Trends in Bioinformatics最新文献_第2页

Trends in Bioinformatics Pub Date : 2016-09-15 DOI: 10.3923/TB.2016.52.58

Y. Faridah, H. Nasir, K. Kadir, S. Safie, Sheroz Khan, T. Gunawan

引用次数: 10

Conservation Pattern, Homology Modeling and Molecular Phylogenetic Study of BMP Ligands BMP配体的保护模式、同源性建模及分子系统发育研究

Trends in Bioinformatics Pub Date : 2016-09-15 DOI: 10.3923/TB.2016.70.80

S. Chatterjee, Madhuri Haque, M. S. Rahman, H. M. Jamil, Naznin Akhtar, S. Abdul-Awal, Md. Shahedur Rahman, S. M. Asaduzzama

{"title":"Conservation Pattern, Homology Modeling and Molecular Phylogenetic Study of BMP Ligands","authors":"S. Chatterjee, Madhuri Haque, M. S. Rahman, H. M. Jamil, Naznin Akhtar, S. Abdul-Awal, Md. Shahedur Rahman, S. M. Asaduzzama","doi":"10.3923/TB.2016.70.80","DOIUrl":"https://doi.org/10.3923/TB.2016.70.80","url":null,"abstract":"Background: Bone Morphogenic Proteins (BMPs) play many important roles in embryogenesis and metamorphosis throughout the life of vertebrates and other animals. The BMPs are multifunctional and some BMPs do similar functions which lead us to believe that it may have existed before the evolution and they may evolve from a single BMP. Additionally, less is known regarding phylogeny and conservation based conserved molecular mechanism of BMPs. Hence, evolutionary relationship of 16 BMP ligands (phylogenetic as well as protein sequence conversed patterns) were done. Materials and Methods: For this study, protein sequences were retrieved from UniProtKB, homology modeling was executed by Swiss-model using 3rjr.1A and 2qcq.1A as template, followed by MSA and phylogeny. Later conserved regions of BMP ligand were compared. Protein subfamily determination was done in Zebra and supported by the phylogenetic data. Results: Remarkably, similar region of conserved area were observed and different disulfide linkage pattern had been identified. It was found notable patterns in C1-C4, C2-C5 and C3-C6 that all but BMP3 and BMP15 do not contain 7th Cys. Phylogeny study indicate, according to evolutionary clock, GDF11 and BMP15 were more distantly diverged taxa, BMP3A and BMP3B had same point origin and GDF5, 6 and 7 are homologous. These seven proteins, as per this study indicates that, those are evolved at simultaneously during evolution, whereas other nine forms monophyletic taxa. Conclusion: However, more studies needs to explore on this. As per homology modelling studied, BMP ligands shares common evolutionary origin, some of the members are highly diverged indicating ancient evolutionary history of these protein. This study will be useful for wet lab once the evolutionary relationship gets established.","PeriodicalId":164864,"journal":{"name":"Trends in Bioinformatics","volume":"222 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128840196","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}

引用次数: 1

Evaluation of solar energy potential in Malaysia 马来西亚太阳能潜力评估

Trends in Bioinformatics Pub Date : 2016-09-15 DOI: 10.3923/TB.2016.35.43

P. D. A. Aziz, S. N. A. Wahid, Y. Arief, N. Aziz

引用次数: 25

Effective Parameters on the Performance of Solar Desiccant Cooling Systems 太阳能干燥剂冷却系统性能的有效参数研究

Trends in Bioinformatics Pub Date : 2016-09-15 DOI: 10.3923/TB.2016.44.51

M. Dezfouli

引用次数: 0

Functional Characterization of Elapid Venom Toxin Proteins and Related Non-Toxin Proteins of Human through Comparative Analysis 通过比较分析研究人类蛇毒毒素蛋白与相关非毒素蛋白的功能特征

Trends in Bioinformatics Pub Date : 2015-03-01 DOI: 10.3923/TB.2015.86.92

Z. Y. Roly, M. Ruhullah, Rafsan Zani Tanvir, M. K. Foyasal, M. R. Bapari, Dipu Roy, Z. Islam, B. Hasan, Md. Mahmudul Islam

{"title":"Functional Characterization of Elapid Venom Toxin Proteins and Related Non-Toxin Proteins of Human through Comparative Analysis","authors":"Z. Y. Roly, M. Ruhullah, Rafsan Zani Tanvir, M. K. Foyasal, M. R. Bapari, Dipu Roy, Z. Islam, B. Hasan, Md. Mahmudul Islam","doi":"10.3923/TB.2015.86.92","DOIUrl":"https://doi.org/10.3923/TB.2015.86.92","url":null,"abstract":"Snake venom contains a diverse array of pharmacologically active proteins and polypeptides that have led to the development of molecular probes and therapeutic agents. Short neurotoxins and cytotoxins are non-enzymatic polypeptides components of snake venom found only in the venoms of Elapidae (cobras, kraits, mambas, coral snakes and Australian elapids) and Hydrophidae (sea snakes). The three-dimensional structure of short neurotoxins and cytotoxins has three beta stranded loops resembling three-fingers of three-finger protein super family. This protein super family has different family members which are employed in various biological functions. The objective of this study is to search out the amino acid compositional (%) profile, physiochemical properties and functional analysis of three finger toxins present in different elapid snake species to be precise, Bungarus fasciatus, Naja naja and Naja kauthia. We analyzed a total of 23 reference protein sequences representing short neurotoxin and cytotoxin of three elapid snakes and related non-toxin proteins of human in terms of functional analysis, amino acid compositional (%) profile, number of amino acids, molecular weight, theoretical isoelectric point (pI), number of positively charged and negatively charged amino acid residues, instability index and grand average of hydropathy using computational tools. From the result it was found that amino acid composition profile represents that all sequences hold a conserved cysteine amount even as differential amount of different amino acid residues have a particular family pattern. It will also assist to know about involvement in various biological functions those are accountable for the vivid amino acid composition profile of these proteins. This comparative analysis of physicochemical properties would play a significant role in understanding the mechanisms of action of toxins and in the development of lead therapeutic molecules.","PeriodicalId":164864,"journal":{"name":"Trends in Bioinformatics","volume":"8 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120820027","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}

引用次数: 2

A Compression Algorithm for DNA Sequences Based on R2G Techniques with Security 基于R2G技术的DNA序列安全压缩算法

Trends in Bioinformatics Pub Date : 2015-03-01 DOI: 10.3923/TB.2015.93.98

S. M. Hossein, P. Mohapatra, D. De

引用次数: 1

Modified k-Tuple Method for the Construction of Phylogenetic Trees 构建系统发育树的改进k元组方法

Trends in Bioinformatics Pub Date : 2015-03-01 DOI: 10.3923/TB.2015.75.85

Geetika, M. Hanmandlu, Ashish Sani, D. Gaur

引用次数: 6

Identification of Putative Therapeutic Targets in Candida tropicalis: An in silico Approach 热带假丝酵母推定治疗靶点的鉴定:一种计算机方法

Trends in Bioinformatics Pub Date : 2015-02-01 DOI: 10.3923/TB.2015.52.62

Haribalaganesh Ravinaraya, R. Coico, K. Sundar

引用次数: 6

Detection of Active Site Residues in Bovine Rhodopsin Using Network Analysis 用网络分析法检测牛紫红质中活性位点残基

Trends in Bioinformatics Pub Date : 2015-02-01 DOI: 10.3923/TB.2015.63.74

I. Emerson, Preeti Tabitha Louis

引用次数: 6

Homology Modeling, Molecular Dynamic Simulations and Docking Studies of a New Cold Active Extracellular Lipase, EnL A from Emericella nidulans NFCCI 3643 新冷活性胞外脂肪酶EnL a同源性建模、分子动力学模拟及对接研究

Trends in Bioinformatics Pub Date : 2015-02-01 DOI: 10.3923/TB.2015.37.51

Suseela Lanka, Venkateswar Rao Tallur, V. Ganesh, J. La

{"title":"Homology Modeling, Molecular Dynamic Simulations and Docking Studies of a New Cold Active Extracellular Lipase, EnL A from Emericella nidulans NFCCI 3643","authors":"Suseela Lanka, Venkateswar Rao Tallur, V. Ganesh, J. La","doi":"10.3923/TB.2015.37.51","DOIUrl":"https://doi.org/10.3923/TB.2015.37.51","url":null,"abstract":"A cold active lipase producing mesophilic fungus was isolated from Palm Oil Mill Effluent (POME) dump sites and identified by 28S rRNA molecular identification studies as Emericella nidulans NFCCI 3643. The BLAST P search with the sequence of the purified cold active lipase obtained by MALDI-TOF/MS analysis revealed that the protein is a hypothetical protein from Emericella nidulans with a gi number 67522685. Search of Lipase Engineering Database (LED) for this protein sequence revealed that this protein belongs to Candida antarctica lipase A like super family and to Aspergillus lipase like homologous family of class Y lipases. In the present study, a 3D structure of EnL A (Emericella nidulans lipase A) was built using homology modeling, the model was further optimized by molecular dynamic simulations and the optimized model was then docked with natural substrates. Secondary structure analysis of EnL A showed 37.11% of its content to be alpha helix making it stable for three dimensional structure modeling. Homology model of EnL A was constructed using the X-ray structure of Candida antarctica Lip A (3 guu.1.A) as a template with which EnL A showed 32.77% sequence identity. The stereo chemical quality and side chain environment of the model was validated by Ramachandran plot, ERRAT and Verify 3D. Natural substrates like tributyrin and trioctanoin were docked in to the optimized 3D model to further investigate the ligand-enzyme interactions.","PeriodicalId":164864,"journal":{"name":"Trends in Bioinformatics","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127984316","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}

引用次数: 6