International Journal of Computational Bioinformatics and In Silico Modeling
ABSTRACT: The pesticide glyphosate is commonly used around the world because of its effectiveness and low persistence in the environment. Based on its solubility and ionic nature, numerous studies since the 70s have suggested that this compound should not be harmful to humans. However, recent studies have shown that it could adversely affect human health, and accumulation of glyphosate in human tissue has been correlated with teratogenic and carcinogenic effects. To affect living organisms, glyphosate must be able to cross biological membranes. In this work, we studied the ability of glyphosate to cross a membrane bilayer composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) at different ratios. Molecular dynamics calculations were used to simulate the diffusion of glyphosate into a coarse grained model of DOPC and DOPS. The preliminary results suggested that glyphosate could cross the model membranes under certain conditions. This knowledge will be useful for assessing the impact of this herbicide on human health.
KeyWords: glyphosate; phospholipid; lipid bilayer; coarse grained model; molecular dynamics.
How to cite: Vito Librando et. al. In silico study of glyphosate entry into lipid bilayers. Int J Comput Bioinfo In Silico Model. 4(6) 2015: 743-748
ABSTRACT: The emerging advanced technologies facilitate the systematic study of the complex agricultural traits and the regulation underlying the phenotype of the biological organisms. In contrast to the classical research before the post-genomic era, the current agricultural research tends to investigate the behaviour of all system components simultaneously. This strategy intends to reveal how the system components collaborate to regulate the system behaviour rather than an attempt to identify the individual function of a component. In context of the agricultural research, the systems based approaches has been exploited to explore the biological regulation controlling agricultural productivity. This report highlighted the importance of Bioinformatics and systems biology tools in OMICS data analysis for mining of important genes/traits linked to agricultural productivity.
KeyWords: Bioinformatics, Systems Biology, Omics, Next-Generation Sequencing, Agricultural Productivity.
How to cite: Anil Kumar et. al. High-throughput Omics Data for mining of important genes/traits linked to Agricultural Productivity: A National Bioinformatics workshop report. Int J Comput Bioinfo In Silico Model. 4(6) 2015: 749-752
ABSTRACT: This is a sequel to the previous study on the structural insight into the homology modeled human N-acetyl-alpha-neuraminidase 3 (NEU3). Further analysis was performed with a software package the Molecular Operating Environment. A human NEU2 (PDB code: 1SNT) was selected as template for the 3D structure modeling of NEU3. The template NEU2 lacks the catalytically important Asp46 that is equivalent to Asp50 in NEU3. The superimposition and root mean square deviation analysis indicated that the modeled NEU3 showed significant 3D similarity to NEU2. However, the molecular electrostatic potential (MEP) map of the NEU3 model exhibited that the model was electrostatically different from the NEU2 model and also the NEU3 model constructed from 1VCU at the ligand-binding site (LBS). Further, docking simulations between the N-acetyl-2,3-dehydro-2-deoxyneuraminic acid (DANA)-NEU2 and DANA-NEU3 complexes revealed the dissimilarity of the ligand-receptor binding orientation between the NEU2 and 3 models. The different binding orientation between the DANA-NEU2 and DANA-NEU3 complexes reflected the different MEP maps at the LBSs between the NEU2 and 3 models. The docking simulation also revealed that DANA was unable to create interactions with the residues that are considered crucial to the DANA-NEU3 binding. These results indicate that missing a very important residue (Asp50) at the LBS can modify the interaction of NEU3 with ligands and possibly nullify its enzyme activity, although the 3D structure of the enzyme remains almost completely intact.
KeyWords: N-acetyl-alpha-neuraminidase 3 (NEU3), residue, LBS, in silico.
How to cite: Katsuyoshi Kamiie et. al. Structural insight into the homology modeled human N-acetyl-alpha-neuraminidase 3 (NEU3): Part2. Int J Comput Bioinfo In Silico Model. 4(6) 2015: 753-760