Journal of proteomics & bioinformatics最新文献

{"title":"Normal Mode Analysis of Thermophilic Cellulase FnCel5A Using Elastic Network Models","authors":"S. Mohammad, F. Ali, M. Rahman, Asim Muhammad","doi":"10.4172/jpb.1000475","DOIUrl":"https://doi.org/10.4172/jpb.1000475","url":null,"abstract":"Normal mode analysis (NMA) based on elastic network models is an efficient, cost-effective and powerful, computational approach for characterizing protein flexibility and the resulting dynamics. In this study, we have analyzed a single protein structure, a hyperthermophylic enzyme (FnCel5A) with a given PDB ID: 3rjy, in order to calculate deformation energies, Eigenvalues, atomic fluctuations and displacements, and overlap and correlation matrices that display correlations among all of the C-alpha-atom motions in the FnCel5A structure. The WEBnm@ server was used to provide a quick automated computational low-frequency normal protein structure mode analysis. Single mode analysis using NMA has been applied on the web server, which can provide recently improved functionality for the single protein structures. This includes new visualization of protein motions, inter-amino acids correlations, and conformational transition analysis applying the overlap analysis. Furthermore, we have studied the structural and single mode FnCel5A (PDB: 3rjy) analysis in order to calculate the lowest and normal frequency protein modes. This study provides enough information about the loop flexibility and highest B-factors regions of FnCel5A which play an important role in rational and semi-rational designing to engineer this enzyme for improved activity.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a Pathway-Based 5-Gene Expression Signature for Predicting Outcomes in Gastric Cancer","authors":"Nikolay Alabi, Dropen Sheka, Mehul Gupta, S. Kannappan","doi":"10.4172/JPB.1000482","DOIUrl":"https://doi.org/10.4172/JPB.1000482","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying the Interaction between Copper-Zinc Superoxide Dismutase (Sod1) and its Copper Chaperone (Ccs1).","authors":"Stefanie D Boyd,&nbsp;Li Liu,&nbsp;Lee Bulla,&nbsp;Duane D Winkler","doi":"10.4172/jpb.1000473","DOIUrl":"https://doi.org/10.4172/jpb.1000473","url":null,"abstract":"<p><p>Immature copper-zinc superoxide dismutase (Sod1) is activated by its copper chaperone (Ccs1). Ccs1 delivers a single copper ion and catalyzes oxidation of an intra-subunit disulfide bond within each Sod1 monomer through a mechanistically ambiguous process. Here, we use residue specific fluorescent labeling of immature Sod1 to quantitate the thermodynamics of the Sod1•Ccs1 interaction while determining a more complete view of Ccs1 function. Ccs1 preferentially binds a completely immature form of Sod1 that is metal deficient and disulfide reduced (E, E-Sod1^SH). However, binding induces structural changes that promote high-affinity zinc binding by the Ccs1-bound Sod1 molecule. This adds further support to the notion that Ccs1 likely plays dual chaperoning roles during the Sod1 maturation process. Further analysis reveals that in addition to the copper-dependent roles during Sod1 activation, the N- and C-terminal domains of Ccs1 also have synergistic roles in securing both Sod1 recognition and its own active conformation. These results provide new and measurable analyses of the molecular determinants guiding Ccs1-mediated Sod1 activation.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/jpb.1000473","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36262893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"“ESI-MSBioinformatics Studies on Crosslinking of αA-Crystallin and Lysozyme using a New Small Aryl Azido-N-HydroxySuccinimidyl Heterobifunctional Crosslinker based on a Metabolite of the Alternative Kynurenine Pathway”.","authors":"S. K. Thakur, Shreya C. Pal, Ankur Kumar, R. Goel, S. Eswaran","doi":"10.4172/0974-276X.1000486","DOIUrl":"https://doi.org/10.4172/0974-276X.1000486","url":null,"abstract":"The use of a new small aryl azido-N-Hydroxysuccinimidyl heterobifunctional crosslinker for crosslinking of αAcrystallin and lysozyme is described here. The crosslinker is based on the small molecule, 3-hydroxy anthranilic acid (3HAA) a part of the kynurenine pathway in Tryptophan metabolism. Enhanced amounts of 3HAA are found in disease states in the human body. The new crosslinker contains a photo labile azido group and an amine reactive, N-hydroxy succinimide (NHS) group. Small crosslinkers capture interacting protein interfaces better, while the larger ones are more useful for identifying interacting partners. Our earlier work has shown that aryl azides in this series lead to ‘long lived’ transients allowing for increased intermolecular reaction rates, otherwise difficult to achieve. Using this crosslinker, successful crosslinking of αA-Crystallin & lysozyme has been demonstrated in two steps i. e. incubation followed by photolysis (366 nm, 6W UV lamp). Previous studies on αACrystallin have mostly used only homobifunctional crosslinkers. As hypothesized by us, the use of a heterobifunctional crosslinker has indeed led to more efficient crosslinking. This has been confirmed using SDS-PAGE, ESI-MS/MS (following trypsinization of the homo and hetero ‘dimer’ bands) and use of StavroX 3.6.0.1, the bioinformatics software especially suited for analyzing intermolecular crosslinking. These investigations are expected to lead to a better understanding of the role of αA-Crystallin in chaperoning mechanism and in cataractogenesis.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Annotating the Function of Protein-coding Genes Based on Gene Ontology Terms of Neighboring Co-expressed Genes","authors":"Vuong Tran, A. Barghash, V. Helms","doi":"10.4172/JPB.1000468","DOIUrl":"https://doi.org/10.4172/JPB.1000468","url":null,"abstract":"Proteins are of key importance in virtually every cellular process but many proteins have still not been annotated with functions due to experimental difficulties involved with functional assays. To address this problem, many computational methods based on sequence homology, three-dimensional structure, genomic context, and gene expression were developed to predict functions of proteins. Here, we tested the performance of a novel approach that is motivated by the concept of bacterial operons. To predict the substrate specificities of membrane transporters we combined genomic context-based methods with Gene Ontology and gene expression data whereby using SVM for classifying genes. We found that in Escherichia coli, the substrate-specificities of membrane transporters can be predicted with ca. 90% accuracy from the biological functions of co-expressed neighboring genes. In Saccharomyces cerevisiae and Homo sapiens, the respective accuracies are lower at around 80%. When applying the same strategy to enzymes of four metabolic classes of Escherichia coli, we found lower accuracies of 77% (2-class prediction) and 68% (4-class prediction), respectively. This suggests that transfer of functional associations between co-expressed neighbor genes may be case-specific","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microarray Gene Expression Statistical Data Analysis of Three Different Clinical Forms of Human Tuberculosis Stimulated Samples in the Bioconductor R Package","authors":"U. Shittu, M. A. Naser, Z. Idris, Maryam Sa","doi":"10.4172/JPB.1000465","DOIUrl":"https://doi.org/10.4172/JPB.1000465","url":null,"abstract":"The overall aim of this research identified and explores the usage of microarray gene expression statistical tools available in Bioconductor R package for image visualization, data quality control, background correction, summarization, normalization and identification of highly differential gene expression from microarray gene expression data of human tuberculosis infections. The stimulated samples with phosphate buffered saline (PBS) of human tuberculosis microarray gene expression data such include pulmonary TB infection (PTB), meningeal TB infection (TBM) and latent TB infection (LTB) image data were collected from GEO-NCBI (Gene Expression Omnibus-National Centre for Biotechnical information’s) database in a form of CEL file format with Accession number: GSE11199 and all the analyses were performed in the R packages. These analyses identified and explore the use of AffyQCReport tool, affycoretools, PCA, MAS 5.0 and GCRMA for microarray gene expression data pre-processing and for the identification of highly significantly expressed genes, LIMMA was used and explore as a statistical tool for such analysis. The statistical analysis from LIMMA indicates that there was a significant difference between the three different forms of human tuberculosis. Therefore, most of the genes significantly expressed in both groups were genes responsible for cellular immune response. The results of three different comparison groups generated from the LIMMA analysis were further analysed using correlation coefficient=1, when p-value<=0.05 and generated Venn diagram, the results from venn diagram shows that majority of the genes were up-regulated indicating less decrease in the rate of gene expression but increase among the regulated genes of stimulated tuberculosis and more genes were observed with higher expression than those with less expression during the three group’s comparison. It suggested recommendation that the results obtained from this study can be utilize in further analysis for detection and control of human tuberculosis infections.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000465","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent Topics in Protein Folding","authors":"T. Kikuchi","doi":"10.4172/JPB.1000469","DOIUrl":"https://doi.org/10.4172/JPB.1000469","url":null,"abstract":"The protein folding is a long-standing problem and there have been a lot of experimental and theoretical/computational studies so far [1-3]. These efforts by many researches have reveals mysterious folding mechanisms of proteins. However, there are still several unsolved problems on protein folding. An interesting one is how the information of the folding mechanism of a protein is encoded in its amino acid sequence. In the present short article, I discuss the remaining interesting problems on protein folding.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide Transcriptional Response during the Shift to N2-fixing Conditions in Heliobacterium modesticaldum","authors":"D. Sheehy, Yih-Kuang Lu, Fawsia Osman, Zana Alattar, Catalina V. Flores, Hallie Sussman, S. Zaare, Maria Dooling, A. Meraban, Patricia L. Baker, J. Touchman, K. Redding","doi":"10.4172/JPB.1000481","DOIUrl":"https://doi.org/10.4172/JPB.1000481","url":null,"abstract":"Heliobacteria are the only known phototrophic Firmicute; all known members of this group appear to be capable of N2 fixation but incapable of CO2 fixation. They are anoxygenic and possess the simplest photosynthetic apparatus known. The sequence of the 3.1-Mb genome of Heliobacterium modesticaldum, a moderate thermophile within the family Heliobacteriaceae, is publicly available. The focus of this study is to understand how this organism operates at a fundamental level by examining changes in its transcriptome during a shift from ammonium-containing medium to N2-fixing conditions. RNA was purified from cells grown with pyruvate as the carbon source and ammonia or N2 as the nitrogen source. After rRNA depletion, the RNA pool was sequenced using the Ion Torrent PGM platform. We found that the nitrogenase gene cluster was only expressed under N2-fixing conditions, concomitant with increased expression of the high-affinity ammonium transporter. Most genes were down-regulated in N2-fixing conditions by a factor of at least three. A drastic down-regulation of the highly expressed genes encoding proteins involved in the cyclic electron transport chain also occurred. The photosynthetic pshA transcript also decreased more than 100-fold but subsequent photochemical analysis demonstrated no large drop in the concentration of the reaction center protein complex. This indicates that there is a role for substantial translational regulation in some genes. The transcriptomic analyses revealed a network of differentially expressed genes in H. modesticaldum. This study represents the first step in the creation of a quantitative genome-scale metabolic model establishing H. modesticaldum as a model organism for the Heliobacteriaceae family. temperatures under which it grows [9]. Nitrogen fixation is catalyzed by the nitrogenase enzyme complex, and results in the reduction of atmospheric dinitrogen (N2) to ammonium (NH4 +) and the production of molecular hydrogen [12]. This process requires large amounts of chemical energy (16 ATP) and reducing power (8 Fdred) to convert one N2 to two molecules of NH4 + [13], which is then assimilated into many biomolecules. Sequence similarity predicts the use of a Mo-Fe group I nitrogenase consisting of a homodimer of NifD/K polypeptides [14]. The primary pathway for NH4 + assimilation in heliobacteria is the glutamine synthetase/glutamate synthase pathway [15]. This pathway is essential for growth, because glutamine is the primary intracellular nitrogen donor for purine and pyrimidine synthesis. Both ATP and reducing power are required in carbon metabolism, nitrogen assimilation, and hydrogen production, inextricably linking these pathways. In H. modesticaldum, the high-energy demand required for nitrogen fixation during diazotrophic growth has resulted in strict regulation of the nif genes encoding for nitrogenase. Thus, the addition of NH4 + to cultures Citation: Sheehy D, Lu YK, Osman F, Alattar Z, Flores C, et al. (2018) Genom","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000481","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum-Chemical Description of Some Physical-Chemical Properties of Proteinogenic Amino Acids","authors":"J. Kereselidze, G. Mikuchadze, Lia Bobokhidze","doi":"10.4172/JPB.1000483","DOIUrl":"https://doi.org/10.4172/JPB.1000483","url":null,"abstract":"We describe an impact of the inductive and steric effects of R-groups of amino acids on the reaction center (carboxy and amine groups) to estimate the propensity of amino acids for the peptide bond formation. These effects were quantitatively evaluated using the orders of the C-O and N-H bonds (PCO and PNH), the charges on the carbon, nitrogen and oxygen atoms of the carboxy, amine and hydroxy groups (q(C3), q(N6), q(O2)) and the dipole moments of all amino acids (μ). The calculations were carried out by means of modern quantum-chemical method Density Functional Theory (DFT). many-electron system can be determined by using functionals, which in this case is the spatially dependent electron density. Hence the name of density functional theory comes from the use of functionals of electron density. DFT is among the most popular and versatile methods available in computational biology. Unlike the wavefunction, which is not a physical reality, electron density is a physical characteristic of molecules. Hybrid methods, as the name suggests, attempt to incorporate some of the more useful features from ab initio methods (specifically Hartree-Fock methods) with some of the improvements of DFT mathematics. Hybrid methods, such as B3LYP [9-11] most commonly used for computational chemistry and Biology. Calculations were performed using software,”Priroda-8” in regime of the reaction coordinate [12]. N","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Structure Prediction, Analysis and Energy Calculation of Retinol Binding Protein7 (RBP7) in Coturnix coturnix japonica (japanese quail)","authors":"Aishwarya Tiwari, V. Saxena, M. Patel","doi":"10.4172/jpb.1000471","DOIUrl":"https://doi.org/10.4172/jpb.1000471","url":null,"abstract":"The biologically dynamic natural occurring retinoid (retinol and its metabolites, vitamin A) is intermediated by extracellular, intracellular, and nuclear proteins in Coturnix japonica or japenese quail. Retinoids mainly transmit by two medium such as Plasma retinoid binding protein (RBP) and Epididymal retinoic acid binding protein (ERABP) carries retinoid in body fluid while cellular retinol binding proteins (CRBPs) and cellular retinoic acid binding proteins(CRABPs) carry retinoids within cells. Accurate description of amino acids of RBP7 is very important to consider when prediction of structure and calculation of energy take place. The aim of the study is prediction the structure of RBP7 in Coturnix japonica using Bioinformatics tools and software approach. Ramachandran plot of the φ, ψ values for the amino acids in a RBP7 protein. Using this computational approach the total energy of RBP7 in Coturnix japonica is 1047.341 KJ/mol. And total minimum energy is 1026.898 KJ/mol in Cotunix japonica or japenese quail. It is also observed that repeating energy trends at each of the molecular, functional group, and atomic levels. Retinols and retinoic acid play essential characters in variation of gene expression and overall growth of embryo in Coturnix japonica. This makes RBP7 more significant in terms of expression of adipose tissues in Coturnix japonica (japenese quail) because RBP7 works as a novel adipose-specific gene.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/jpb.1000471","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}