In Silico Biology - Volume 8, issue 3-4

Authors: Sharma, Babita

Article Type: Research Article

Abstract: Malaria is caused by the protozoan Plasmodium. The parasite Plasmodium completes its life cycle inside two hosts, i.e. human and mosquito. Among all known Plasmodium species, Plasmodium falciparum is known to cause maximum mortality. Various studies done on the mosquito stages of the parasite suggest that the proteins present on the parasite's surface are responsible for its survival under the adverse conditions prevailing in the mosquito midgut. When human blood containing Plasmodium …gametocytes enters the mosquito gut, the gametocytes form gametes which then fuse to form zygotes. At this stage two closely related proteins, Pfs25 and Pfs28 are expressed on the surface of the parasite which continue to express up to the young oocyst stage. These proteins present on zygotes, ookinetes and young oocysts of Plasmodium are categorized in P25 and P28 families and are well known malaria vaccine candidate proteins. In this study, we have done sequence analysis, homology modeling and docking studies of a typical member of the P25 family of ookinete surface protein, i.e. Pfs25 from Plasmodium falciparum. We have built a 3D model of Pfs25 based on the X-ray crystallographic structure of Pvs25 from Plasmodium vivax. Also we have modeled the Fv region of the malaria transmission blocking monoclonal antibody 4B7. This antibody is the transmission blocking monoclonal antibody for Pfs25 protein. Pfs25 and 4B7 scFv (single chain variable fragment only) docking results indicate that EGF domain III of the Pfs25 protein interacts with the scFv region of modeled 4B7 antibody forming seven hydrogen bonds out of which six are formed with heavy chain of scFv region. Docking results of Pfs25 with gamma chain of laminin also suggest a possible role of Pfs25 protein in host parasite interaction. Show more

Keywords: Homology modeling, docking, EGF-domain, GPI anchor, Pfs25

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 193-206, 2008

Authors: Unni Vinod, Palakkad Krishnan | Venkatesh, Kareenhalli V.

Article Type: Research Article

Abstract: Occurrence of multiple upstream activation sites (UASs) is a structural motif that is observed within the promoter of eukaryotic genes for coordinating gene expression. Transcriptional activation depends on the ability of transcriptional activators to bind to its specific UASs, which are kept inaccessible due to the nucleosomal organization of the chromatin. Targeting of chromatin remodeling complexes by a sequence specific transcriptional activator is shown to be detrimental for transcriptional initiation. Here, we analyze …such a regulatory structure involving ordered recruitment of transcriptional activators and chromatin remodeling complexes with respect to activation of a flocculin gene, FLO11 involved in the filamentous growth to gain insights into its regulation. We develop a steady state model for the transcriptional regulation of FLO11 by primary transcriptional activators Flo8p, Ste12p, Tec1p and Mss11p, which are under a complex network comprising of cAMP and MAPK pathways. Our analysis predicts that the FLO11 promoter should undergo varying chromatin remodeling activity from partial to complete disassembly depending upon the concentration of Ste12p. This variation should be sensitive and sharply shift to saturate with Ste12p concentration. Overexpression of Ste12p can increase the overall chromatin remodeling activity by increasing the local concentration of remodeling complex through active recruitment. Further, we demonstrate that the chromatin remodeling activity brings about amplification of cAMP and MAPK signal and in absence of either of the signals, the input signal required for the other increases. We also discuss the results obtained from our steady state analysis in respect to other eukaryotic genes. Show more

Keywords: Multiple transcriptional activators, FLO11, STA1, chromatin remodeling, signal integration

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 207-222, 2008

Authors: Pundhir, Sachin | Vijayvargiya, Hemant | Kumar, Anil

Article Type: Research Article

Abstract: Pathogenicity Islands (PAIs) are the sub-sets of Genomic Islands (GIs) that are acquired by horizontal gene transfer (HGT) and are generally shown to have a significant deviation in G + C, dinucleotide or codon frequency from core genome. Major approaches used for PAI identification are based on composition bias and/or similarity with known PAIs. These approaches either limit the search to GIs or to regions similar to previously annotated PAIs. PredictBias is a web application for …the identification of genomic and pathogenicity islands in prokaryotes based on composition bias, presence of insertion elements, proximity with virulence-associated genes and absence in related non-pathogenic species. A profile database of virulence factors (VFPD) has been developed using 213 protein families associated to virulence retrieved from Pfam and PRINTS database. PredictBias performs a RPSBLAST search for regions with significant composition bias against VFPD. If a region encodes for at least one protein related to virulence then it is marked as potential PAI (biased-composition) otherwise as GI. Regions involved in virulence but having unsuspicious composition bias due to ancient HGT are identified by scanning genome segments (8 ORFs) with more than four significant hits to VFPD and are marked as potential PAI (unbiased-composition). The relative absence of potential PAIs in related non-pathogenic species can be investigated using 'compare genome feature' of PredictBias that further aids in validating the results and defining boundaries for PAIs. Performance measure analysis showed that the output of PredictBias is in agreement with the known findings. PredictBias is available at www.davvbiotech.res.in/PredictBias. Show more

Keywords: Pathogenicity islands, genomic islands, web server

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 223-234, 2008

Authors: Krishnadev, Oruganty | Srinivasan, Narayanaswamy

Article Type: Research Article

Abstract: Lack of large-scale efforts aimed at recognizing interactions between host and pathogens limits our understanding of many diseases. We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection. This dataset of putative in vitro interactions …is combined with large-scale datasets of expression and sub-cellular localization. This integrated approach reduces drastically the number of false positives and hence can be used for generating testable hypotheses. We could recognize known interactions previously suggested in the literature. We also propose new predictions which involve interactions of some of the parasite proteins of yet unknown function. The method described is generally applicable to any host-pathogen pair and can thus be of general value to studies of host-pathogen protein-protein interactions. Show more

Keywords: Host-pathogen interactions, protein-protein interactions, data integration method

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 235-250, 2008

Authors: Ram, Siya | Singh, Ram Lakhan | Shanker, Rishi

Article Type: Research Article

Abstract: Rapid diagnostics and risk assessment of the pathogens is possible by Real-Time Polymerase Chain Reaction (PCR) probes like TaqMan, Molecular Beacon (MB) and FRET. However, validation of such probes for real-life samples is an expensive and time consuming proposition. Hence, development and comparison of real-time probes in silico can be the first step in selection of most appropriate probe chemistry. The virulence genes specific for a model pathogen, Escherichia coli O157:H7, transmitted worldwide by …contaminated water and food, were chosen to compare probe chemistries. MB was observed to be the best probe chemistry for virulence genes stx1, stx2 and eae, while FRET was preferred for hlyA gene, based on T_{m} and free energy values for self-dimer, hairpin and cross-dimer. Secondary structure analysis indicated that MB design was flexible and less dependent on nucleotide arrangement and repetitive sequences in the genes compared to TaqMan and FRET probes. In addition, multiplexed MB probes could be a feasible option using a single non-fluorescent quencher for high throughput diagnostics. Show more

Keywords: Real-time PCR, probes, in silico PCR, Escherichia coli

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 251-259, 2008

Authors: Anand, Sudha | Anbarasu, Anand | Sethumadhavan, Rao

Article Type: Research Article

Abstract: We have explored the roles played by C-H…π hydrogen bonds in interleukins. Main-chain to side-chain C-H…π interactions are the predominant type of interactions in interleukins. There was an average of 15 C-H…π interactions per protein and also there was an average of one significant C-H…π interaction for every 14 residues in the interleukins investigated. Significant contribution to C-H…π interactions was only from Asp, Gly, His, Lys, Phe, Pro, Ser, Thr, Trp and Tyr in interleukins. Trp …contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain 5 member aromatic ring and side-chain to side-chain C-H…π interactions. Short and medium-range C-H…π interactions are the predominant type of interactions in interleukins. More than 50% of C-H…π interacting residues had a conservation score of ⩾ 6. Significant percentage of C-H…π interacting residues had one or more stabilization centers; hence these residues may also contribute additional stability to structure of interleukins. Show more

Keywords: C-H…π interactions, solvent accessibility, short range interactions, stabilization centers, interleukins

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 261-273, 2008

Authors: Sengupta, Dipankar | Verma, Deeptak | Naik, Pradeep Kumar

Article Type: Research Article

Abstract: Nevirapine and its synthetic analogues, a class of non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), have been the objective of numerous studies focused to prepare better and safer anti-HIV drugs. We developed a library of nevirapine analogues (47) using combinatorial design and with structural modification at X, Y and R substituents in the parent structure of nevirapine. Their molecular interactions and binding affinities with reverse transcriptase (3HVT and 1VRT) have been studied using …the docking-molecular mechanics based generalized Born/surface area (MM-GB/SA) solvation model. Final screening of these analogues is based on absorption, distribution, metabolism and excretion (ADME) properties. The proposed NNRTI analogues dock in a similar position and orientation in the active site of RT as co-crystallized nevirapine. In addition a linear correlation was observed between the calculated free energy of binding (FEB) and pIC_{50} for the inhibitors with correlation coefficient R^{2} of 0.9948, suggesting that the docked structure orientation and the interaction energies are reasonable. The electrostatic energy terms estimated by GB/SA showed important role on prediction of binding affinity (R^{2} = 17.2%. Since we used two different HIV-1 RT crystal structures (3HVT and 1VRT), which are at different resolution (2.9 and 2.2 Å, we propose that structures with resolutions better than 3 Å can be used to produce reasonable docking results. Few analogues showed high binding affinity and activity with RT in compare to co-crystallized nevirapine. These analogues also well qualify ADME properties and showed good druggable characters. The work addressed to modify the X, Y and R substituents in the nevirapine scaffold to prepare synthetic analogues for second generation drug development against RT. Show more

Keywords: HIV-I RT, nevirapine and its analogues, docking, glide, MM-GB/SA, free energy of binding, ADME

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 275-289, 2008

Authors: Wen, Jiayu | Frickey, Tancred | Weiller, Georg F.

Article Type: Research Article

Abstract: Identification and analysis of miRNAs enhances our understanding of the important roles that small RNAs play in complex regulatory networks. It is often difficult to perform large-scale validation of miRNA expression that is predicted from genomic regions. Expressed transcripts provide an alternative resource to facilitate identification of miRNAs and their targets. We developed a computational pipeline to scan for miRNA genes from polyadenylated transcripts that were associated with limited protein coding potentials, …corresponding to the intergenic regions of Medicago truncatula genomic sequences. Each predicted miRNA was required to have a near perfect match with target genes. We also searched for miRNA conservation in other plant species, clustered highly similar miRNAs, and provided a functional classification of target genes. The data is represented in the Medicago-MIRATdb (MiRNA And Target gene Data Base). The database provides detailed information on the sequences of the predicted miRNAs, their precursors, and potential target genes. It also details sequence source information such as the EST library, tissue category, and the number of EST clones. Information regarding miRNA conservation in other species, functional classification of target genes, and clusters of similar miRNAs is also provided. The web interface to the database provides researchers with the ability to narrow their search for miRNAs and target genes of interest by using a variety of filters. To our knowledge, this work represents the first systematic effort to identify candidate miRNAs and targets in the model legume M. truncatula. The database is freely accessible at http://bioinfoserver.rsbs.anu.edu.au/utils/MIRATdb/Medicago/v1/. Show more

Keywords: miRNAs, plant, Medicago truncatula, model legume, database, mRNA-like ncRNA, ncRNA, EST

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 291-306, 2008

Authors: Kanagarajadurai, Karuppiah | Sowdhamini, Ramanathan

Article Type: Research Article

Abstract: Interleukin-8 and related chemokines are small proteins that bind to receptors belonging to the large family of G-protein-coupled receptors. They can cause migration of cells like neutrophils and eosinophils and some of them are implicated in angiogenic diseases. More than 40 subfamilies of these ligands are known that share poor sequence similarity and display receptor specificity. There is very little structural information about the mode of binding between ligands and the receptors. We have employed multi-fold …sensitive sequence search methods to provide a repertoire of 252 putative interleukin-8 proteins and homologues, which are shared across humans, aves and fish. The sequences can be organized into five major known clusters. The propensity of occurrence of certain amino acid alphabets is found to be specific in different locations of the polypeptide fold. The sequence dispersion is also observed to be cluster-specific when examined by Evolutionary Trace procedure. Amino acid alphabet analysis and Evolutionary Trace procedure reveal cluster-specific amino acid distribution that provide clues about how the small fold of the ligand could display remarkable receptor specificity. We notice regions, like the β_{1} -β_{2} loop of the fold, that are potentially involved in receptor recognition and specificity that could be potential sites for residue mutations. Systematic studies of the distribution patterns enable better understanding of the evolution and molecular recognition of this important and diverse protein superfamily. Show more

Keywords: GPCR ligand superfamily, clustering by phylogeny, structure-function relationship, Amino Acid Alphabet propensity

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 307-330, 2008

Authors: Sharma, Vibhuti | Gupta, Preeti | Dixit, Aparna

Article Type: Research Article

Abstract: Aeromonas hydrophila is a major pathogen both of aquatic and terrestrial organisms, including humans. Infection with A. hydrophila results in severe economic losses to the aquaculture industry. In humans, Aeromonas hydrophila infections are known to cause gastroenteritis and wound infections. Investigations for developing a potential vaccine for its control are underway. The availability of the complete sequence information of A. hydrophila strain ATCC 7966^{T} genome has made it possible to carry …out the in silico analysis of its genome for various aspects of its biology. Keeping in view the possible risks that A. hydrophila poses to humans, in silico analysis of the A. hydrophila genome was carried out for the identification of potential vaccine and drug targets. Our study revealed 2097 genes which are non-homologous to human genome. Screening these genes using the Database of Essential Genes (DEG) resulted in the identification of 379 genes as essential genes of the bacteria. Further analysis of the identified essential genes, using the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways database, revealed 87 enzymes of A. hydrophila that may be used as drug targets, as they are not present in humans. Of these, 15 enzymes belong to pathways present only in the bacteria, whereas 72 enzymes are from the pathways that are common to both human and the bacteria. These can be used as a platform for further investigation to develop effective drugs against A. hydrophila. Show more

Keywords: Aeromonas hydrophila, Homo sapiens, comparative microbial genomics, KEGG, homology, potential drug targets, enzyme targets

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 331-338, 2008

Authors: Akiyama, Kenji | Chikayama, Eisuke | Yuasa, Hiroaki | Shimada, Yukihisa | Tohge, Takayuki | Shinozaki, Kazuo | Hirai, Masami Yokota | Sakurai, Tetsuya | Kikuchi, Jun | Saito, Kazuki

Article Type: Research Article

Abstract: PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research and analysis workflows ranging from metabolome to transcriptome analysis. The site provides access to a growing collection of standardized measurements of metabolites obtained by using NMR, GC-MS, LC-MS, and CE-MS, and metabolomics tools that support related analyses (SpinAssign for the identification of metabolites by means of NMR, KNApSAcK for searches within metabolite …databases). In addition, the transcriptomics tools provide Correlated Gene Search, and Cluster Cutting for the analysis of mRNA expression. Use of the tools and database can contribute to the analysis of biological events at the levels of metabolites and gene expression, and we describe one example of such an analysis for Arabidopsis thaliana using the batch-learning self-organizing map (BL-SOM), which is provided via the Web site. Show more

Keywords: Metabolome, transcriptome, correlation analysis, spectrum database, analytical platform

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 339-345, 2008

Authors: Kamasawa, Masami | Horiuchi, Jun-ichi

Article Type: Research Article

Abstract: A large-scale analysis of human polyadenylation signals was carried out in silico. The most canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in human genes were used to search for polyadenylation signals in the terminal sequences. Out of 18,277 poly(A) sites that were identified from 26,414 human genes, 82.5% of the sites were found to contain at least one of these 12 hexamers as a polyadenylation signal within 40 nucleotides upstream of …the poly(A) site. The rest (17.5%) did not contain any of these hexamers, which suggests the existence of yet unknown signals. A total of 20,347 terminal sequences in close proximity to 12 polyadenylation signals were collected using modified EST clustering technique to establish a large-scale database of polyadenylation signals. To characterize the 12 hexamers, the locations of polyadenylation signals that were identified as "authentic" and the uracil contents of the downstream region of the signal were examined. Based on this analysis, the 11 variants of the canonical AAUAAA were identified as possibly forming "functional" signals as AAUAAA. Moreover, the observed frequency of 41.9% for AAUAAA was significantly lower than those of other reports, suggesting that the non-canonical variants are more important in the polyadenylation process than frequently recognized. Since the poly(A) sites processed by those non-canonical variants have not been generally annotated in major gene databases, it is important to determine whether the variant hexamers could work as polyadenylation signals that may be responsible for generating heterogeneity of mRNAs by alternative polyadenylation. Show more

Keywords: Polyadenylation signal, poly(A) site, downstream sequence element, upstream sequence element, single-nucleotide variants, 3'-untranslated region

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 347-361, 2008

Authors: Khalid, Sabah | Khan, Mohsin | Gorle, Chandrasekhar Babu | Fraser, Karl | Wang, Ping | Liu, Xiaohui | Li, Suling

Article Type: Research Article

Abstract: Microarray gene expression datasets are continually being placed in public repositories. As a result, one of the most important emerging challenges is that which enables researchers to take full advantage of such previously accumulated data to discover or validate common genes in similar biological systems. In light of this we have designed the MaXlab software to not only cross-compare available array data from different laboratories but also extract further knowledge from gene expression patterns embedded within …published data. More importantly MaXlab offers a flexible and automated solution applicable for microarray technologies including cDNA and Affymetrix gene chips generating expression profiles for common genes with biological significance. We have identified several sets of genes previously unknown to be commonly expressed across studies investigating related biological questions. Among them is the identification of 17 genes involved in the dysregulation of immune tolerance including the crucial transcription factor Egr2. In addition, we have identified 175 genes commonly expressed in basal and luminal breast tumours in response to the chemotherapeutic drug doxorubicin. The universal expression and characterisation of these encouraging genes identified through MaXlab suggests that they may play a common role in the mechanism of disease and hence act as an incentive for further investigation for identifying potential therapeutic targets. Overall, MaXlab is an attractive application for molecular biologists extracting the intersection between microarray datasets together with the gene expression profiles, from which biologists are able to infer further biological insights. The software together with file formats and additional material is freely available at http://www.immuno-software.org. Show more

Keywords: Microarray, cross-comparison, meta-analysis, multi-platform, data-fusion

Citation: In Silico Biology, vol. 8, no. 3-4, pp. 363-376, 2008