Cloning, Phylogenetic Analysis and 3D Modeling of a Putative Lysosomal Acid Lipase from the Camel, Camelus dromedarius

Ataya, Farid S.

doi:10.3390/molecules170910399

Cited by 5 publications

(4 citation statements)

References 25 publications

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“…The 3D structure of yak IGF2 was predicted using a Swiss-model server base on homology structure model [ 47 ]. The similarities between modeled human IGF2 and IGF1 structure, the catalytic and enzymatically important residues and DNA backbone interaction residues in IGF2 were superimposed on IGF2 using Pymol software (delino Scientific, New York, NY, USA) [ 48 ]. The quality of the superimposed 3D structures was assessed using PDBe on the EMBL-EBI server [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens

Zhang

Gong

et al. 2014

IJMS

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The IGF family is essential for normal embryonic and postnatal development and plays important roles in the immune system, myogenesis, bone metabolism and other physiological functions, which makes the study of its structure and biological characteristics important. Tianzhu white yak (Bos grunniens) domesticated under alpine hypoxia environments, is well adapted to survive and grow against severe hypoxia and cold temperatures for extended periods. In this study, a full coding sequence of the IGF2 gene of Tianzhu white yak was amplified by reverse transcription PCR and rapid-amplification of cDNA ends (RACE) for the first time. The cDNA sequence revealed an open reading frame of 450 nucleotides, encoding a protein with 179 amino acids. Its expression in different tissues was also studied by Real time PCR. Phylogenetic tree analysis indicated that yak IGF2 was similar to Bos taurus, and 3D structure showed high similarity with the human IGF2. The putative full CDS of yak IGF2 was amplified by PCR in five tissues, and cDNA sequence analysis showed high homology to bovine IGF2. Moreover the super secondary structure prediction showed a similar 3D structure with human IGF2. Its conservation in sequence and structure has facilitated research on IGF2 and its physiological function in yak.

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Section: Methodsmentioning

confidence: 99%

Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens

Zhang

Gong

et al. 2014

IJMS

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“…In addition, 3D structural analysis methods have been applied to lipid-degrading enzymes in various organisms, including humans and animals (Fendri et al 2006;Lampidonis et al 2008;Cornaciu et al 2011;Ataya 2012;Bouchaâla et al 2015;Ganesan et al 2015;Mahankali et al 2015). Specifically, structural studies of lipid-degrading enzymes in microbes have been reported (Vasel et al 1993;Gaskin et al 2001;Mandrich et al 2004;Jan et al 2015).…”

Section: Three-dimensional Structural Analysis Of Lipase Enzymesmentioning

confidence: 99%

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Vorapreeda

Thammarongtham

Laoteng

2016

World J Microbiol Biotechnol

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Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

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“…Expression of the test sample is compared with that of a steadily expressed gene known as a housekeeping gene. RT-PCR can be used to analyze the expression of many genes in a quantitative manner during treatment or in different tissues of the same organism [13,36].…”

Section: Profiling Gene Expression Of Protein Targetmentioning

confidence: 99%

Bioinformatics, Genomics, and Proteomics Tools in Drug Design

Fs¹

2019

J Drug Res Dev

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Unraveling of human genome sequences had enabled the discovery of new drugs, studies of their effects, and determination of their main targets. Integrated genomics, proteomics, and bioinformatics have led to powerful new strategies for solving many biochemical issues and developing new techniques which give new biomedical products. Among the applications were analyses of DNA and genome annotation, predicting target structure, and understanding the genetics of disease. As a result, a new trend in research had evolved to illustrate the mechanism of drug action, predict of drug resistance, and discover biomarkers for many diseases. The discovery of new drugs is complex process. Drug design is based on 2 main strategies: ligand-based drug design and structure-based drug design. Studying protein structure and function was the key to develop drug in which modern techniques were used based on combinatorial approaches like proteomics, genomics, bioinformatics, molecular docking and mass spectrometry. To successfully design a new drug, it is important to identify the cell or tissue targeted by this drug. No absolute confirmation that the suspected drug will be effective in vivo. In this review, an overview on the combinatorial approaches of proteomics, genomics and bioinformatics that help understanding the process of drug design is discussed.

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Cloning, Phylogenetic Analysis and 3D Modeling of a Putative Lysosomal Acid Lipase from the Camel, Camelus dromedarius

Cited by 5 publications

References 25 publications

Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens

Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Bioinformatics, Genomics, and Proteomics Tools in Drug Design

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