H-alpha .. O=C (D)Leu(9) distance 3.27 Angstrom C-alpha-H .. O angle 176 degrees, and O .. H-alpha distance 2.29 Angstrom. This structure suggests that insertion of contiguous D-residues may provide a handle for the generation of designed structures containing more than one helical segment folded in a compact manner. (C) 2000 Academic Press.

Characterization of a mercury-reducing Bacillus cereus strain isolated from the Pulicat Lake sediments, south east coast of India

Pulicat Lake sediments are often severely polluted with the toxic heavy metal mercury. Several mercury-resistant strains of Bacillus species were isolated from the sediments and all the isolates exhibited broad spectrum resistance (resistance to both organic and inorganic mercuric compounds). Plasmid curing assay showed that all the isolated Bacillus strains carry chromosomally borne mercury resistance. Polymerase chain reaction and southern hybridization analyses using merA and merB3 gene primers/probes showed that five of the isolated Bacillus strains carry sequences similar to known merA and merB3 genes. Results of multiple sequence alignment revealed 99% similarity with merA and merB3 of TnMERI1 (class II transposons). Other mercury resistant Bacillus species lacking homology to these genes were not able to volatilize mercuric chloride, indicating the presence of other modes of resistance to mercuric compounds.

Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Reactions of bis(isonitrosoethylacetoacetato)palladium(II) with straight chain aliphatic primary amines influence of concentration of the reacting amines on the nature of the products

Reactions of bis(isonitrosoethylacetoacetato)palladium(II), Pd(IEAA)2,with straight chain non-bulky alkylamines, RNH2(R = CH3, C2H5, n-C3H7or n-C4H9) in the mole ratio 1:1 gave bis (B-alkylisonitrosoethylacetoacetateimino)Palladium(II), Pd(R-IEAI)2. In this reaction the coordinated carbonyl groups of Pd(IEAA)2 undergo condensation with amines fo rming Schiff bases (>CNR). On the other hand, the reactions of Pd(IEAA)2 with a large excess of amine yielded N-alkylamido bridgedisonitrosoethylacetoacetatedipalladium(II), μ-(NHR)2[Pd(IEAA)]2 complexes. The complexes are characterized by elemental analyses, magnetic susceptib ility, i.r., p.m.r. and in some cases, nitrogen 1s X-ray photoelectron and mass spectral studies.

Characterization of a mercury-reducing Bacillus cereus strain isolated from the Pulicat Lake sediments, south east coast of India

Pulicat Lake sediments are often severely polluted with the toxic heavy metal mercury. Several mercury-resistant strains of Bacillus species were isolated from the sediments and all the isolates exhibited broad spectrum resistance (resistance to both organic and inorganic mercuric compounds). Plasmid curing assay showed that all the isolated Bacillus strains carry chromosomally borne mercury resistance. Polymerase chain reaction and southern hybridization analyses using merA and merB3 gene primers/probes showed that five of the isolated Bacillus strains carry sequences similar to known merA and merB3 genes. Results of multiple sequence alignment revealed 99% similarity with merA and merB3 of TnMERI1 (class II transposons). Other mercury resistant Bacillus species lacking homology to these genes were not able to volatilize mercuric chloride, indicating the presence of other modes of resistance to mercuric compounds.

X-ray studies on crystalline complexes involving amino acids and peptides. XV. Crystal structures of L-lysine D-glutamate and L-lysine D-aspartate monohydrate and the effect of chirality on molecular aggregation

L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

An algorithm to find distant repeats in a pair of protein sequences

Distant repeats between a pair of protein sequences can be exploited to study the various aspects of proteins such as structure-function relationship, disorders due to protein malfunction, evolutionary analysis, etc. An in-depth analysis of the distant repeats would facilitate to establish a stable evolutionary relation of the repeats with respect to their three-dimensional structure. To this effect, an algorithm has been devised to identify the distant repeats in a pair of protein sequences by essentially using the scores of PAM (Percent Accepted Mutation) matrices. The proposed algorithm will be of much use to researchers involved in the comparative study of various organisms based on the amino-acid repeats in protein sequences. (C) 2010 Elsevier B.V. All rights reserved.

Performance comparison of dynamical decoupling sequences for a qubit in a rapidly fluctuating spin bath

Avoiding the loss of coherence of quantum mechanical states is an important prerequisite for quantum information processing. Dynamical decoupling (DD) is one of the most effective experimental methods for maintaining coherence, especially when one can access only the qubit system and not its environment (bath). It involves the application of pulses to the system whose net effect is a reversal of the system-environment interaction. In any real system, however, the environment is not static, and therefore the reversal of the system-environment interaction becomes imperfect if the spacing between refocusing pulses becomes comparable to or longer than the correlation time of the environment. The efficiency of the refocusing improves therefore if the spacing between the pulses is reduced. Here, we quantify the efficiency of different DD sequences in preserving different quantum states. We use C-13 nuclear spins as qubits and an environment of H-1 nuclear spins as the environment, which couples to the qubit via magnetic dipole-dipole couplings. Strong dipole-dipole couplings between the proton spins result in a rapidly fluctuating environment with a correlation time of the order of 100 mu s. Our experimental results show that short delays between the pulses yield better performance if they are compared with the bath correlation time. However, as the pulse spacing becomes shorter than the bath correlation time, an optimum is reached. For even shorter delays, the pulse imperfections dominate over the decoherence losses and cause the quantum state to decay.

Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes

Sixteen million nucleotide sequence of genome of various organisms have been analysed to detect and study the extent of occurrence of simple repetitive sequences. Two sequence motifs (TG/CA)n and (CT/AG)n capable of adopting unusual DNA structures, left handed Z-conformation and triple-helical conformation respectively, are found to be abundant in rodent and human genomes, but almost completely absent in bacterial genome. (TG/CA)n and (CT/AG)n sequences are present mostly in the intron or 5'/3' flanking regions of the genes. The presence of such repeat motifs in genomic sequence of higher eukaryotes has been correlated with their possible functional significance in nucleosome organization, recombination and gene expression.

C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

The serendipitous observation of a C–Hcdots, three dots, centeredO hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).