Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Interactions of 3' terminal and 5' terminal regions of physalis mottle virus genomic RNA with its replication complex

Physalis mottle virus (PhMV) belongs to the tymogroup of positive-strand RNA viruses with a genome size of 6 kb. Crude membrane preparations from PhMV-infected Nicotiana glutinosa plants catalyzed the synthesis of PhMV genomic RNA from endogenously bound template. Addition of exogenous genomic RNA enhanced the synthesis which was specifically inhibited by the addition of sense and antisense transcripts corresponding to 3' terminal 242 nucleotides as well as the 5' terminal 458 nucleotides of PhMV genomic RNA while yeast tRNA or ribosomal RNA failed to inhibit the synthesis. This specific inhibition suggested that the 5' and 3' non-coding regions of PhMV RNA might play an important role in viral replication.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

An analysis on WDM components in flat gain regions of EDFA

Wavelength-division multiplexing (WDM) technology, by which multiple optical channels can be simultaneously transmitted at different wavelengths through a single optical fiber, is a useful means of making full use of the low-loss characteristics of optical fibers over a wide-wavelength region. The present day multifunction RADARs with multiple transmit receive modules requires various kinds of signal distribution for real time operation. If the signal distribution can be achieved through optical networks by using Wavelength Division Multiplexing (WDM) methods, it results in a distribution scheme with less hardware complexity and leads to the reduction in the weight of the antenna arrays In addition, being an Optical network it is free from Electromagnetic interference which is a crucial requirement in an array environment. This paper discusses about the analysis performed on various WDM components of distribution optical network for radar applications. The analysis is performed by considering the feasible constant gain regions of Erbium doped fiber amplifier (EDFA) in Matlab environment. This will help the user in the selection of suitable components for WDM based optical distribution networks.

A divide and conquer strategy for scaling weather simulations with multiple regions of interest

Accurate and timely prediction of weather phenomena, such as hurricanes and flash floods, require high-fidelity compute intensive simulations of multiple finer regions of interest within a coarse simulation domain. Current weather applications execute these nested simulations sequentially using all the available processors, which is sub-optimal due to their sub-linear scalability. In this work, we present a strategy for parallel execution of multiple nested domain simulations based on partitioning the 2-D processor grid into disjoint rectangular regions associated with each domain. We propose a novel combination of performance prediction, processor allocation methods and topology-aware mapping of the regions on torus interconnects. Experiments on IBM Blue Gene systems using WRF show that the proposed strategies result in performance improvement of up to 33% with topology-oblivious mapping and up to additional 7% with topology-aware mapping over the default sequential strategy.

On the absence of shear cracking and grain boundary cavitation in secondary tensile regions of Ti-6Al-4V-0.1B alloy during hot (alpha plus beta)-compression

Deformation instabilities, such as shear cracking and grain boundary cavitation, which are observed in the secondary tensile region of Ti-6Al-4V alloy during compressive deformation in the (+)-phase field, do not form in Ti-6Al-4V-0.1B alloy when processed under the same conditions. This has been attributed to the microstructural modifications, e.g. the absence of grain boundary and adjacent grain boundary retained layers and a lower proportion of 90(o)-misoriented -colonies that occur with boron addition.

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

Neonatal exposure to 17 beta-estradiol down-regulates the expression of synaptogenesis related genes in selected brain regions of adult female rats

Aims: Administration of estradiol or compounds with estrogenic activity to newborn female rats results in irreversible masculinization as well as defeminization in the brain and the animals exhibit altered reproductive behavior as adults. The cellular and molecular mechanism involved in inducing the irreversible changes is largely unknown. In the present study, we have monitored the changes in the expression of selected synaptogenesis related genes in the sexually dimorphic brain regions such as POA, hypothalamus and pituitary following 17 beta-estradiol administration to neonatal female rats. Main methods: Female Wistar rats which were administered 17 beta-estradiol on day 2 and 3 after birth were sacrificed 120 days later and the expression levels of genes implicated in synaptogenesis were monitored by semi-quantitative reverse transcription PCR. Since estradiol induced up-regulation of COX-2 in POA is a marker for estradiol induced masculinization as well as defeminization, in the present study only animals in which the increase in expression of COX-2 gene was observed in POA were included in the study. Key findings: Down-regulation of genes such as NMDA-2B, NETRIN-1, BDNF, MT-5 MMP and TNF-alpha was observed in the pre-optic area of neonatally E2 treated female rat brain but not in hypothalamus and pituitary compared to the vehicle- treated controls as assessed by RT-PCR and Western blot analysis. Significance: Our results suggest a possibility that down-regulation of genes associated with synaptogenesis in POA, may be resulting in disruption of the cyclical regulation of hormone secretion by pituitary the consequence of which could be infertility and altered reproductive behavior. (C) 2015 Elsevier Inc. All rights reserved.

The degree of predictability of earthquakes in several regions of China: statistical analysis of historical data

The stress release model, a stochastic version of the elastic-rebound theory, is applied to the historical earthquake data from three strong earthquake-prone regions of China, including North China, Southwest China, and the Taiwan seismic regions. The results show that the seismicity along a plate boundary (Taiwan) is more active than in intraplate regions (North and Southwest China). The degree of predictability or regularity of seismic events in these seismic regions, based on both the Akaike information criterion (AIC) and fitted sensitivity parameters, follows the order Taiwan, Southwest China, and North China, which is further identified by numerical simulations. (c) 2004 Elsevier Ltd. All rights reserved.

PICES Climate Change and Carrying Capacity Workshop on the Development of Cooperative Research in Coastal Regions of the North Pacific, October 17-18, 1997, Pusan, Republic of Korea

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Bag and size limit analyses for red drum in Northern and Southern Regions of the U.S. Atlantic

Assessments of the Atlantic red drum for the northern (North Carolina and north) and southern (South Carolina through east coast of Florida) regions along the U. S. Atlantic coast were recently completed. The joint Red Drum Technical Committee (SAFMC/ASMFC) selected the most appropriate catch matrix (incorporating an assumption on size of recreationally-released fish), selectivity of age 3 relative to age 2, and virtual population analysis (FADAPT). Given gear- and age-specific estimates of fishing mortality (F) for the 1992-1998 period, analyses were made of potential gains in escapement through age 4 and static spawning potential ratio (SPR) from further reductions in fishing mortality due to changes in slot and bag limits. Savings from bag limits were calculated given a particular slot size for the recreational fishery, with no savings for the commercial fisheries in the northern region due to their being managed primarily through a quota. Relative changes in catch-at-age estimates were used to adjust age-specific F and hence calculated escapement through age 4 and static SPR. Adjustment was made with the recreational savings to account for release mortality (10%, as in the stock assessment). Alternate runs for the northern region commercial fishery considered 25% release mortality for lengths outside the slot (instead of 0% for the base run), and 0% vs. 10% gain or loss across legal sizes in F. These results are summarized for ranges of bag limits with increasing minimum size limit (for fixed maximum size), and with decreasing maximum size limit (for fixed minimum size limit). For the southern region, a bag limit of one-fish per angler trip would be required to attain the stated target of 40% static SPR if the current slot limit were not changed. However, for the northern region, a bag limit of one-fish per angler trip appears to be insufficient to attain the stated target of 40% static SPR while maintaining the current slot limit. (PDF contains 41 pages)