Journal of proteomics & bioinformatics最新文献

{"title":"Biopharmaceutical Potential of ACE-Inhibitory Peptides","authors":"Praveen P. Balgir, M. Sharma","doi":"10.4172/JPB.1000437","DOIUrl":"https://doi.org/10.4172/JPB.1000437","url":null,"abstract":"Bioactive peptides are defined as peptides with hormone or drug like activity that bind to specific receptors leading to induction of physiological responses with a positive impact on body functions and health. Though pharmaceuticals are available, the responses to these drugs show variability and outright toxicity in some patients. Peptides of food origin have been reported to play an important role in the prevention and treatment of hypertension therefore researchers are extensively exploring food based strategies to produce functional food products with antihypertensive properties. These peptides act by intervening in different biochemical pathways that control blood pressure, fluid and electrolyte balance. Some targeted pathways are the renin-angiotensin system, kinin-kallikrein system, sympathetic nervous system, ion regulation system, sodium-transport system and the endothelin-converting enzyme system. These peptides are more reactive than their native proteins and have been produced by fermentation and enzymatic hydrolysis of food sources. Recombinant DNA technology has opened more avenues of production of antihypertensive peptides. In the present work antihypertensive Angiotensin-Converting-Enzyme (ACE) inhibitor peptides (2-5 in length and from food source) were selected from BIOPEP database and validated in silico for anti-hypertensive activity using web-based software Molsoft and Molinspiration. An overall drug-likeness score for the selected peptides was calculated using Molsoft. The more positive the value of drug-likeness scores the more active the peptide is. The molecular properties like hydrophobicity, electron distribution, hydrogen bonding characteristics and molecular size of active peptides were predicted using Molinspiration. In comparison with others only eight peptides WP, PLW, YPR, LPP, FP, LW, YW, RW showed positive drug-likeness score and bioactivity score (not violating Lipinski’s rule).","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000437","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43731224","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":"Comparison of Physicochemical Studies of Single Tailed and Gemini Cyclohexanoxy Carbonyl Pyridinium Cationic Amphiphiles","authors":"Rajni Aggarwal","doi":"10.4172/JPB.1000438","DOIUrl":"https://doi.org/10.4172/JPB.1000438","url":null,"abstract":"In the present research work, the physicochemical studies of surface active Cyclohexanoxy carbonyl Pyridinium single tailed and Gemini amphiphiles had been compared. Thermal stability, size of aggregates in aqueous system and interaction with a globular protein, Bovine Serum Albumin (BSA), was done by using TGA analysis, DLS, UV-visible, steady-state fluorescence and synchronous fluorescence and TEM respectively. On the basis of the experiments, it had been concluded that the Gemini amphiphile possessed less cytotoxicity, high thermally stability, form small sized compact aggregates and stable complex with BSA. The results have further been supported by higher value of Stern-Volmer quenching constant (KSV) and a higher binding constants for Gemini amphiphiles as compared to single tailed amphiphiles. Moreover, on the basis of synchronous fluorescence spectra and UV spectra, it has been concluded that both the amphiphiles mainly interact with tryptophan residues. The less cytotoxicity values and stabilization of secondary structure of BSA in low concentration of ionic liquids implies that these ionic liquids can replaced the conventional surfactants in the detergent industries and used as a potential vehicles for the drug and gene delivery.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000438","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43409551","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":"High Abundance Proteins: ProteomerâÂÂs Thorns in the Flesh?","authors":"Ravi Gupta","doi":"10.4172/jpb.1000e35","DOIUrl":"https://doi.org/10.4172/jpb.1000e35","url":null,"abstract":"Identification of low-abundance proteins is one of the major challenges in Proteomics because of the high dynamic range of the protein concentration in the biological samples [1]. Therefore, one of the prime objectives of the proteomers is to reduce the dynamic protein concentration range to shed a light on the “low-abundance proteome” or sometimes referred as “Hidden Proteome” [2]. The development and utilization of latest mass spectrometers have increased the sensitivity of the protein identification, fostering the identification of proteins present in extremely small amounts (up to attomoles, in isolation) [3]. However, the identification of low-abundance proteins during the analysis of whole cell/tissue proteome is still not achievable without any prefractionation of the samples [4]. One of the major reasons of this limited resolution, during total proteome analysis, is the presence of high-abundance proteins which occupies a major portion of the cell/ tissue proteome. Albumin in blood [1], RuBisCO in green leaves [5], and storage proteins in seeds, tubers, and roots [6] are some of the common examples of the high-abundance proteins in the biological samples. These high abundance proteins are products of the genes which are present in large copy numbers and inevitably impede the identification and characterization of low abundance proteins. Biomarkers or signaling/regulatory proteins are generally lowabundance in nature and are masked by the presence of these abundant proteins which are present in numbers 105-106 copies per cell [2,7,8]. As an example, 22 most abundant proteins, in the human blood plasma, constitute approximately 99% of the total plasma proteome with lowabundance proteins present as only 1% of the total plasma proteome [9]. Because of the presence of these high-abundance proteins, proteomics studies majorly ends up with the repeated identification of different components of these abundant or house-keeping proteins and thus actual information of the biological phenomenon remains concealed. The possibility to look beyond these abundant proteins or go further lies on the successful enrichment and identification of the lowabundance proteins which are present less than 100 copies per cell [7].","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42126206","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":"Structural Model of TaNAM-B1 Transcription Factor from Wheat ( Triticum aestivum ) Insight into the Nutritional Grain Quality","authors":"Murtaza Malik, P. Saurabh, Ey, K. Tripathi, Rashmi Jain, T. Kaul","doi":"10.4172/JPB.1000441","DOIUrl":"https://doi.org/10.4172/JPB.1000441","url":null,"abstract":"Wheat is a propitious crop which renders several health benefits, but the modern wheat lacks essential micronutrients like zinc and iron. In this paper, various bioinformatics tools and molecular modeling approaches have been embodied for the development and exploration of structure and various properties, respectively. The NAM-B1 gene is a NAC transcription factor which plays an essential role in the translation machinery. It is also responsible for maintaining the nutritional seed grain quality in wheat. NAM-B1 gene is accountable for the Fe and Zn concentration in wheat and is also held responsible for delayed senescence in the crop by three weeks. In this study, we have developed the structural model of the NAM-B1 protein using the structure of 3ULX as template by Modeller 9.12. The resultant model was further processed and refined using various tools such as PROCHECK, ProSA, Verify3D and RMSD. As a result, the model developed was found to be conceivable with 62% a.a sequence identity with the template. Investigation revealed that conserved region found was accountable of the response generated during the improvement of the nutritional quality of grain. TaNAM-B1 plays an ingenious role in leaf senescence and abiotic stress tolerance in plants.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48024517","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":"Proteomics and Bioinformatics: A Modern Way to Elucidate the Resistome in Mycobacterium tuberculosis","authors":"D. Sharma, Nirmala Deo, D. Bisht","doi":"10.4172/JPB.1000E33","DOIUrl":"https://doi.org/10.4172/JPB.1000E33","url":null,"abstract":"Tuberculosis (TB) remains one of the world’s biggest threats which are caused by Mycobacterium tuberculosis. According to WHO 2016 report, 10.4 million people were infected worldwide with 1.8 million deaths including 0.4 million individuals with HIV-TB coinfection [1]. Vaccines, diagnostics and drugs are the available current tools to control this situation. Over the half century, Mycobacterium bovis bacille Calmette Guérin (BCG) is still the only vaccine against TB worldwide, despite showing highly variable efficacy (0–80%) in different trials [2]. Worldwide, sputum smear microscopy and culture remains the commonly used TB diagnostic and gold standard method respectively. However, use of rapid molecular testing like Line Probe Assay (LPA) has been used for detection of Rifampicin and isoniazid drug resistant Mycobacterium tuberculosis strains. Recently in India, Revised National TB Control Programme (RNTCP) has approved a study for the Validation of second line LPA for detecting resistance to fluoroquinolones, aminoglycosides (kanamycin, amikacin) and cyclic peptides (capreomycin). First and second line anti-TB drugs are effective and necessary component of short course chemotherapy. The treatment failure can lead to the emergence of resistant strains [Multidrug-resistant Tuberculosis (MDR-TB), Extensively Drug Resistant Tuberculosis (XDR-TB) and Totally Drug Resistant Tuberculosis (TDR-TB)] and consequently spread of the resistant form of the disease which have worsened the situation and became a major threat to community. The reasons for this are complex and multifactorial. These drug resistant M. tuberculosis strains or bad bugs can resist the action of drugs by the various mechanisms. These includes target gene mutations [3], drug modifying enzymes [4], over expression of efflux pumps and porins alterations [5,6], drugs trapping and overexpression of proteins showed drug neutralizing effects [7-13]. Majorly of drug resistance is contributed by target gene mutation however remaining part of drug resistance is due to various other mechanisms. Our existing gadgets (vaccines, diagnostics and therapeutics) are incapable to provide the complete protection against these deadly situations.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44280513","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":"Indices of Codon Usage Bias","authors":"A. Uddin","doi":"10.4172/JPB.1000E34","DOIUrl":"https://doi.org/10.4172/JPB.1000E34","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000E34","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48068156","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":"Tissue specific secretomes - A treasure chest for the identification of disease related marker proteins","authors":"S. Lehr","doi":"10.4172/0974-276X-C1-096","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-096","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915277","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":"Comparative peptidome analysis of the mucus from seven gastropod species","authors":"Viroj Tachapuripunya Sittiruk Roytrakul Pramote Chuamnanpuen, Teerasak Ekobon","doi":"10.4172/0974-276X-C1-097","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-097","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915304","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":"Modulation of fish allergenicity towards the production of a low allergen farmed fish: A proteomics approach","authors":"Pedro M L Rodrigues, D. Schrama","doi":"10.4172/0974-276X-C1-098","DOIUrl":"https://doi.org/10.4172/0974-276X-C1-098","url":null,"abstract":"F allergies are a significant public health concern throughout the world. Fish is a food product increasingly consumed worldwide due to its high nutritional value and healthy meat. Unfortunately, like many food sources, fish can cause adverse immune-mediate reactions in some individuals. This allergic reaction to food affects 1-3% of the population and about 4-6% of children. The main fish allergen is β-parvalbumin; a small and highly stable muscle protein. Fish parvalbumins are highly conserved proteins, which are binding bivalent ions, calcium or magnesium. In fish-allergic patients, specific IgE cross-react mostly with parvalbumins from different fish, especially when recognizing highly identical protein regions involved in the ion binding. Other fish allergens have been identified as well such as enolases, aldolases or fish gelatin-but their importance has been only shown for a limited number of fish species. Currently, there is no cure available for fish allergies with the clinical management of fish allergy solely relying on a strict avoidance diet. Modulation of fish allergenicity towards the production of a low allergen farmed fish was firstly attempted by our group. This has been done with specifically designed fish diets, enriched in components and small changes introduced in the fish farming process that target the expression or inactivation of the main fish allergen; parvalbumin. Proteomics is the chosen technique to access fish allergen characterization and expression in muscle while IgE assays are used to confirm the lower allergenic potential of this fish are conducted in patients with history of fish allergies.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70915429","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 Modeling and Characterization of Hypothetical Protein YP_004590319.1 Present in Enterobacter aerogens","authors":"Ritika Gupta, Ankita Dey, Anu Vijan, Bitu Gartia","doi":"10.4172/JPB.1000436","DOIUrl":"https://doi.org/10.4172/JPB.1000436","url":null,"abstract":"Transfer RNAs anticodon post-transcriptional modifications are responsible to the high fidelity of protein synthesis. In eubacteria, two genome-encoded transfer RNA (tRNA) species bear the same CAU sequence as the anticodons, which are differentiated by modified cytidines at the wobble positions. We have determined the structure model of the hypothetical protein. The structure unexpectedly reveals an idiosyncratic RNA helicase module fused with a GCN5-related N-acetyltransferase (GNAT) fold, which intimately cross interact. The stereo chemical quality of the protein model was checked by using in silico analysis with SWISS- MODEL, PyMol, PROCHECK, ProSA and QMEAN servers. These results may be helpful for further investigations for determining crystal structure of the hypotheitical protein and developing target molecules to inhibit Enterobacter aerogenes.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/JPB.1000436","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47157604","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}