Journal of proteomics & bioinformatics最新文献

{"title":"Synthesis, biological evaluation and molecular simulation studies of new arylated benzo[h]quinolines compounds as potential anticancer agents","authors":"Dharmendra Kumar, Mihyun Kim","doi":"10.4172/0974-276X-C1-106","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-106","url":null,"abstract":"D is a major active ingredient and principal component in several plants, Derris trifoliata Lour. (Leguminosae), Mundulea sericea (Leguminosae), Tephrosia vogelii Hook.f. (Leguminosae) and potential molecule to target cancer cell signaling pathway proteins. As a complex natural extract, deguelin interacts with various molecular targets to exert its anti-tumor properties at nanomolar levels. Deguelin induced cell apoptosis by blocking anti-apoptotic pathways, while inhibiting tumor cell propagation and malignant transformation through p27-cyclin-E-pRb-E2F1cell cycle control and HIF-1αVEGF antiangiogenic pathways. Our research explores the deguelin and its derivatives interaction with crystal structure of cyclin D1 (PDB ID: 2W96) and cyclin E (PDB ID: 2AST) to understand the better molecular insights. Molecular modelling of ligands (deguelin and its derivatives) were carried out by Avogadro software till stable confirmation obtained. The partial charges for the ligands were assigned as per standard protocol for molecular docking. All docking simulation were performed with AutoDock Vina on workstation. Virtual screening was done for all docked molecules based on binding energy and hydrogen bonding affinity. Molecular dynamics (MD) and Simulation (10 ns and 12 ns for cyclin D1 and cyclin E1 respectively) was done using GROMACS 5.1.1 software to explore the interaction stability. All the stable confirmations for cyclin D1 and cyclin E proteins trajectories was captured at various time intervals. Few compounds screened based on high affinity as inhibitors for cyclin D1 and cyclin E and may inhibit the cell cycle in cancer cell signaling under in vitro and in vivo experiments.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915342","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":"A Novel Methodology for Structural, Functional and Toxicological Analysis of Mutant Angiogenin Protein in Human","authors":"M. Hassan, Aqib Zafar Khan, B. Haidar, M. Nawaz, R. Mumtaz, S. Manzoor","doi":"10.4172/jpb.1000450","DOIUrl":"https://doi.org/10.4172/jpb.1000450","url":null,"abstract":"Introduction: Angiogenin is a protein of 14.1 kDa encoded by ANG gene and belongs to a superfamily of pancreatic ribonuclease A. Angiogenin is an effective stimulator of new blood vessels formation. It plays a vital role in the pathological as well as physiological mechanisms by regulating cell proliferation, differentiation and invasion. Mutation in ANG leads to a disease called amyotrophic lateral sclerosis 9. Amyotrophic lateral sclerosis 9 is a motor neuron disease that causes the decease of neurons, which controls the voluntary muscles of body. \u0000Material and Methods: The mutations F12S, P20S, Q36L, Y38H, K41E, D46G, S52N, R55K, C63W, K64I, I70V, K84E, P136L, V137I and H138R were selected for this study to investigate the single amino acid substitution effects on structure, function, stability and pathological impression on the protein. \u0000Results: The study revealed that the mutations Q36L, C63W, K64I, P136L, V137R and H138R have strong functional, structural and conformational effects compared to F12S, P20S, Y38H, K41E, S52N, R55K and K84E suggesting a high rate of disorder tendency. \u0000Conclusion: The in silico analysis of angiogenin identified several point mutations which may cause ALS9. The results of this study may be useful in planning and conducting clinical work on the ANG gene to find out, which mutation is responsible for the major cause of amyotrophic lateral sclerosis 9.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"260-266"},"PeriodicalIF":0.0,"publicationDate":"2017-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41886130","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":"Protein Biomarker Validation: A Mass Spectrometry Approach","authors":"M. Qoronfleh","doi":"10.4172/JPB.1000448","DOIUrl":"https://doi.org/10.4172/JPB.1000448","url":null,"abstract":"This concept communication describes a mass spectrometry workflow specific to biomarker assay development and validation. The primary objective of this workflow is to significantly decrease the cost and timeline for assay development and biomarker validation. The biomarker development workflow can be separated into five development stages that take less than 6 months to complete.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"246-251"},"PeriodicalIF":0.0,"publicationDate":"2017-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000448","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46761698","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":"On the importance of intrinsically disordered segments in multidomain proteins: The example of the interplay between STAM2, AMSH and polyubiquitin chains","authors":"O. Martin, Henry Y. Kim","doi":"10.4172/0974-276X-C1-101","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-101","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915456","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":"Detection of Folding Sites of β-Trefoil Fold Proteins Based on Amino Acid Sequence Analyses and Structure-Based Sequence Alignment","authors":"T. Kirioka, Panyavut Aumpuchin, T. Kikuchi","doi":"10.4172/JPB.1000446","DOIUrl":"https://doi.org/10.4172/JPB.1000446","url":null,"abstract":"The information on the 3D structure of a protein including its folding mechanism is encoded in its amino acid sequence. A β-trefoil protein is well known to have a remarkable 3D structure property, that is, the pseudo three-fold symmetry without clear hydrophobic packing. It is interesting to investigate how information on the folding mechanism to form such a topology is encoded in the amino acid sequence of a protein. In this study, analyses based on inter-residue average distance statistics and the conservation of hydrophobic residues are performed for sequences of 26 β-trefoil proteins to identify significant sites for the initial folding. Results are compared with the native 3D structures. The conserved hydrophobic residues are defined by multiple sequence alignment based on the 3D structures. It is confirmed that a conserved hydrophobic residue is always located in a β-strand. In particular, β-strands 5 and 6 are significant for the initial folding from the analyses based on the inter-residue average distance statistics. These results coincide well with the experimental data obtained so far for folding of some of the β-trefoil proteins. It is also confirmed that the conserved hydrophobic residues defined in this study contribute to form hydrophobic packing in β-trefoil proteins in general. Twelve conserved hydrophobic residue pairs are almost always observed to form packing in the 26 β-trefoil proteins from different superfamilies. We elucidate how the conserved hydrophobic residues in β-strands 5 and 6 contribute to the initial stage of folding of a β-trefoil protein. The common packing of the 12 conserved hydrophobic residue pairs are significant to form the whole β-trefoil fold structure.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"222-235"},"PeriodicalIF":0.0,"publicationDate":"2017-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000446","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46340842","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":"Mechanisms of Plasmid Replication","authors":"N. Khan","doi":"10.4172/jpb.1000444","DOIUrl":"https://doi.org/10.4172/jpb.1000444","url":null,"abstract":"Plasmids are small, circular extra fragments of DNA, commonly found in bacteria that are capable of replicating independent of the host genome, though plasmids are not required for survival of a living organism. But encodes essential genetic determinants that enable an organism to adapt and resist unfavourable conditions for better survival. Rolling circle, Col E1 type and iteron-containing replicons are the common modes through which plasmid replicates, each mechanism with unique significance to the organism.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"212-213"},"PeriodicalIF":0.0,"publicationDate":"2017-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/jpb.1000444","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48230470","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":"Mitochondrial COI Gene Sequence Analyses of Puntius ticto and Compared with Seven Species of Genus Puntius of Family Cyprinidae: A Finding for Phylogenetic Positioning and DNA Barcoding as Model Study for Cryptic Species","authors":"R. Garg, N. Dubey, N. Batav, P. Pooja, Ey, RK Singh","doi":"10.4172/JPB.1000445","DOIUrl":"https://doi.org/10.4172/JPB.1000445","url":null,"abstract":"Over the last three decades, mitochondrial DNA (mtDNA) has declared as the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of a species. The present study examined partial mitochondrial cytochrome c oxidase subunit I gene sequence of mitochondrial DNA for phylogenetic positioning of Puntius ticto among eight species of genus Puntius and its suitability to determine the genetic differentiation in among genus Puntius. The 05 samples of P. ticto were collected from Halali reservoir were analyzed mtcox1 gene of mitochondrial partial regions were sequenced and compared with the online database available on NCBI (National Centre for Biotechnology Information, USA) for rest of seven species (P. sophore, P. sarana, P. amphibious, P. chola, P. conchonius, P. dorsalis and P. gelius). Sequencing of 668 bp of mtcox1 gene revealed 18 haplotypes (h) with haplotype (gene) diversity (Hd) 0.981 ± 0.023 and nucleotide diversity (Pi) 0.658. 504 variable sites and parsimony sites have been recorded and conserved positions were observed at equal frequency in the nucleotide sequence and the variable regions were mostly visualized between nucleotide 27 to 76. The results concluded that the partial mtcox1 is polymorphic and can be a potential marker to determining phylogenetic positioning of Puntius ticto with rest of seven species. Present investigation may be treated model study for wildlife scientists for banding smuggling protected species under false pretenses and the importance of DNA barcoding in stopping such illegal trade.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"214-221"},"PeriodicalIF":0.0,"publicationDate":"2017-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000445","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43698657","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 Structural and Functional Prediction of Phaseolus vulgaris Hypothetical Protein PHA VU_004G136400g","authors":"Zohaib Bashir, Muhammad Rizwan, Kanwal Mushtaq, Anum Munir, Ishtiaq Ali","doi":"10.4172/JPB.1000443","DOIUrl":"https://doi.org/10.4172/JPB.1000443","url":null,"abstract":"Hypothetical proteins (HPs) are the proteins whose occurrence has been predicted, yet in vivo function has not been manufactured up. Illustrating the structural and functional confidential visions of these HPs might likewise prompt a superior understanding of the protein-protein relations or networks in diverse varieties of life. Common bean (Phaseolus vulgaris) is the most important food legume for direct human consumption in the world, most important grain legume for human consumption and has a role in sustainable agriculture helping to its ability to fix atmospheric nitrogen. However, in spite of the importance of this crop species, its genetics have been poorly characterized. In the present study, the hypothetical protein of Phaseolus vulgaris (Common bean) was chosen for analysis, and modeling by distinctive Bioinformatics apparatuses and databases. As indicated by primary and secondary structure analysis, XP_007152511.1 is a stable hydrophobic protein containing a noteworthy extent of α-helices; Homology modeling was utilized SWISS-MODEL server where the templates identity with XP_007152511.1 protein was less which demonstrated novelty of our protein. The Ab initial strategy was conducted to produce its 3D structure. A few evaluations of quality assessment and validation parameters determined the generated protein model as stable with genuinely great quality. Functional analysis was completed by ProtFun 2.2, and KEGG (KAAS), recommended that the hypothetical protein is a translation factor with nuclear domain. The protein was observed to be energetic for translation process, involved in trans-membrane barriers, signaling and cellular processes, and protein binding. It is suggested that further test approval would help to anticipate the structures and functions of other uncharacterized proteins of different plants and living being.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"207-211"},"PeriodicalIF":0.0,"publicationDate":"2017-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43948681","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":"Molecular Docking Studies: The Success Should Overrule the Doubts?","authors":"A. Shrivastava","doi":"10.4172/JPB.1000442","DOIUrl":"https://doi.org/10.4172/JPB.1000442","url":null,"abstract":"The capability of molecular docking in drug discovery can never be underestimated. The success of number of FDA approved drugs for several dreadful diseases have enhanced the speed of drug discovery. Although the inconsistent track record of computational screening may increase the doubts that how well the docking methods can rank the New Chemical Entity. If the method is studied correctly the docking method can have capability to screen and rank a true ligand from false ligand. \u0000 \u0000Here, the performance of molecular docking studies has been evaluated by correlations of experimental binding affinities of 3D ligand-enzyme complexes of Bcr-Abl. Here we evaluate the effect of the protein-ligand complex with the different scoring function and explained how to screen the analogs in better way by using existing computational approach. \u0000 \u0000This review and computational work will certainly boost the confidence of computational biologists.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"202-206"},"PeriodicalIF":0.0,"publicationDate":"2017-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000442","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41821224","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":"Selection of Significant Clusters of Genes based on Ensemble Clustering and Recursive Cluster Elimination (RCE)","authors":"Loai Abdallah, Waleed Khalifa, L. Showe, M. Yousef","doi":"10.4172/JPB.1000439","DOIUrl":"https://doi.org/10.4172/JPB.1000439","url":null,"abstract":"Background: Advances in technology have facilitated the generation of gene expression data from large numbers of samples and the development of “Big Data” approaches to analysing gene expression in basic and biomedical systems. That being said, the data still includes relatively small numbers of samples and tens of thousands of variables/gene expression. A variety of different approaches have been developed for searching these gene spaces in order to select the most informative variables that can accurately distinguish one class of subjects/ samples from another. However, there is still a need for new approaches that can accurately distinguish biologically different classes of subjects with similar gene expression profiles. We describe a new and promising approach for selecting the most informative differentially expressed genes that addresses this problem. We describe a method for identifying significant differentially expressed clusters of genes using a process of Recursive Cluster Elimination (RCE) that is based on an ensemble clustering approach. We refer to this approach as SVM-RCE-EC (Ensemble Clustering). We show that SVM-RCE-EC improves gene selection, classification accuracy as compared to other methods including the traditional SVM-RCE approach, and that this is particularly evident when applied to difficult data sets that are poorly resolved by other approaches. \u0000Methods: To implement SVM-RCE-EC we first applied an ensemble-clustering method, to identify robust gene clusters. We then applied Support Vector Machines (SVMs), with cross validation to score (rank) those clusters of genes based on their contributions to classification accuracy. The clusters of genes that are least significant are progressively removed by the procedure of RCE with the most significant clusters being retained until one identifies the most robust, significantly differentially expressed genes between the two classes. We compare the classification performance of SVM-RCE-EC to a variety of published classification algorithms. \u0000Results and Conclusion: Utilization of gene clusters selected using the ensemble method enhances classification performance as compared to other methods and identifies sets of significant genes that appear to be more biologically meaningful to the system being analyzed. We show that SVM-RCE-EC outperforms several other methods on data that represent highly similar sample classes that are difficult to distinguish and is comparable to other methods when applied to data where the classes are more easily separated. The improved performance of SVM-RCE-EC on difficult data sets is likely due to the fact that the significant clusters, as determined by the ensemble approach, capture the native structure of the data while SVM-RCE leaves that determination to the user. This hypothesis is supported by the observations that the performance of the clusters generated by SVM-RCE-EC is more robust. \u0000Availability: The Matlab version of SVM-RCE-EC is availab","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"10 1","pages":"186-192"},"PeriodicalIF":0.0,"publicationDate":"2017-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41379018","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}