Journal of proteomics & bioinformatics最新文献

{"title":"Inflammation: An Important Parameter in Prostate Cancer Biomarkers","authors":"Francesco Andelli","doi":"10.35248/0974-276X.21.14.540","DOIUrl":"https://doi.org/10.35248/0974-276X.21.14.540","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961584","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":"ROS and MAPK Cascades in the Post-harvest Senescence of Horticultural Products","authors":"M. Gouda, Chun-Rong Zhang, Junhao Wang, Sijia Peng, Yu-ru Chen, Haibo Luo, Lijuan Yu","doi":"10.35248/0974-276x.1000508","DOIUrl":"https://doi.org/10.35248/0974-276x.1000508","url":null,"abstract":"Plants are naturally sessile and cannot move away from adverse environmental conditions. Environmental stress may induce loss of membrane integrity, which is a seminal feature of premature senescence. Therefore, plants must respond in other ways to protect themselves from abiotic and biotic stresses that involve protein kinases, which are crucial to signal transduction pathways. Protein kinases are involved in the phosphorylation of serine/threonine and tyrosine side chains of proteins. Among these protein kinases, mitogen-activated protein kinase (MAPK) cascade genes are key components of signal transduction pathways that help transduce extracellular signals to intracellular responses in animals, plants, and fungi. Interestingly, reactive oxygen species (ROS) are important and common messengers that are produced in various biotic and abiotic stresses; ROS are known to activate many of the MAPKs. In this review, we highlight the mechanisms of crosstalk between ROS and MAPK cascades in the post-harvest senescence of horticultural products and summarize recent findings about MAPK regulation and functioning in various cellular processes.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961185","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":"Editorial Note for Journal of Proteomics & Bioinformatics","authors":"Susan Williams","doi":"10.35248/0974-276X.1000512","DOIUrl":"https://doi.org/10.35248/0974-276X.1000512","url":null,"abstract":"","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69960880","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":"Understanding the Role of Natural Medicinal Compounds Such as Curcumin and Allicin against SARS-CoV-2 Proteins as Potential Treatment against COVID-19: An In silico Approach","authors":"V. Bastikar, Alpana Bastikar, S. Chhajed","doi":"10.35248/0974-276X.1000510","DOIUrl":"https://doi.org/10.35248/0974-276X.1000510","url":null,"abstract":"The COVID-19 pandemic has caused greater deaths worldwide and is continuing to do so. India is no exception to this and the number of positive cases in India at increasing at an alarming rate. With no vaccine or medicine to either prevent or cure it, the medical fraternity and people worldwide are relying on basic precautionary measures. There is an utmost need of a drug to cure the pandemic. Various studies have been reported for the genomic and proteomic structure of the virus SARS-CoV-2, which causes the COVID-19. There are many important proteins in the viral genome which can be targeted for drug design and discovery. The current paper focuses on Main protease and RNA dependent RNA polymerase (RdRp) proteins for the drug design against COVID-19. Two important molecules such as Curcumin and Allicin having medicinal properties were studied for their antiviral activity against the SARS-CoV-2 proteins. Hexahydrocurcumin and Hexahydrourcuminol amongst the Curcumin derivatives were found to show good binding affinity against the Main protease; Dihydrocurcumin glucuronide and Curcumin sulphate showed good binding against RdRp. Amongst the Allicin derivatives, Allicin and Ajoene showed good binding affinity for both Main protease as well as RdRp protein. Thus these molecules can be further studied for their in vitro and in vivo activity testing against COVID-19.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961261","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":"Fungal Infestation of Garri Sold Around Dutsinma Metropolis","authors":"J. Orpin, I. Mzungu, H. Usman-Sani","doi":"10.35248/0974-276X.1000511","DOIUrl":"https://doi.org/10.35248/0974-276X.1000511","url":null,"abstract":"This study was conducted to determine the fungal contaminants of garri in Dutsinma metropolis. A total of 150 samples were bought at random, 75 each of white and red garri from three different markets including Wednesday market, Abuja road market and Old market respectively. The fungi isolated using standard microbiological techniques were Alternaria spp. (3.7%), Aspergillus spp. (14.8%), Cladosporium spp. (27.8%), Fusarium spp. (9.3%), Mucor spp. (12.9%), Penicillium spp. (16.7%) and Rhizopus spp. (14.8%) in white garri. For yellow garri: Alternaria spp. (2.9%), Aspergillus spp. (8.8%), Cladosporium spp. (29.4%), Fusarium spp. (8.8%), Mucor spp. (11.8%), Penicillium spp. (20.6%) and Rhizopus spp. (17.6%) with Cladosporium and Rhizopus recording the highest occurrence in both white and yellow garri. Higher fungi species were isolated from white garri (54) compared to yellow (34) samples. Moisture content recorded showed higher content in white garri than in the yellow garri. Identification of the isolated fungi based on their morphological and cultural characteristics was carried out. The results show that consumers are exposed to the risk of aflatoxin poisoning. Efforts should therefore be made to improve the quality of Cassava farina by addressing its handling and processing practices.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69960811","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":"Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data","authors":"S. Srivastava, M. Merchant, A. Rai, S. Rai","doi":"10.35248/0974-276X.19.12.500","DOIUrl":"https://doi.org/10.35248/0974-276X.19.12.500","url":null,"abstract":"Introduction: The proteomics experiments involve several steps and there are many choices available for each step in the workflow. Therefore, standardization of proteomics workflow is an essential task for design of proteomics experiments. However, there are challenges associated with the quantitative measurements based on liquid chromatography-mass spectrometry such as heterogeneity due to technical variability and missing values. Methods: We introduce a web application, Proteomics Workflow Standardization Tool (PWST) to standardize the proteomics workflow. The tool will be helpful in deciding the most suitable choice for each step of the experimentation. This is based on identifying steps/choices with least variability such as comparing Coefficient of Variation (CV). We demonstrate the tool on data with categorical and continuous variables. We have used the special cases of general linear model, analysis of covariance and analysis of variance with fixed effects to study the effects due to various sources of variability. We have provided various options that will aid in finding the contribution of sum of squares for each variable and the CV. The user can analyze the data variability at protein and peptide level even in the presence of missing values. Availability and implementation: The source code for “PWST” is written in R and implemented as shiny web application that can be accessed freely from https://ulbbf.shinyapps.io/pwst/.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44374762","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 active sites interaction of different protein molecules in case of formation Nap1-Nap1, Mdm2-Mdm2 and P53-Mdm2","authors":"pT V Koshlan, K. G. Kulikovp","doi":"10.4172/0974-276X-C3-118","DOIUrl":"https://doi.org/10.4172/0974-276X-C3-118","url":null,"abstract":"In this report, two algorithms are developed, algorithm 1 and algorithm 2. Algorithm 1 was developed in order to search for the interaction of a polypeptide chain of a full-length protein with short active region. Algorithm 2 was developed to determine the most active sites of interaction between fulllength proteins when dimers are formed in the direction from the N terminus to C terminus. Numerical calculations were made using proteins Mdm2, Nap1, P53. For modern proteomics, research and prediction of protein interactions are very important tasks, since they determine the function of proteins at levels from the cell to the whole organism. For proteins whose structure is known, the search for intermolecular interactions according to known data on the conformation of their tertiary structure reduces to the problem of searching for geometric complementarity of the sections of two interacting molecular surfaces and modeling their contacts, the so-called molecular docking. The task of molecular docking is the task of a conformational search algorithm, which reduces to a search for the conformational space of the formed biological complex due to the variation of the torsion angles of protein molecules. Modern conformational search algorithms in most cases find conformations that are generally close to the experimentally found structures in a relatively short time. However, there are factors that also have a significant impact on the success of the docking, which are often not taken into account in standard algorithms. One such factor is the conformational mobility of the target protein. The mobility range can be different beginning with a small adjustment of the side chains and ending with scale domain movements. These movements play an important role. At first glance, the most logical solution to this problem is to take into account the mobility of the protein in a docking program. Unfortunately, modern computational tools do not allow such modeling to be performed in an acceptable time frame since a protein molecule is very large, and allowing for mobility over all degrees of freedom can lead to a so-called combinatorial explosion (an astronomical increase in the number of possible variants). Only in some programs is there a limited mobility of protein binding sites (usually at the level of a small adaptation of conformations of the side chains of the active center residues). Another approach to this problem consists in docking the same protein in several different conformations and then selecting the best solutions from each docking run. The third approach is to find a universal structure of the target protein in which docking would produce fairly good results for different classes of ligands. In this case, the number of missed (but correct) solutions decreases, but the number of incorrect options also increases significantly. It should also be noted that most programs for the theoretical docking of proteins work according to the following principl","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70916017","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":"Bioinformatics analysis of novel 18s ribosomal RNA genomic sequence of mentha spicata","authors":"pAbdul Nasir Adnan Akbar, Samina Shakeelp","doi":"10.4172/0974-276X-C3-119","DOIUrl":"https://doi.org/10.4172/0974-276X-C3-119","url":null,"abstract":"Ribosomal RNAs (rRNAs) are all around circulated and known for their useful equality among all the known creatures. Examination of little subunit rRNAs (16-18S rRNAs) can allow the precise factual estimation of an expansive scope of phylogenetic connections because of exceptionally rationed arrangements. Along these lines, we recognized and halfway sequenced novel isoforms of 18S rRNA quality from 7 wild, therapeutic plants (Ferocactus glaucescens, Capparis decidua, Calatropis procera, Maytenus royleana, Prosopis Juliflora, Ficus carica and Mentha spicata) and three developed plants (Cyamopsis tetragonoloba, Eruca sativa and Solanum lycopersicum). The genomic arrangements of 18S rRNA from these various plants were dissected and affirmed by utilizing bioinformatics devices and submitted to genebank. We utilized ClustalW for pairwise arrangement of these novel groupings with other known 18S rRNA successions to discover their phylogenetic connections. Our outcomes have demonstrated exceptionally saved nature of 18S rRNA with variable areas may be signs of some authentic signs. Optional structure compels of rRNA can influence their phylogenetic understandings once in a while. These epic 18S rRNA groupings can likewise be utilized as inside controls for a few sorts of sub-atomic investigation after exact approvals of their steady articulation in the given plant species in future examinations, as less is thought about these housekeeping qualities of wild plants. Mentha spicata (Spearmint) is a Medicinal plant has a place with family Lamiaceae utilized in the treatment of fevers, bronchitis, chills, cramps, interminable gastritis and basic virus. Diffreent Bioinformatics instruments i.e Mega5, T-espresso arrangement, Pepstats, Signal P4.1, Pepwindow, NEBV 2.0 Cutter, NetPhos 2.0, SOPMA, Phyre2, BioEdit and Prosite, product used to recognize Phylogency, homology, Physiochemical properties, Signal peptide, Hydropathy Plot, Restriction planning, Phosphorylation destinations, auxiliary structure, Protein 3D structure, Nucleotide organization and Pattern acknowledgment individually.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70916085","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 Multidimensional Approach to Explore the Use of a Small Heterobifunctional Crosslinker based on a Metabolite of the Kynurenine Pathway","authors":"S. K. Thakur, Mitul Srivastava, Ankur Kumar, R. Goel, Shailendra Asthana, S. Eswaran","doi":"10.4172/0974-276x.1000491","DOIUrl":"https://doi.org/10.4172/0974-276x.1000491","url":null,"abstract":"This study describes the use of a new small heterobifunctional crosslinker for crosslinking of proteins (e.g. lysozyme). This crosslinker is based on 3-hydroxy anthranilic acid (3HAA) that is part of the kynurenine pathway of the degradation of Tryptophan. 3HAA is found in enhanced amounts in disease states in the human body. Small crosslinkers capture interacting protein interfaces better, while the larger ones are more useful for identifying interacting partners. The new crosslinker described here, functions presumably via a ‘long lived’ transient, leading to enhanced rate of intermolecular crosslinking, which is otherwise difficult to achieve. It contains a photo labile azido group and an amine reactive N-hydroxysuccinimide (NHS) group. Successful crosslinking in two steps (incubation followed by photolysis (366 nm, 6W UV lamp) , has been confirmed using SDS-PAGE, ESI-MS/MS, and bioinformatics analysis via StavroX 3.6.0.1 Docking followed by molecular dynamics simulation studies, have provided detailed structural insights into the ‘dimer’ formation of lysozyme. Identical conclusions have been obtained, using two different software, and providing a more refined 3D view of the interfaces during protein-protein interactions.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907580","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":"Developing High Sensitivity/Specificity Detection Systems for Studying Protein Interactions","authors":"R. Khan","doi":"10.35248/0974-276x.19.12.498","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.498","url":null,"abstract":"The study of proteomics succeeds the deciphering of the genetic code; this growing burgeoning area is set to dominate scientific research well into the next decade. Current tools employed in studying protein-protein interactions include antibodies, non-protein scaffolds, fluorescence imaging, split enzymes and the relatively new tool termed Adhirons designed by researchers at Leeds University. Antibodies have been used extensively in protein studies due to the high degree of affinity and specificity however the rise in cost and the length of time required to make antibodies has fuelled efforts to find better alternatives. In this work we report whether Adhirons owing to their small size and high stability can be adapted to assay interactions in cells. It will explore whether current tools widely used in protein studies can debunk the davinchi code for protein-protein interactions. Most biological processes are governed by protein interactions and at the heart of most disease states particularly cancer lies a signalling cascade triggered by a plethora of protein interactions. We review current research into proteomics to evaluate and appreciate the work achieved thus far by international scientist crossing east and west divide. The journey into proteomics has already begun and at the present juncture has made significant milestones.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961096","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}