Journal of proteomics & bioinformatics最新文献

{"title":"Clinical Proteomics and Bioinformatics: Exploring Drug Resistant Tuberculosis","authors":"D. Sharma, D. Bisht, Rijuved Garg","doi":"10.4172/0974-276X.1000E37","DOIUrl":"https://doi.org/10.4172/0974-276X.1000E37","url":null,"abstract":"Tuberculosis (TB) is a major public health problem across the globe. As per WHO, 10.4 million new TB cases and 1.8 million deaths occur annually [1]. In developing countries, TB burden among the healthcare workers is a serious issue [2] and spreading of drug-resistant Mycobacterium tuberculosis strains further worsened the situation which leads to the emergence of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDRTB) and totally drug-resistant tuberculosis (TDR-TB). Use of effective diagnostics and therapeutics strategies are the only valid options to combat the situation of global antibiotic resistance [3,4]. Researchers have paid attention in this direction and trying to develop alternative strategies against global antibiotic resistance. Repurposing of the drugs against the antibiotics resistant M. tuberculosis infection has been considered as an effective strategy and might be shown the positive outcomes in the treatment of MDR-TB, XDR-TB and TDR-TB [4]. Still, our current therapeutic strategies are unable to give complete protection against antibiotics resistant TB infections. Therefore, an urgent need is required for developing the possible diagnostics and therapeutic strategies against the antibiotics resistance.","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":"70908071","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":"Bladder Carcinoma Treatment Challenges and Future Directions of Immunotherapy","authors":"Barnali Deb, Prashant Kumar","doi":"10.4172/0974-276X.1000E38","DOIUrl":"https://doi.org/10.4172/0974-276X.1000E38","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":"70908145","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":"Optimizing Workflows for LC/MS Analysis of Co-Immunoprecipitated Protein Complexes - \"Soap Opera(tions)\".","authors":"Matthew A Held, Don M Wojchowski","doi":"10.4172/jpb.1000e36","DOIUrl":"https://doi.org/10.4172/jpb.1000e36","url":null,"abstract":"The ability to define specific, and often dynamic proteinprotein associations within interactomes is critical to advancing an understanding of cell signal transduction pathways, drug design and the actions of therapeutic agents [1]. Standard approaches to assessing protein-protein interactions commonly have involved the retrieval of target proteins (“bait”) plus partner protein coimmunoprecipitates; the isolation of partner proteins from 1D or 2D gels; and the identification of retrieved partners via LC-MS/MS [2]. The use of in vivo biotinylation [3,4] or HALO tagging of target / bait proteins [5,6] can further extend the detection of protein partnerships [7]. Limitations, however, can include the need for multi-step workflows, relatively large-scale preparations, and/or the construction of labeled baits. Shotgun approaches including MudPIT (multidimensional protein identification technologies) [8] also continue to be advanced that can bypass SDS-PAGE, and in certain formats avoid the need for elution of immune complexes from adsorbent gels. In RIME (Rapid Immunoprecipitation Mass Spectrometry) co-IP LC/MS, for example, immune complexes are proteolyzed from Ig or Igprotein A/G/L beads and are analyzed directly by LC/MS [9,10]. Beyond this, in silico procedures also have recently been developed to guide cell lysis and/or subcellular fraction extraction methods, and co-IP workflows [11,12]. For LCMS/MS data analysis, advanced algorithms and reference databases also continue to be developed (e.g., DIA/SWATH) [13]. During the earlier fundamental steps of cell lysate preparation and target/ bait plus partner protein immunoprecipitation, the choice of detergents also becomes a point of central importance. This relates to the need to solubilize, but not disrupt protein complexes, while avoiding detergent incompatibilities with LC/MS. In a context of cell signal transduction, membrane proteins additionally can be key components (including transmembrane receptors), and this brings further attention to detergent considerations [14]. In particular, this includes a requirement to retain the solubility of hydrophobic proteins, while also maintaining protein-protein partnerships [15,16]. One non-ionic detergent frequently suggested as a potentially advantageous choice for this challenge is octyl beta-D-glucoside (OBG). This is based on OBG’s effectiveness in solubilizing and retrieving membrane proteins [17,18], and OBG’s exceptional property of rapid micelle disassembly upon dilution or dialysis [17,19]. In published studies, however, comparably few examples exist for OBG’s use in cell lysis and co-IP (compared, for example, with Triton-X-100, Igepal, DOC, CHAPS). This includes systems that use FLAG-epitope tagged target/bait proteins. In a workflow context, a challenge also exists during immune complex isolation for replacing OBG (an LC-MS incompatible detergent) with an LC-MS compatible detergent that continues to preserve solubilized co-IP complexes. For L","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 7","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/jpb.1000e36","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36832003","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":"A Classification Approach for Genome Structural Variations Detection","authors":"Eman Alzaid, Achraf El Allali, Hatim Aboalsamh","doi":"10.4172/0974-276X.1000488","DOIUrl":"https://doi.org/10.4172/0974-276X.1000488","url":null,"abstract":"Background: Finding accurate genome structural variations (SVs) is important for understanding phenotype diversity and complex diseases. Limited research using classification to find SVs from next-generation sequencing is available. Additionally, the existing algorithms are mainly dependent on an analysis of the alignment signatures of paired-end reads for the prediction of different types of variations. Here, the candidate SV regions and their features are computed using single reads only. Classification is used to predict the variation types of these regions. Results: Our approach utilizes reads with multi-part alignments to define a possible set of SV regions. To annotate these regions, we extract novel features based on the reads at the breakpoints. We then build three random forest classifiers to identify regions with deletions, inversions, or tandem duplications. Conclusions: This paper proposes a random forest-based classification approach, MPRClassify, which addresses the issue of finding SVs using single reads only. These single-reads are used to define candidate regions and extract their features. Experimental results show that single reads are sufficient to find SVs without the need for paired-end read signatures. Our proposed approach outperforms existing approaches and serves as a basis for future studies finding SVs using single reads.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"211-218"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907510","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 TRIP Back in Time to TRIP","authors":"E. Bhat, I. Rather","doi":"10.4172/JPB.1000480","DOIUrl":"https://doi.org/10.4172/JPB.1000480","url":null,"abstract":"TRAF-interacting protein (TRIP, TRAIP and RNF206) was initially known as a binding partner that prevented NF-kβ activation. Currently, it is defined as a protein encoded as TRIP gene in humans. TRIP gene encodes an amino acid that has N-terminal RING finger motif. The same murine protein associates with TNFR-linked factor 1 also known as TRAF 1. It also interacts with TRAF 2 and cylindromatosis. The association with TRAF 2 leads to cell activation such as NF-κB activation. Tumor Necrosis factor receptor (TNFR) associated factors are primary adapter molecules in the TNF-signaling pathway and induce a wide range of biological processes including cell proliferation, activation, differentiation, and apoptosis. TRIP can also be defined as a novel binding protein that detrimentally influences and regulates the NF-KB activation via the TNFR2and CD30 signaling complexes. Nonetheless, studies show that TRIP being part of several processes such as DNA stability and cell cycle progression by direct association with other binding partners is not evidence enough for its integral role. Irrespective of TRIP, being an influencing factor in cell signaling and human diseases, the physiological importance and the exact role of TRIP is not clear. As such, the review seeks to demystify, and explain the role of TRIP in various signaling pathway based on recent published research. induce a wide range of biological processes including cell proliferation, activation, differentiation, and apoptosis. TRAF members directly interact with the TNFR super-family via their cytoplasmic domains [1]. Cytoplasmic domains of TNFR lack catalytic activity and possess no significant homology to each other or other known proteins [2]. To date, TRAF1-7 has been identified. Except for TRAF7, other TRAF members possess a conserved TRAF domain which is composed of (~230 amino acid length) TRAF-N and TRAF-C domain which plays a pivotal role in TRAF signaling complexes by interacting directly via cytoplasmic regions of TNFR superfamily. It is now clear that TRAF-N domain mediates the interaction with different intracellular signaling molecules. TNFR super-family members recruit several types of signal transducer molecules which have been identified to initiates different signaling pathways. Moreover, one class of signalTransducing molecules are recruited to Fas (CD90) or TNFR1 via their death domain. For example, through their respective Death domain interactions, Fas (CD95) and TNFR1 recruit FADD (MORT1)/RIP or TRADD/FADD/RIP. Association of these signal transducers lead to the recruitment of FLICE/MACH and finally causes cell death [3]. Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are second class of signal transducers, recruited by TNFR superfamily via their cytoplasmic interactions and either activates or suppresses the NF-Kb or JNK pathway. The ability of TRAF’s to bind TNFR2, CD30, CD40, and LT-BR has been identified by their biochemical studies. The interaction of th","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.1000480","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324784","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 Fat Storage-Inducing Transmembrane Proteins 1 and 2 as Putative Therapeutic Targets for Heart Failure by Integrated Analysis of Proteome and Transcriptome","authors":"Natsumi Nishihama","doi":"10.4172/JPB.1000484","DOIUrl":"https://doi.org/10.4172/JPB.1000484","url":null,"abstract":"Cardiovascular disease constitutes a major health burden globally, for which novel cardiotonic agents are still required. Cardiac failure is thought to be caused by dysfunctions of the sarcoplasmic/endoplasmic reticulum (SR/ ER) in cardiomyocytes. Therefore, in this study, we searched for novel pharmaceutical targets in SR/ER. Tissue and organelle specific proteome profiling by liquid chromatography coupled with mass spectrometry after gel electrophoresis separation identified 3,638 proteins in heart and liver SR/ER samples from a mouse transverse aortic constriction (TAC) model (heart failure). We also analyzed the transcriptome of heart tissue from the TAC model (heart failure, hypertrophy) and a myocardial infarction model using microarrays to identify differentially expressed genes in the diseased heart. Several genes were chosen for further studies following the proteome and transcriptome analyses. Of these, fat storage-inducing transmembrane proteins 1 and 2 (FITM1 and FITM2) were highly expressed in mouse and human heart and skeletal muscle. We investigated the functions of FITM1 and FITM2 in vitro and confirmed that they mediated lipid droplet (LD) formation and directly bound to triglycerides. FITM1 and/ or FITM2 overexpression in cells altered the levels of Ero1-Lα and PDI, which are ER stress marker proteins that protect against heart failure and affect cellular metabolism. Together, these results indicate that FITM1 and FITM2 are expressed in heart tissue and that their modulated expression or function can change LD formation, ER function, and cellular metabolism in cells. Thus, FITM1 and FITM2 are good drug target candidates. Tmem38A: Transmembrane Protein 38A; Tmem38B: Transmembrane Protein 38B; Tmem242: Transmembrane Protein 242; UPR: Unfolded Protein Response.","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":"70324930","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":"QSAR Model Generation of Phthalazinones as Poly (ADP-Ribose) Polymerase Inhibitors by the Genetic Algorithm and Multiple Linear Regression (GA-MLR) Method: A Ligand-Based Approach for Cancer Drug Design","authors":"G. Ambrose, O. Afees, U. J. Kalu, Abiodun Wisdom Oshireku, Afolayan Daniel Todimu, O. Oluwasegun, Toba Olatoye, Fagbemi Ranti-Ade Rebecca, Adekunle Precious","doi":"10.4172/0974-276X.1000485","DOIUrl":"https://doi.org/10.4172/0974-276X.1000485","url":null,"abstract":"Poly (ADP-ribose) polymerase-1 (PARP-1), an enzyme known for catalyzing the attachment (covalently) of polymers of ADP-ribose moieties on itself and its target proteins, has been reported in recent study to regulate gene expression in prostate cancer. BRCA mutations are associated in the sensitivity of PARP inhibitors. The present study aimed to develop a Quantitative Structure-Activity Relationship (QSAR) model with Phthalazinones, inhibitors of PARP-1. Phthalazinones were divided into training and test sets to build the QSAR model. Among the several topological, constitutional, geometrical, electronic and hybrid descriptors generated as inputs to the model, three variables were selected by adopting the genetic algorithm subset selection method (GA). The correctness of the proposed model was accounted for by using the following evaluation techniques: Y-randomization, Validation of the external data test set and cross-validation. The model was found to have a good predictive ability and could be used for designing similar group of compounds.","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/10.4172/0974-276X.1000485","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907434","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":"Investigation of Differentially Expressed Proteins of Candida tropicalis Biofilm in Response to Citral","authors":"A. Chatrath, P. Kumari, R. Gangwar, R. Prasad","doi":"10.4172/JPB.1000466","DOIUrl":"https://doi.org/10.4172/JPB.1000466","url":null,"abstract":"Candida tropicalis is an opportunistic human pathogen with an ability to cause superficial as well as systemic infections in immunocompromised patients. C. tropicalis biofilms can cause persistent infections which are difficult to treat due to acquired resistance. Citral has been used as antifungal agents against Candida species and biofilms. In the present study, we used one-dimensional polyacrylamide gel electrophoresis (1D-PAGE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/TOF-MS) to identify the changes in the protein expression of C. tropicalis in response to the sub-lethal concentration of citral. A total of six differential proteins involved inoxidative stress (Tsa1p, Psa2p), amino acid biosynthesis (Met6p, Gln1p), heme biosynthesis (Hem13p) and glucose metabolism (Eno1p) pathways were detected. Our results revealed citral-induced proteins of C. tropicalis biofilm. This study will further help in the interpretation of mode of action of citral and development of novel antifungal agents against these potential protein targets.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324514","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":"Proteomic Analyses of Exothermic Processes in Rat Brain Homogenate","authors":"Y. Voynikov, L. Velkova, L. Tancheva, P. Mladenov, A. Dolashki, L. Alova, W. Voelter, P. Dolashka","doi":"10.4172/JPB.1000470","DOIUrl":"https://doi.org/10.4172/JPB.1000470","url":null,"abstract":"Alzheimer’s disease (AD) is the most widespread neurodegenerative disorder which can be induced by scopolamine, but the underlying molecular mechanism is poorly understood. Recently, differential scanning calorimetry (DSC) has been used to study healthy and scopolamine-treated mice. A well-expressed exothermic transition minimum in the range of 35 - 45°C was determined in the DSC profiles of healthy mice supernatants. To explain this process, using two-dimensional gel electrophoresis (2D-PAGE) coupled with MALDI-TOF-TOF, poorly soluble membrane proteins in hippocampal proteome of rat brain tissue were identified. The different behavior of the hippocampal proteome from the healthy rats before and after heating to 45oC was identified. Due to the demonstrated change in protein level of tau protein and tubulin in the rat hippocampus after heating to 45°C, it was suggested that the observed exothermic process at 35-45°C in rat may be due to the partial unfolding of tau protein, which leads to the release of tubulin. Both proteins together are involved in protein fibrillation and aggregation. Another important result is the discovery of different profiles for the proteome of hippocampal rat homogenates with scopolamine-induced neurodegenerative disorder and its characteristics of healthy rats. The reported results from this study can help clarify the molecular mechanisms of scopolamine-induced dementia and neurodegenerative processes in general.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000470","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324614","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":"Mutation Based Structural Modelling and Dynamics Study of Alpha Fetoprotein: An Insight to Inhibitory Mechanism in Breast Cancer","authors":"Priyam Patel, P. Panda, Sneha S. Patil, Hetalkumar Panchal","doi":"10.4172/JPB.1000462","DOIUrl":"https://doi.org/10.4172/JPB.1000462","url":null,"abstract":"The incidence of breast cancer is amassed in the current era due to the advent in urbanization, increase in sophisticated vicissitude living, and espousal of western lifestyles. Alpha- fetoprotein, a serum glycoprotein produced during embryonic development tends to act as the curative mediator and has anti-estrotrophic properties to inhibit the growth of estrogen- dependent tumor’s in breast cancer and metastasis. This oncofetal protein exhibits pharmaceutical activity during en route cancer metastasis and pathways lead to tumor cell progression and proliferation. In this work, the maximal inhibitory action of the peptide derived from the active site segment, which was previously suggested in experimental works against mice xenografts (8-mer Peptide), was derived from the structural model generated by homology modelling that retains the inhibitory activity exhibited by the derived AFPep P489- P496 (EMTPVNPG). A comparable mutation study has been undertaken in the derived peptide region to maximize the inhibitory action of the above-said activities. Comparative molecular dynamics study of each mutation has been carried out to know the stability of the octapeptide 489-496 to ensure the curative perspective that is indulged in inhibiting the progression and proliferation of oncofetal proteins in breast cancer. Another modification to the derived peptide was done by addition of hydroxyproline group to the region selected that was previously suggested with the combined effect of tamoxifen and hydroxyproline associated peptide. Molecular docking studies have also been carried out for the octapeptide against Hsp70 which might help in stabilising the anti tumour associated peptide AFPep for better binding efficacy for maximal inhibitory action and treatment of breast cancer.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":"11 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000462","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70324957","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}